pysam-0.7.7/0000775000076400007650000000000012241575073012513 5ustar andreasandreaspysam-0.7.7/tabix/0000775000076400007650000000000012241575073013622 5ustar andreasandreaspysam-0.7.7/tabix/bedidx.c0000660000076400007650000000727612162637166015241 0ustar andreasandreas#include #include #include #include #include #include "ksort.h" KSORT_INIT_GENERIC(uint64_t) #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 8192) typedef struct { int n, m; uint64_t *a; int *idx; } bed_reglist_t; #include "khash.h" KHASH_MAP_INIT_STR(reg, bed_reglist_t) #define LIDX_SHIFT 13 typedef kh_reg_t reghash_t; int *bed_index_core(int n, uint64_t *a, int *n_idx) { int i, j, m, *idx; m = *n_idx = 0; idx = 0; for (i = 0; i < n; ++i) { int beg, end; beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT; if (m < end + 1) { int oldm = m; m = end + 1; kroundup32(m); idx = realloc(idx, m * sizeof(int)); for (j = oldm; j < m; ++j) idx[j] = -1; } if (beg == end) { if (idx[beg] < 0) idx[beg] = i; } else { for (j = beg; j <= end; ++j) if (idx[j] < 0) idx[j] = i; } *n_idx = end + 1; } return idx; } void bed_index(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { bed_reglist_t *p = &kh_val(h, k); if (p->idx) free(p->idx); ks_introsort(uint64_t, p->n, p->a); p->idx = bed_index_core(p->n, p->a, &p->m); } } } int bed_overlap_core(const bed_reglist_t *p, int beg, int end) { int i, min_off; if (p->n == 0) return 0; min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT]; if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here int n = beg>>LIDX_SHIFT; if (n > p->n) n = p->n; for (i = n - 1; i >= 0; --i) if (p->idx[i] >= 0) break; min_off = i >= 0? p->idx[i] : 0; } for (i = min_off; i < p->n; ++i) { if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end) return 1; // find the overlap; return } return 0; } int bed_overlap(const void *_h, const char *chr, int beg, int end) { const reghash_t *h = (const reghash_t*)_h; khint_t k; if (!h) return 0; k = kh_get(reg, h, chr); if (k == kh_end(h)) return 0; return bed_overlap_core(&kh_val(h, k), beg, end); } void *bed_read(const char *fn) { reghash_t *h = kh_init(reg); gzFile fp; kstream_t *ks; int dret; kstring_t *str; // read the list fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) return 0; str = calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name int beg = -1, end = -1; bed_reglist_t *p; khint_t k = kh_get(reg, h, str->s); if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(str->s); k = kh_put(reg, h, s, &ret); memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); if (dret != '\n') { // if the lines has other characters if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) { beg = atoi(str->s); // begin if (dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) end = atoi(str->s); // end } } } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column if (beg >= 0 && end > beg) { if (p->n == p->m) { p->m = p->m? p->m<<1 : 4; p->a = realloc(p->a, p->m * 8); } p->a[p->n++] = (uint64_t)beg<<32 | end; } } ks_destroy(ks); gzclose(fp); free(str->s); free(str); bed_index(h); return h; } void bed_destroy(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); free(kh_val(h, k).idx); free((char*)kh_key(h, k)); } } kh_destroy(reg, h); } pysam-0.7.7/tabix/index.c.pysam.c0000664000076400007650000006410312162637166016456 0ustar andreasandreas#include "pysam.h" #include #include #include #include "khash.h" #include "ksort.h" #include "kstring.h" #include "bam_endian.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #include "tabix.h" #define TAD_MIN_CHUNK_GAP 32768 // 1<<14 is the size of minimum bin. #define TAD_LIDX_SHIFT 14 typedef struct { uint64_t u, v; } pair64_t; #define pair64_lt(a,b) ((a).u < (b).u) KSORT_INIT(offt, pair64_t, pair64_lt) typedef struct { uint32_t m, n; pair64_t *list; } ti_binlist_t; typedef struct { int32_t n, m; uint64_t *offset; } ti_lidx_t; KHASH_MAP_INIT_INT(i, ti_binlist_t) KHASH_MAP_INIT_STR(s, int) struct __ti_index_t { ti_conf_t conf; int32_t n, max; khash_t(s) *tname; khash_t(i) **index; ti_lidx_t *index2; }; struct __ti_iter_t { int from_first; // read from the first record; no random access int tid, beg, end, n_off, i, finished; uint64_t curr_off; kstring_t str; const ti_index_t *idx; pair64_t *off; }; typedef struct { int tid, beg, end, bin; } ti_intv_t; ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 }; ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 }; ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 }; ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 }; ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 }; /*************** * read a line * ***************/ /* int ti_readline(BGZF *fp, kstring_t *str) { int c, l = 0; str->l = 0; while ((c = bgzf_getc(fp)) >= 0 && c != '\n') { ++l; if (c != '\r') kputc(c, str); } if (c < 0 && l == 0) return -1; // end of file return str->l; } */ /* Below is a faster implementation largely equivalent to the one * commented out above. */ int ti_readline(BGZF *fp, kstring_t *str) { return bgzf_getline(fp, '\n', str); } /************************************* * get the interval from a data line * *************************************/ static inline int ti_reg2bin(uint32_t beg, uint32_t end) { --end; if (beg>>14 == end>>14) return 4681 + (beg>>14); if (beg>>17 == end>>17) return 585 + (beg>>17); if (beg>>20 == end>>20) return 73 + (beg>>20); if (beg>>23 == end>>23) return 9 + (beg>>23); if (beg>>26 == end>>26) return 1 + (beg>>26); return 0; } static int get_tid(ti_index_t *idx, const char *ss) { khint_t k; int tid; k = kh_get(s, idx->tname, ss); if (k == kh_end(idx->tname)) { // a new target sequence int ret, size; // update idx->n, ->max, ->index and ->index2 if (idx->n == idx->max) { idx->max = idx->max? idx->max<<1 : 8; idx->index = realloc(idx->index, idx->max * sizeof(void*)); idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t)); } memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t)); idx->index[idx->n++] = kh_init(i); // update ->tname tid = size = kh_size(idx->tname); k = kh_put(s, idx->tname, strdup(ss), &ret); kh_value(idx->tname, k) = size; assert(idx->n == kh_size(idx->tname)); } else tid = kh_value(idx->tname, k); return tid; } int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv) { int i, b = 0, id = 1, ncols = 0; char *s; intv->ss = intv->se = 0; intv->beg = intv->end = -1; for (i = 0; i <= len; ++i) { if (line[i] == '\t' || line[i] == 0) { ++ncols; if (id == conf->sc) { intv->ss = line + b; intv->se = line + i; } else if (id == conf->bc) { // here ->beg is 0-based. intv->beg = intv->end = strtol(line + b, &s, 0); if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg; else ++intv->end; if (intv->beg < 0) intv->beg = 0; if (intv->end < 1) intv->end = 1; } else { if ((conf->preset&0xffff) == TI_PRESET_GENERIC) { if (id == conf->ec) intv->end = strtol(line + b, &s, 0); } else if ((conf->preset&0xffff) == TI_PRESET_SAM) { if (id == 6) { // CIGAR int l = 0, op; char *t; for (s = line + b; s < line + i;) { long x = strtol(s, &t, 10); op = toupper(*t); if (op == 'M' || op == 'D' || op == 'N') l += x; s = t + 1; } if (l == 0) l = 1; intv->end = intv->beg + l; } } else if ((conf->preset&0xffff) == TI_PRESET_VCF) { // FIXME: the following is NOT tested and is likely to be buggy if (id == 4) { if (b < i) intv->end = intv->beg + (i - b); } else if (id == 8) { // look for "END=" int c = line[i]; line[i] = 0; s = strstr(line + b, "END="); if (s == line + b) s += 4; else if (s) { s = strstr(line + b, ";END="); if (s) s += 5; } if (s) intv->end = strtol(s, &s, 0); line[i] = c; } } } b = i + 1; ++id; } } /* if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) { if (ncols == 1) fprintf(pysamerr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line); else fprintf(pysamerr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line); exit(1); } */ if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; return 0; } static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv) { ti_interval_t x; intv->tid = intv->beg = intv->end = intv->bin = -1; if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) { int c = *x.se; *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c; intv->beg = x.beg; intv->end = x.end; intv->bin = ti_reg2bin(intv->beg, intv->end); return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1; } else { fprintf(pysamerr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s); return -1; } } /************ * indexing * ************/ // requirement: len <= LEN_MASK static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end) { khint_t k; ti_binlist_t *l; int ret; k = kh_put(i, h, bin, &ret); l = &kh_value(h, k); if (ret) { // not present l->m = 1; l->n = 0; l->list = (pair64_t*)calloc(l->m, 16); } if (l->n == l->m) { l->m <<= 1; l->list = (pair64_t*)realloc(l->list, l->m * 16); } l->list[l->n].u = beg; l->list[l->n++].v = end; } static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset) { int i, beg, end; beg = _beg >> TAD_LIDX_SHIFT; end = (_end - 1) >> TAD_LIDX_SHIFT; if (index2->m < end + 1) { int old_m = index2->m; index2->m = end + 1; kroundup32(index2->m); index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); } if (beg == end) { if (index2->offset[beg] == 0) index2->offset[beg] = offset; } else { for (i = beg; i <= end; ++i) if (index2->offset[i] == 0) index2->offset[i] = offset; } if (index2->n < end + 1) index2->n = end + 1; return (uint64_t)beg<<32 | end; } static void merge_chunks(ti_index_t *idx) { khash_t(i) *index; int i, l, m; khint_t k; for (i = 0; i < idx->n; ++i) { index = idx->index[i]; for (k = kh_begin(index); k != kh_end(index); ++k) { ti_binlist_t *p; if (!kh_exist(index, k)) continue; p = &kh_value(index, k); m = 0; for (l = 1; l < p->n; ++l) { if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v; else p->list[++m] = p->list[l]; } // ~for(l) p->n = m + 1; } // ~for(k) } // ~for(i) } static void fill_missing(ti_index_t *idx) { int i, j; for (i = 0; i < idx->n; ++i) { ti_lidx_t *idx2 = &idx->index2[i]; for (j = 1; j < idx2->n; ++j) if (idx2->offset[j] == 0) idx2->offset[j] = idx2->offset[j-1]; } } ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf) { int ret; ti_index_t *idx; uint32_t last_bin, save_bin; int32_t last_coor, last_tid, save_tid; uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp; kstring_t *str; str = calloc(1, sizeof(kstring_t)); idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); idx->conf = *conf; idx->n = idx->max = 0; idx->tname = kh_init(s); idx->index = 0; idx->index2 = 0; save_bin = save_tid = last_tid = last_bin = 0xffffffffu; save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu; while ((ret = ti_readline(fp, str)) >= 0) { ti_intv_t intv; ++lineno; if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { last_off = bgzf_tell(fp); continue; } get_intv(idx, str, &intv); if ( intv.beg<0 || intv.end<0 ) { fprintf(pysamerr,"[ti_index_core] the indexes overlap or are out of bounds\n"); exit(1); } if (last_tid != intv.tid) { // change of chromosomes if (last_tid>intv.tid ) { fprintf(pysamerr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1); exit(1); } last_tid = intv.tid; last_bin = 0xffffffffu; } else if (last_coor > intv.beg) { fprintf(pysamerr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno); exit(1); } tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off); if (last_off == 0) offset0 = tmp; if (intv.bin != last_bin) { // then possibly write the binning index if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record insert_offset(idx->index[save_tid], save_bin, save_off, last_off); save_off = last_off; save_bin = last_bin = intv.bin; save_tid = intv.tid; if (save_tid < 0) break; } if (bgzf_tell(fp) <= last_off) { fprintf(pysamerr, "[ti_index_core] bug in BGZF: %llx < %llx\n", (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off); exit(1); } last_off = bgzf_tell(fp); last_coor = intv.beg; } if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp)); merge_chunks(idx); fill_missing(idx); if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) { int i, beg = offset0>>32, end = offset0&0xffffffffu; for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0; } free(str->s); free(str); return idx; } void ti_index_destroy(ti_index_t *idx) { khint_t k; int i; if (idx == 0) return; // destroy the name hash table for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) { if (kh_exist(idx->tname, k)) free((char*)kh_key(idx->tname, k)); } kh_destroy(s, idx->tname); // destroy the binning index for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; ti_lidx_t *index2 = idx->index2 + i; for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) free(kh_value(index, k).list); } kh_destroy(i, index); free(index2->offset); } free(idx->index); // destroy the linear index free(idx->index2); free(idx); } /****************** * index file I/O * ******************/ void ti_index_save(const ti_index_t *idx, BGZF *fp) { int32_t i, size, ti_is_be; khint_t k; ti_is_be = bam_is_big_endian(); bgzf_write(fp, "TBI\1", 4); if (ti_is_be) { uint32_t x = idx->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &idx->n, 4); assert(sizeof(ti_conf_t) == 24); if (ti_is_be) { // write ti_conf_t; uint32_t x[6]; memcpy(x, &idx->conf, 24); for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4); } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t)); { // write target names char **name; int32_t l = 0; name = calloc(kh_size(idx->tname), sizeof(void*)); for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) if (kh_exist(idx->tname, k)) name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k); for (i = 0; i < kh_size(idx->tname); ++i) l += strlen(name[i]) + 1; if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4); else bgzf_write(fp, &l, 4); for (i = 0; i < kh_size(idx->tname); ++i) bgzf_write(fp, name[i], strlen(name[i]) + 1); free(name); } for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; ti_lidx_t *index2 = idx->index2 + i; // write binning index size = kh_size(index); if (ti_is_be) { // big endian uint32_t x = size; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &size, 4); for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) { ti_binlist_t *p = &kh_value(index, k); if (ti_is_be) { // big endian uint32_t x; x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4); x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } bgzf_write(fp, p->list, 16 * p->n); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } else { bgzf_write(fp, &kh_key(index, k), 4); bgzf_write(fp, &p->n, 4); bgzf_write(fp, p->list, 16 * p->n); } } } // write linear index (index2) if (ti_is_be) { int x = index2->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &index2->n, 4); if (ti_is_be) { // big endian int x; for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); bgzf_write(fp, index2->offset, 8 * index2->n); for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); } else bgzf_write(fp, index2->offset, 8 * index2->n); } } static ti_index_t *ti_index_load_core(BGZF *fp) { int i, ti_is_be; char magic[4]; ti_index_t *idx; ti_is_be = bam_is_big_endian(); if (fp == 0) { fprintf(pysamerr, "[ti_index_load_core] fail to load index.\n"); return 0; } bgzf_read(fp, magic, 4); if (strncmp(magic, "TBI\1", 4)) { fprintf(pysamerr, "[ti_index_load] wrong magic number.\n"); return 0; } idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); bgzf_read(fp, &idx->n, 4); if (ti_is_be) bam_swap_endian_4p(&idx->n); idx->tname = kh_init(s); idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t)); // read idx->conf bgzf_read(fp, &idx->conf, sizeof(ti_conf_t)); if (ti_is_be) { bam_swap_endian_4p(&idx->conf.preset); bam_swap_endian_4p(&idx->conf.sc); bam_swap_endian_4p(&idx->conf.bc); bam_swap_endian_4p(&idx->conf.ec); bam_swap_endian_4p(&idx->conf.meta_char); bam_swap_endian_4p(&idx->conf.line_skip); } { // read target names int j, ret; kstring_t *str; int32_t l; uint8_t *buf; bgzf_read(fp, &l, 4); if (ti_is_be) bam_swap_endian_4p(&l); buf = calloc(l, 1); bgzf_read(fp, buf, l); str = calloc(1, sizeof(kstring_t)); for (i = j = 0; i < l; ++i) { if (buf[i] == 0) { khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret); kh_value(idx->tname, k) = j++; str->l = 0; } else kputc(buf[i], str); } free(str->s); free(str); free(buf); } for (i = 0; i < idx->n; ++i) { khash_t(i) *index; ti_lidx_t *index2 = idx->index2 + i; uint32_t key, size; khint_t k; int j, ret; ti_binlist_t *p; index = idx->index[i] = kh_init(i); // load binning index bgzf_read(fp, &size, 4); if (ti_is_be) bam_swap_endian_4p(&size); for (j = 0; j < (int)size; ++j) { bgzf_read(fp, &key, 4); if (ti_is_be) bam_swap_endian_4p(&key); k = kh_put(i, index, key, &ret); p = &kh_value(index, k); bgzf_read(fp, &p->n, 4); if (ti_is_be) bam_swap_endian_4p(&p->n); p->m = p->n; p->list = (pair64_t*)malloc(p->m * 16); bgzf_read(fp, p->list, 16 * p->n); if (ti_is_be) { int x; for (x = 0; x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } } // load linear index bgzf_read(fp, &index2->n, 4); if (ti_is_be) bam_swap_endian_4p(&index2->n); index2->m = index2->n; index2->offset = (uint64_t*)calloc(index2->m, 8); bgzf_read(fp, index2->offset, index2->n * 8); if (ti_is_be) for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); } return idx; } ti_index_t *ti_index_load_local(const char *fnidx) { BGZF *fp; fp = bgzf_open(fnidx, "r"); if (fp) { ti_index_t *idx = ti_index_load_core(fp); bgzf_close(fp); return idx; } else return 0; } #ifdef _USE_KNETFILE static void download_from_remote(const char *url) { const int buf_size = 1 * 1024 * 1024; char *fn; FILE *fp; uint8_t *buf; knetFile *fp_remote; int l; if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; l = strlen(url); for (fn = (char*)url + l - 1; fn >= url; --fn) if (*fn == '/') break; ++fn; // fn now points to the file name fp_remote = knet_open(url, "r"); if (fp_remote == 0) { fprintf(pysamerr, "[download_from_remote] fail to open remote file.\n"); return; } if ((fp = fopen(fn, "w")) == 0) { fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory.\n"); knet_close(fp_remote); return; } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) fwrite(buf, 1, l, fp); free(buf); fclose(fp); knet_close(fp_remote); } #else static void download_from_remote(const char *url) { return; } #endif static char *get_local_version(const char *fn) { struct stat sbuf; char *fnidx = (char*)calloc(strlen(fn) + 5, 1); strcat(strcpy(fnidx, fn), ".tbi"); if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { char *p, *url; int l = strlen(fnidx); for (p = fnidx + l - 1; p >= fnidx; --p) if (*p == '/') break; url = fnidx; fnidx = strdup(p + 1); if (stat(fnidx, &sbuf) == 0) { free(url); return fnidx; } fprintf(pysamerr, "[%s] downloading the index file...\n", __func__); download_from_remote(url); free(url); } if (stat(fnidx, &sbuf) == 0) return fnidx; free(fnidx); return 0; } const char **ti_seqname(const ti_index_t *idx, int *n) { const char **names; khint_t k; *n = idx->n; names = calloc(idx->n, sizeof(void*)); for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k) if (kh_exist(idx->tname, k)) names[kh_val(idx->tname, k)] = kh_key(idx->tname, k); return names; } ti_index_t *ti_index_load(const char *fn) { ti_index_t *idx; char *fname = get_local_version(fn); if (fname == 0) return 0; idx = ti_index_load_local(fname); if (idx == 0) fprintf(pysamerr, "[ti_index_load] fail to load the index: %s\n", fname); free(fname); return idx; } int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx) { char *fnidx; BGZF *fp, *fpidx; ti_index_t *idx; if ((fp = bgzf_open(fn, "r")) == 0) { fprintf(pysamerr, "[ti_index_build2] fail to open the file: %s\n", fn); return -1; } idx = ti_index_core(fp, conf); bgzf_close(fp); if (_fnidx == 0) { fnidx = (char*)calloc(strlen(fn) + 5, 1); strcpy(fnidx, fn); strcat(fnidx, ".tbi"); } else fnidx = strdup(_fnidx); fpidx = bgzf_open(fnidx, "w"); if (fpidx == 0) { fprintf(pysamerr, "[ti_index_build2] fail to create the index file.\n"); free(fnidx); return -1; } ti_index_save(idx, fpidx); ti_index_destroy(idx); bgzf_close(fpidx); free(fnidx); return 0; } int ti_index_build(const char *fn, const ti_conf_t *conf) { return ti_index_build2(fn, conf, 0); } /******************************************** * parse a region in the format chr:beg-end * ********************************************/ int ti_get_tid(const ti_index_t *idx, const char *name) { khiter_t iter; const khash_t(s) *h = idx->tname; iter = kh_get(s, h, name); /* get the tid */ if (iter == kh_end(h)) return -1; return kh_value(h, iter); } int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end) { char *s, *p; int i, l, k; l = strlen(str); p = s = (char*)malloc(l+1); /* squeeze out "," */ for (i = k = 0; i != l; ++i) if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i]; s[k] = 0; for (i = 0; i != k; ++i) if (s[i] == ':') break; s[i] = 0; if ((*tid = ti_get_tid(idx, s)) < 0) { free(s); return -1; } if (i == k) { /* dump the whole sequence */ *begin = 0; *end = 1<<29; free(s); return 0; } for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break; *begin = atoi(p); if (i < k) { p = s + i + 1; *end = atoi(p); } else *end = 1<<29; if (*begin > 0) --*begin; free(s); if (*begin > *end) return -1; return 0; } /******************************* * retrieve a specified region * *******************************/ #define MAX_BIN 37450 // =(8^6-1)/7+1 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN]) { int i = 0, k; if (beg >= end) return 0; if (end >= 1u<<29) end = 1u<<29; --end; list[i++] = 0; for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; return i; } ti_iter_t ti_iter_first() { ti_iter_t iter; iter = calloc(1, sizeof(struct __ti_iter_t)); iter->from_first = 1; return iter; } ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end) { uint16_t *bins; int i, n_bins, n_off; pair64_t *off; khint_t k; khash_t(i) *index; uint64_t min_off; ti_iter_t iter = 0; if (beg < 0) beg = 0; if (end < beg) return 0; // initialize the iterator iter = calloc(1, sizeof(struct __ti_iter_t)); iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1; // random access bins = (uint16_t*)calloc(MAX_BIN, 2); n_bins = reg2bins(beg, end, bins); index = idx->index[tid]; if (idx->index2[tid].n > 0) { min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1] : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT]; if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4 int n = beg>>TAD_LIDX_SHIFT; if (n > idx->index2[tid].n) n = idx->index2[tid].n; for (i = n - 1; i >= 0; --i) if (idx->index2[tid].offset[i] != 0) break; if (i >= 0) min_off = idx->index2[tid].offset[i]; } } else min_off = 0; // tabix 0.1.2 may produce such index files for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) n_off += kh_value(index, k).n; } if (n_off == 0) { free(bins); return iter; } off = (pair64_t*)calloc(n_off, 16); for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) { int j; ti_binlist_t *p = &kh_value(index, k); for (j = 0; j < p->n; ++j) if (p->list[j].v > min_off) off[n_off++] = p->list[j]; } } if (n_off == 0) { free(bins); free(off); return iter; } free(bins); { int l; ks_introsort(offt, n_off, off); // resolve completely contained adjacent blocks for (i = 1, l = 0; i < n_off; ++i) if (off[l].v < off[i].v) off[++l] = off[i]; n_off = l + 1; // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing for (i = 1; i < n_off; ++i) if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; { // merge adjacent blocks for (i = 1, l = 0; i < n_off; ++i) { if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; else off[++l] = off[i]; } n_off = l + 1; } } iter->n_off = n_off; iter->off = off; return iter; } const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) { if (iter->finished) return 0; if (iter->from_first) { int ret; if ((ret = ti_readline(fp, &iter->str)) < 0) { iter->finished = 1; return 0; } else { if (len) *len = iter->str.l; return iter->str.s; } } if (iter->n_off == 0) return 0; while (1) { int ret; if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk if (iter->i == iter->n_off - 1) break; // no more chunks if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET); iter->curr_off = bgzf_tell(fp); } ++iter->i; } if ((ret = ti_readline(fp, &iter->str)) >= 0) { ti_intv_t intv; iter->curr_off = bgzf_tell(fp); if (iter->str.s[0] == iter->idx->conf.meta_char) continue; get_intv((ti_index_t*)iter->idx, &iter->str, &intv); if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed else if (intv.end > iter->beg && iter->end > intv.beg) { if (len) *len = iter->str.l; return iter->str.s; } } else break; // end of file } iter->finished = 1; return 0; } void ti_iter_destroy(ti_iter_t iter) { if (iter) { free(iter->str.s); free(iter->off); free(iter); } } int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func) { ti_iter_t iter; const char *s; int len; iter = ti_iter_query(idx, tid, beg, end); while ((s = ti_iter_read(fp, iter, &len)) != 0) func(len, s, data); ti_iter_destroy(iter); return 0; } const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; } /******************* * High-level APIs * *******************/ tabix_t *ti_open(const char *fn, const char *fnidx) { tabix_t *t; BGZF *fp; if ((fp = bgzf_open(fn, "r")) == 0) return 0; t = calloc(1, sizeof(tabix_t)); t->fn = strdup(fn); if (fnidx) t->fnidx = strdup(fnidx); t->fp = fp; return t; } void ti_close(tabix_t *t) { if (t) { bgzf_close(t->fp); if (t->idx) ti_index_destroy(t->idx); free(t->fn); free(t->fnidx); free(t); } } int ti_lazy_index_load(tabix_t *t) { if (t->idx == 0) { // load index if (t->fnidx) t->idx = ti_index_load_local(t->fnidx); else t->idx = ti_index_load(t->fn); if (t->idx == 0) return -1; // fail to load index } return 0; } ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end) { if (tid < 0) return ti_iter_first(); if (ti_lazy_index_load(t) != 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } ti_iter_t ti_querys(tabix_t *t, const char *reg) { int tid, beg, end; if (reg == 0) return ti_iter_first(); if (ti_lazy_index_load(t) != 0) return 0; if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end) { int tid; if (name == 0) return ti_iter_first(); // then need to load the index if (ti_lazy_index_load(t) != 0) return 0; if ((tid = ti_get_tid(t->idx, name)) < 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } const char *ti_read(tabix_t *t, ti_iter_t iter, int *len) { return ti_iter_read(t->fp, iter, len); } pysam-0.7.7/tabix/bgzip.c.pysam.c0000664000076400007650000001351312162637166016461 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "bgzf.h" static const int WINDOW_SIZE = 64 * 1024; static int bgzip_main_usage() { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: bgzip [options] [file] ...\n\n"); fprintf(pysamerr, "Options: -c write on standard output, keep original files unchanged\n"); fprintf(pysamerr, " -d decompress\n"); fprintf(pysamerr, " -f overwrite files without asking\n"); fprintf(pysamerr, " -b INT decompress at virtual file pointer INT\n"); fprintf(pysamerr, " -s INT decompress INT bytes in the uncompressed file\n"); fprintf(pysamerr, " -h give this help\n"); fprintf(pysamerr, "\n"); return 1; } static int write_open(const char *fn, int is_forced) { int fd = -1; char c; if (!is_forced) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) { fprintf(pysamerr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn); scanf("%c", &c); if (c != 'Y' && c != 'y') { fprintf(pysamerr, "[bgzip] not overwritten\n"); exit(1); } } } if (fd < 0) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) { fprintf(pysamerr, "[bgzip] %s: Fail to write\n", fn); exit(1); } } return fd; } static void fail(BGZF* fp) { fprintf(pysamerr, "Error: %d\n", fp->errcode); exit(1); } int main(int argc, char **argv) { int c, compress, pstdout, is_forced; BGZF *fp; void *buffer; long start, end, size; compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){ switch(c){ case 'h': return bgzip_main_usage(); case 'd': compress = 0; break; case 'c': pstdout = 1; break; case 'b': start = atol(optarg); break; case 's': size = atol(optarg); break; case 'f': is_forced = 1; break; } } if (size >= 0) end = start + size; if (end >= 0 && end < start) { fprintf(pysamerr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end); return 1; } if (compress == 1) { struct stat sbuf; int f_src = fileno(stdin); int f_dst = fileno(stdout); if ( argc>optind ) { if ( stat(argv[optind],&sbuf)<0 ) { fprintf(pysamerr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } if ((f_src = open(argv[optind], O_RDONLY)) < 0) { fprintf(pysamerr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } if (pstdout) f_dst = fileno(stdout); else { char *name = malloc(strlen(argv[optind]) + 5); strcpy(name, argv[optind]); strcat(name, ".gz"); f_dst = write_open(name, is_forced); if (f_dst < 0) return 1; free(name); } } else if (!pstdout && isatty(fileno((FILE *)stdout)) ) return bgzip_main_usage(); fp = bgzf_dopen(f_dst, "w"); buffer = malloc(WINDOW_SIZE); while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0) if (bgzf_write(fp, buffer, c) < 0) fail(fp); // f_dst will be closed here if (bgzf_close(fp) < 0) fail(fp); if (argc > optind && !pstdout) unlink(argv[optind]); free(buffer); close(f_src); return 0; } else { struct stat sbuf; int f_dst; if ( argc>optind ) { if ( stat(argv[optind],&sbuf)<0 ) { fprintf(pysamerr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } char *name; int len = strlen(argv[optind]); if ( strcmp(argv[optind]+len-3,".gz") ) { fprintf(pysamerr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]); return 1; } fp = bgzf_open(argv[optind], "r"); if (fp == NULL) { fprintf(pysamerr, "[bgzip] Could not open file: %s\n", argv[optind]); return 1; } if (pstdout) { f_dst = fileno(stdout); } else { name = strdup(argv[optind]); name[strlen(name) - 3] = '\0'; f_dst = write_open(name, is_forced); free(name); } } else if (!pstdout && isatty(fileno((FILE *)stdin)) ) return bgzip_main_usage(); else { f_dst = fileno(stdout); fp = bgzf_dopen(fileno(stdin), "r"); if (fp == NULL) { fprintf(pysamerr, "[bgzip] Could not read from stdin: %s\n", strerror(errno)); return 1; } } buffer = malloc(WINDOW_SIZE); if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp); while (1) { if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE); else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); if (c == 0) break; if (c < 0) fail(fp); start += c; write(f_dst, buffer, c); if (end >= 0 && start >= end) break; } free(buffer); if (bgzf_close(fp) < 0) fail(fp); if (!pstdout) unlink(argv[optind]); return 0; } } pysam-0.7.7/tabix/index.c0000660000076400007650000006402112162637166015100 0ustar andreasandreas#include #include #include #include "khash.h" #include "ksort.h" #include "kstring.h" #include "bam_endian.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #include "tabix.h" #define TAD_MIN_CHUNK_GAP 32768 // 1<<14 is the size of minimum bin. #define TAD_LIDX_SHIFT 14 typedef struct { uint64_t u, v; } pair64_t; #define pair64_lt(a,b) ((a).u < (b).u) KSORT_INIT(offt, pair64_t, pair64_lt) typedef struct { uint32_t m, n; pair64_t *list; } ti_binlist_t; typedef struct { int32_t n, m; uint64_t *offset; } ti_lidx_t; KHASH_MAP_INIT_INT(i, ti_binlist_t) KHASH_MAP_INIT_STR(s, int) struct __ti_index_t { ti_conf_t conf; int32_t n, max; khash_t(s) *tname; khash_t(i) **index; ti_lidx_t *index2; }; struct __ti_iter_t { int from_first; // read from the first record; no random access int tid, beg, end, n_off, i, finished; uint64_t curr_off; kstring_t str; const ti_index_t *idx; pair64_t *off; }; typedef struct { int tid, beg, end, bin; } ti_intv_t; ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 }; ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 }; ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 }; ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 }; ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 }; /*************** * read a line * ***************/ /* int ti_readline(BGZF *fp, kstring_t *str) { int c, l = 0; str->l = 0; while ((c = bgzf_getc(fp)) >= 0 && c != '\n') { ++l; if (c != '\r') kputc(c, str); } if (c < 0 && l == 0) return -1; // end of file return str->l; } */ /* Below is a faster implementation largely equivalent to the one * commented out above. */ int ti_readline(BGZF *fp, kstring_t *str) { return bgzf_getline(fp, '\n', str); } /************************************* * get the interval from a data line * *************************************/ static inline int ti_reg2bin(uint32_t beg, uint32_t end) { --end; if (beg>>14 == end>>14) return 4681 + (beg>>14); if (beg>>17 == end>>17) return 585 + (beg>>17); if (beg>>20 == end>>20) return 73 + (beg>>20); if (beg>>23 == end>>23) return 9 + (beg>>23); if (beg>>26 == end>>26) return 1 + (beg>>26); return 0; } static int get_tid(ti_index_t *idx, const char *ss) { khint_t k; int tid; k = kh_get(s, idx->tname, ss); if (k == kh_end(idx->tname)) { // a new target sequence int ret, size; // update idx->n, ->max, ->index and ->index2 if (idx->n == idx->max) { idx->max = idx->max? idx->max<<1 : 8; idx->index = realloc(idx->index, idx->max * sizeof(void*)); idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t)); } memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t)); idx->index[idx->n++] = kh_init(i); // update ->tname tid = size = kh_size(idx->tname); k = kh_put(s, idx->tname, strdup(ss), &ret); kh_value(idx->tname, k) = size; assert(idx->n == kh_size(idx->tname)); } else tid = kh_value(idx->tname, k); return tid; } int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv) { int i, b = 0, id = 1, ncols = 0; char *s; intv->ss = intv->se = 0; intv->beg = intv->end = -1; for (i = 0; i <= len; ++i) { if (line[i] == '\t' || line[i] == 0) { ++ncols; if (id == conf->sc) { intv->ss = line + b; intv->se = line + i; } else if (id == conf->bc) { // here ->beg is 0-based. intv->beg = intv->end = strtol(line + b, &s, 0); if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg; else ++intv->end; if (intv->beg < 0) intv->beg = 0; if (intv->end < 1) intv->end = 1; } else { if ((conf->preset&0xffff) == TI_PRESET_GENERIC) { if (id == conf->ec) intv->end = strtol(line + b, &s, 0); } else if ((conf->preset&0xffff) == TI_PRESET_SAM) { if (id == 6) { // CIGAR int l = 0, op; char *t; for (s = line + b; s < line + i;) { long x = strtol(s, &t, 10); op = toupper(*t); if (op == 'M' || op == 'D' || op == 'N') l += x; s = t + 1; } if (l == 0) l = 1; intv->end = intv->beg + l; } } else if ((conf->preset&0xffff) == TI_PRESET_VCF) { // FIXME: the following is NOT tested and is likely to be buggy if (id == 4) { if (b < i) intv->end = intv->beg + (i - b); } else if (id == 8) { // look for "END=" int c = line[i]; line[i] = 0; s = strstr(line + b, "END="); if (s == line + b) s += 4; else if (s) { s = strstr(line + b, ";END="); if (s) s += 5; } if (s) intv->end = strtol(s, &s, 0); line[i] = c; } } } b = i + 1; ++id; } } /* if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) { if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line); else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line); exit(1); } */ if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1; return 0; } static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv) { ti_interval_t x; intv->tid = intv->beg = intv->end = intv->bin = -1; if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) { int c = *x.se; *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c; intv->beg = x.beg; intv->end = x.end; intv->bin = ti_reg2bin(intv->beg, intv->end); return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1; } else { fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s); return -1; } } /************ * indexing * ************/ // requirement: len <= LEN_MASK static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end) { khint_t k; ti_binlist_t *l; int ret; k = kh_put(i, h, bin, &ret); l = &kh_value(h, k); if (ret) { // not present l->m = 1; l->n = 0; l->list = (pair64_t*)calloc(l->m, 16); } if (l->n == l->m) { l->m <<= 1; l->list = (pair64_t*)realloc(l->list, l->m * 16); } l->list[l->n].u = beg; l->list[l->n++].v = end; } static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset) { int i, beg, end; beg = _beg >> TAD_LIDX_SHIFT; end = (_end - 1) >> TAD_LIDX_SHIFT; if (index2->m < end + 1) { int old_m = index2->m; index2->m = end + 1; kroundup32(index2->m); index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); } if (beg == end) { if (index2->offset[beg] == 0) index2->offset[beg] = offset; } else { for (i = beg; i <= end; ++i) if (index2->offset[i] == 0) index2->offset[i] = offset; } if (index2->n < end + 1) index2->n = end + 1; return (uint64_t)beg<<32 | end; } static void merge_chunks(ti_index_t *idx) { khash_t(i) *index; int i, l, m; khint_t k; for (i = 0; i < idx->n; ++i) { index = idx->index[i]; for (k = kh_begin(index); k != kh_end(index); ++k) { ti_binlist_t *p; if (!kh_exist(index, k)) continue; p = &kh_value(index, k); m = 0; for (l = 1; l < p->n; ++l) { if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v; else p->list[++m] = p->list[l]; } // ~for(l) p->n = m + 1; } // ~for(k) } // ~for(i) } static void fill_missing(ti_index_t *idx) { int i, j; for (i = 0; i < idx->n; ++i) { ti_lidx_t *idx2 = &idx->index2[i]; for (j = 1; j < idx2->n; ++j) if (idx2->offset[j] == 0) idx2->offset[j] = idx2->offset[j-1]; } } ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf) { int ret; ti_index_t *idx; uint32_t last_bin, save_bin; int32_t last_coor, last_tid, save_tid; uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp; kstring_t *str; str = calloc(1, sizeof(kstring_t)); idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); idx->conf = *conf; idx->n = idx->max = 0; idx->tname = kh_init(s); idx->index = 0; idx->index2 = 0; save_bin = save_tid = last_tid = last_bin = 0xffffffffu; save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu; while ((ret = ti_readline(fp, str)) >= 0) { ti_intv_t intv; ++lineno; if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) { last_off = bgzf_tell(fp); continue; } get_intv(idx, str, &intv); if ( intv.beg<0 || intv.end<0 ) { fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n"); exit(1); } if (last_tid != intv.tid) { // change of chromosomes if (last_tid>intv.tid ) { fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1); exit(1); } last_tid = intv.tid; last_bin = 0xffffffffu; } else if (last_coor > intv.beg) { fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno); exit(1); } tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off); if (last_off == 0) offset0 = tmp; if (intv.bin != last_bin) { // then possibly write the binning index if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record insert_offset(idx->index[save_tid], save_bin, save_off, last_off); save_off = last_off; save_bin = last_bin = intv.bin; save_tid = intv.tid; if (save_tid < 0) break; } if (bgzf_tell(fp) <= last_off) { fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n", (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off); exit(1); } last_off = bgzf_tell(fp); last_coor = intv.beg; } if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp)); merge_chunks(idx); fill_missing(idx); if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) { int i, beg = offset0>>32, end = offset0&0xffffffffu; for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0; } free(str->s); free(str); return idx; } void ti_index_destroy(ti_index_t *idx) { khint_t k; int i; if (idx == 0) return; // destroy the name hash table for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) { if (kh_exist(idx->tname, k)) free((char*)kh_key(idx->tname, k)); } kh_destroy(s, idx->tname); // destroy the binning index for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; ti_lidx_t *index2 = idx->index2 + i; for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) free(kh_value(index, k).list); } kh_destroy(i, index); free(index2->offset); } free(idx->index); // destroy the linear index free(idx->index2); free(idx); } /****************** * index file I/O * ******************/ void ti_index_save(const ti_index_t *idx, BGZF *fp) { int32_t i, size, ti_is_be; khint_t k; ti_is_be = bam_is_big_endian(); bgzf_write(fp, "TBI\1", 4); if (ti_is_be) { uint32_t x = idx->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &idx->n, 4); assert(sizeof(ti_conf_t) == 24); if (ti_is_be) { // write ti_conf_t; uint32_t x[6]; memcpy(x, &idx->conf, 24); for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4); } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t)); { // write target names char **name; int32_t l = 0; name = calloc(kh_size(idx->tname), sizeof(void*)); for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) if (kh_exist(idx->tname, k)) name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k); for (i = 0; i < kh_size(idx->tname); ++i) l += strlen(name[i]) + 1; if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4); else bgzf_write(fp, &l, 4); for (i = 0; i < kh_size(idx->tname); ++i) bgzf_write(fp, name[i], strlen(name[i]) + 1); free(name); } for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; ti_lidx_t *index2 = idx->index2 + i; // write binning index size = kh_size(index); if (ti_is_be) { // big endian uint32_t x = size; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &size, 4); for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) { ti_binlist_t *p = &kh_value(index, k); if (ti_is_be) { // big endian uint32_t x; x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4); x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } bgzf_write(fp, p->list, 16 * p->n); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } else { bgzf_write(fp, &kh_key(index, k), 4); bgzf_write(fp, &p->n, 4); bgzf_write(fp, p->list, 16 * p->n); } } } // write linear index (index2) if (ti_is_be) { int x = index2->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &index2->n, 4); if (ti_is_be) { // big endian int x; for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); bgzf_write(fp, index2->offset, 8 * index2->n); for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); } else bgzf_write(fp, index2->offset, 8 * index2->n); } } static ti_index_t *ti_index_load_core(BGZF *fp) { int i, ti_is_be; char magic[4]; ti_index_t *idx; ti_is_be = bam_is_big_endian(); if (fp == 0) { fprintf(stderr, "[ti_index_load_core] fail to load index.\n"); return 0; } bgzf_read(fp, magic, 4); if (strncmp(magic, "TBI\1", 4)) { fprintf(stderr, "[ti_index_load] wrong magic number.\n"); return 0; } idx = (ti_index_t*)calloc(1, sizeof(ti_index_t)); bgzf_read(fp, &idx->n, 4); if (ti_is_be) bam_swap_endian_4p(&idx->n); idx->tname = kh_init(s); idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t)); // read idx->conf bgzf_read(fp, &idx->conf, sizeof(ti_conf_t)); if (ti_is_be) { bam_swap_endian_4p(&idx->conf.preset); bam_swap_endian_4p(&idx->conf.sc); bam_swap_endian_4p(&idx->conf.bc); bam_swap_endian_4p(&idx->conf.ec); bam_swap_endian_4p(&idx->conf.meta_char); bam_swap_endian_4p(&idx->conf.line_skip); } { // read target names int j, ret; kstring_t *str; int32_t l; uint8_t *buf; bgzf_read(fp, &l, 4); if (ti_is_be) bam_swap_endian_4p(&l); buf = calloc(l, 1); bgzf_read(fp, buf, l); str = calloc(1, sizeof(kstring_t)); for (i = j = 0; i < l; ++i) { if (buf[i] == 0) { khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret); kh_value(idx->tname, k) = j++; str->l = 0; } else kputc(buf[i], str); } free(str->s); free(str); free(buf); } for (i = 0; i < idx->n; ++i) { khash_t(i) *index; ti_lidx_t *index2 = idx->index2 + i; uint32_t key, size; khint_t k; int j, ret; ti_binlist_t *p; index = idx->index[i] = kh_init(i); // load binning index bgzf_read(fp, &size, 4); if (ti_is_be) bam_swap_endian_4p(&size); for (j = 0; j < (int)size; ++j) { bgzf_read(fp, &key, 4); if (ti_is_be) bam_swap_endian_4p(&key); k = kh_put(i, index, key, &ret); p = &kh_value(index, k); bgzf_read(fp, &p->n, 4); if (ti_is_be) bam_swap_endian_4p(&p->n); p->m = p->n; p->list = (pair64_t*)malloc(p->m * 16); bgzf_read(fp, p->list, 16 * p->n); if (ti_is_be) { int x; for (x = 0; x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } } // load linear index bgzf_read(fp, &index2->n, 4); if (ti_is_be) bam_swap_endian_4p(&index2->n); index2->m = index2->n; index2->offset = (uint64_t*)calloc(index2->m, 8); bgzf_read(fp, index2->offset, index2->n * 8); if (ti_is_be) for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); } return idx; } ti_index_t *ti_index_load_local(const char *fnidx) { BGZF *fp; fp = bgzf_open(fnidx, "r"); if (fp) { ti_index_t *idx = ti_index_load_core(fp); bgzf_close(fp); return idx; } else return 0; } #ifdef _USE_KNETFILE static void download_from_remote(const char *url) { const int buf_size = 1 * 1024 * 1024; char *fn; FILE *fp; uint8_t *buf; knetFile *fp_remote; int l; if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; l = strlen(url); for (fn = (char*)url + l - 1; fn >= url; --fn) if (*fn == '/') break; ++fn; // fn now points to the file name fp_remote = knet_open(url, "r"); if (fp_remote == 0) { fprintf(stderr, "[download_from_remote] fail to open remote file.\n"); return; } if ((fp = fopen(fn, "w")) == 0) { fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n"); knet_close(fp_remote); return; } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) fwrite(buf, 1, l, fp); free(buf); fclose(fp); knet_close(fp_remote); } #else static void download_from_remote(const char *url) { return; } #endif static char *get_local_version(const char *fn) { struct stat sbuf; char *fnidx = (char*)calloc(strlen(fn) + 5, 1); strcat(strcpy(fnidx, fn), ".tbi"); if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { char *p, *url; int l = strlen(fnidx); for (p = fnidx + l - 1; p >= fnidx; --p) if (*p == '/') break; url = fnidx; fnidx = strdup(p + 1); if (stat(fnidx, &sbuf) == 0) { free(url); return fnidx; } fprintf(stderr, "[%s] downloading the index file...\n", __func__); download_from_remote(url); free(url); } if (stat(fnidx, &sbuf) == 0) return fnidx; free(fnidx); return 0; } const char **ti_seqname(const ti_index_t *idx, int *n) { const char **names; khint_t k; *n = idx->n; names = calloc(idx->n, sizeof(void*)); for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k) if (kh_exist(idx->tname, k)) names[kh_val(idx->tname, k)] = kh_key(idx->tname, k); return names; } ti_index_t *ti_index_load(const char *fn) { ti_index_t *idx; char *fname = get_local_version(fn); if (fname == 0) return 0; idx = ti_index_load_local(fname); if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname); free(fname); return idx; } int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx) { char *fnidx; BGZF *fp, *fpidx; ti_index_t *idx; if ((fp = bgzf_open(fn, "r")) == 0) { fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn); return -1; } idx = ti_index_core(fp, conf); bgzf_close(fp); if (_fnidx == 0) { fnidx = (char*)calloc(strlen(fn) + 5, 1); strcpy(fnidx, fn); strcat(fnidx, ".tbi"); } else fnidx = strdup(_fnidx); fpidx = bgzf_open(fnidx, "w"); if (fpidx == 0) { fprintf(stderr, "[ti_index_build2] fail to create the index file.\n"); free(fnidx); return -1; } ti_index_save(idx, fpidx); ti_index_destroy(idx); bgzf_close(fpidx); free(fnidx); return 0; } int ti_index_build(const char *fn, const ti_conf_t *conf) { return ti_index_build2(fn, conf, 0); } /******************************************** * parse a region in the format chr:beg-end * ********************************************/ int ti_get_tid(const ti_index_t *idx, const char *name) { khiter_t iter; const khash_t(s) *h = idx->tname; iter = kh_get(s, h, name); /* get the tid */ if (iter == kh_end(h)) return -1; return kh_value(h, iter); } int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end) { char *s, *p; int i, l, k; l = strlen(str); p = s = (char*)malloc(l+1); /* squeeze out "," */ for (i = k = 0; i != l; ++i) if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i]; s[k] = 0; for (i = 0; i != k; ++i) if (s[i] == ':') break; s[i] = 0; if ((*tid = ti_get_tid(idx, s)) < 0) { free(s); return -1; } if (i == k) { /* dump the whole sequence */ *begin = 0; *end = 1<<29; free(s); return 0; } for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break; *begin = atoi(p); if (i < k) { p = s + i + 1; *end = atoi(p); } else *end = 1<<29; if (*begin > 0) --*begin; free(s); if (*begin > *end) return -1; return 0; } /******************************* * retrieve a specified region * *******************************/ #define MAX_BIN 37450 // =(8^6-1)/7+1 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN]) { int i = 0, k; if (beg >= end) return 0; if (end >= 1u<<29) end = 1u<<29; --end; list[i++] = 0; for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; return i; } ti_iter_t ti_iter_first() { ti_iter_t iter; iter = calloc(1, sizeof(struct __ti_iter_t)); iter->from_first = 1; return iter; } ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end) { uint16_t *bins; int i, n_bins, n_off; pair64_t *off; khint_t k; khash_t(i) *index; uint64_t min_off; ti_iter_t iter = 0; if (beg < 0) beg = 0; if (end < beg) return 0; // initialize the iterator iter = calloc(1, sizeof(struct __ti_iter_t)); iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1; // random access bins = (uint16_t*)calloc(MAX_BIN, 2); n_bins = reg2bins(beg, end, bins); index = idx->index[tid]; if (idx->index2[tid].n > 0) { min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1] : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT]; if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4 int n = beg>>TAD_LIDX_SHIFT; if (n > idx->index2[tid].n) n = idx->index2[tid].n; for (i = n - 1; i >= 0; --i) if (idx->index2[tid].offset[i] != 0) break; if (i >= 0) min_off = idx->index2[tid].offset[i]; } } else min_off = 0; // tabix 0.1.2 may produce such index files for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) n_off += kh_value(index, k).n; } if (n_off == 0) { free(bins); return iter; } off = (pair64_t*)calloc(n_off, 16); for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) { int j; ti_binlist_t *p = &kh_value(index, k); for (j = 0; j < p->n; ++j) if (p->list[j].v > min_off) off[n_off++] = p->list[j]; } } if (n_off == 0) { free(bins); free(off); return iter; } free(bins); { int l; ks_introsort(offt, n_off, off); // resolve completely contained adjacent blocks for (i = 1, l = 0; i < n_off; ++i) if (off[l].v < off[i].v) off[++l] = off[i]; n_off = l + 1; // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing for (i = 1; i < n_off; ++i) if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; { // merge adjacent blocks for (i = 1, l = 0; i < n_off; ++i) { if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; else off[++l] = off[i]; } n_off = l + 1; } } iter->n_off = n_off; iter->off = off; return iter; } const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) { if (iter->finished) return 0; if (iter->from_first) { int ret; if ((ret = ti_readline(fp, &iter->str)) < 0) { iter->finished = 1; return 0; } else { if (len) *len = iter->str.l; return iter->str.s; } } if (iter->n_off == 0) return 0; while (1) { int ret; if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk if (iter->i == iter->n_off - 1) break; // no more chunks if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET); iter->curr_off = bgzf_tell(fp); } ++iter->i; } if ((ret = ti_readline(fp, &iter->str)) >= 0) { ti_intv_t intv; iter->curr_off = bgzf_tell(fp); if (iter->str.s[0] == iter->idx->conf.meta_char) continue; get_intv((ti_index_t*)iter->idx, &iter->str, &intv); if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed else if (intv.end > iter->beg && iter->end > intv.beg) { if (len) *len = iter->str.l; return iter->str.s; } } else break; // end of file } iter->finished = 1; return 0; } void ti_iter_destroy(ti_iter_t iter) { if (iter) { free(iter->str.s); free(iter->off); free(iter); } } int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func) { ti_iter_t iter; const char *s; int len; iter = ti_iter_query(idx, tid, beg, end); while ((s = ti_iter_read(fp, iter, &len)) != 0) func(len, s, data); ti_iter_destroy(iter); return 0; } const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; } /******************* * High-level APIs * *******************/ tabix_t *ti_open(const char *fn, const char *fnidx) { tabix_t *t; BGZF *fp; if ((fp = bgzf_open(fn, "r")) == 0) return 0; t = calloc(1, sizeof(tabix_t)); t->fn = strdup(fn); if (fnidx) t->fnidx = strdup(fnidx); t->fp = fp; return t; } void ti_close(tabix_t *t) { if (t) { bgzf_close(t->fp); if (t->idx) ti_index_destroy(t->idx); free(t->fn); free(t->fnidx); free(t); } } int ti_lazy_index_load(tabix_t *t) { if (t->idx == 0) { // load index if (t->fnidx) t->idx = ti_index_load_local(t->fnidx); else t->idx = ti_index_load(t->fn); if (t->idx == 0) return -1; // fail to load index } return 0; } ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end) { if (tid < 0) return ti_iter_first(); if (ti_lazy_index_load(t) != 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } ti_iter_t ti_querys(tabix_t *t, const char *reg) { int tid, beg, end; if (reg == 0) return ti_iter_first(); if (ti_lazy_index_load(t) != 0) return 0; if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end) { int tid; if (name == 0) return ti_iter_first(); // then need to load the index if (ti_lazy_index_load(t) != 0) return 0; if ((tid = ti_get_tid(t->idx, name)) < 0) return 0; return ti_iter_query(t->idx, tid, beg, end); } const char *ti_read(tabix_t *t, ti_iter_t iter, int *len) { return ti_iter_read(t->fp, iter, len); } pysam-0.7.7/tabix/khash.h0000660000076400007650000004021212162637166015070 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* An example: #include "khash.h" KHASH_MAP_INIT_INT(32, char) int main() { int ret, is_missing; khiter_t k; khash_t(32) *h = kh_init(32); k = kh_put(32, h, 5, &ret); if (!ret) kh_del(32, h, k); kh_value(h, k) = 10; k = kh_get(32, h, 10); is_missing = (k == kh_end(h)); k = kh_get(32, h, 5); kh_del(32, h, k); for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k)) kh_value(h, k) = 1; kh_destroy(32, h); return 0; } */ /* 2008-09-19 (0.2.3): * Corrected the example * Improved interfaces 2008-09-11 (0.2.2): * Improved speed a little in kh_put() 2008-09-10 (0.2.1): * Added kh_clear() * Fixed a compiling error 2008-09-02 (0.2.0): * Changed to token concatenation which increases flexibility. 2008-08-31 (0.1.2): * Fixed a bug in kh_get(), which has not been tested previously. 2008-08-31 (0.1.1): * Added destructor */ #ifndef __AC_KHASH_H #define __AC_KHASH_H /*! @header Generic hash table library. @copyright Heng Li */ #define AC_VERSION_KHASH_H "0.2.2" #include #include #include typedef uint32_t khint_t; typedef khint_t khiter_t; #define __ac_HASH_PRIME_SIZE 32 static const uint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] = { 0ul, 3ul, 11ul, 23ul, 53ul, 97ul, 193ul, 389ul, 769ul, 1543ul, 3079ul, 6151ul, 12289ul, 24593ul, 49157ul, 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul, 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul, 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul, 3221225473ul, 4294967291ul }; #define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) #define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) #define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) #define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) #define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) #define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) #define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) static const double __ac_HASH_UPPER = 0.77; #define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ typedef struct { \ khint_t n_buckets, size, n_occupied, upper_bound; \ uint32_t *flags; \ khkey_t *keys; \ khval_t *vals; \ } kh_##name##_t; \ static inline kh_##name##_t *kh_init_##name() { \ return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \ } \ static inline void kh_destroy_##name(kh_##name##_t *h) \ { \ if (h) { \ free(h->keys); free(h->flags); \ free(h->vals); \ free(h); \ } \ } \ static inline void kh_clear_##name(kh_##name##_t *h) \ { \ if (h && h->flags) { \ memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(uint32_t)); \ h->size = h->n_occupied = 0; \ } \ } \ static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ { \ if (h->n_buckets) { \ khint_t inc, k, i, last; \ k = __hash_func(key); i = k % h->n_buckets; \ inc = 1 + k % (h->n_buckets - 1); last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \ else i += inc; \ if (i == last) return h->n_buckets; \ } \ return __ac_iseither(h->flags, i)? h->n_buckets : i; \ } else return 0; \ } \ static inline void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ { \ uint32_t *new_flags = 0; \ khint_t j = 1; \ { \ khint_t t = __ac_HASH_PRIME_SIZE - 1; \ while (__ac_prime_list[t] > new_n_buckets) --t; \ new_n_buckets = __ac_prime_list[t+1]; \ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \ else { \ new_flags = (uint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \ memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(uint32_t)); \ if (h->n_buckets < new_n_buckets) { \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) \ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } \ } \ } \ if (j) { \ for (j = 0; j != h->n_buckets; ++j) { \ if (__ac_iseither(h->flags, j) == 0) { \ khkey_t key = h->keys[j]; \ khval_t val; \ if (kh_is_map) val = h->vals[j]; \ __ac_set_isdel_true(h->flags, j); \ while (1) { \ khint_t inc, k, i; \ k = __hash_func(key); \ i = k % new_n_buckets; \ inc = 1 + k % (new_n_buckets - 1); \ while (!__ac_isempty(new_flags, i)) { \ if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \ else i += inc; \ } \ __ac_set_isempty_false(new_flags, i); \ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ __ac_set_isdel_true(h->flags, i); \ } else { \ h->keys[i] = key; \ if (kh_is_map) h->vals[i] = val; \ break; \ } \ } \ } \ } \ if (h->n_buckets > new_n_buckets) { \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) \ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } \ free(h->flags); \ h->flags = new_flags; \ h->n_buckets = new_n_buckets; \ h->n_occupied = h->size; \ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ } \ } \ static inline khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ { \ khint_t x; \ if (h->n_occupied >= h->upper_bound) { \ if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \ else kh_resize_##name(h, h->n_buckets + 1); \ } \ { \ khint_t inc, k, i, site, last; \ x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \ if (__ac_isempty(h->flags, i)) x = i; \ else { \ inc = 1 + k % (h->n_buckets - 1); last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (__ac_isdel(h->flags, i)) site = i; \ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \ else i += inc; \ if (i == last) { x = site; break; } \ } \ if (x == h->n_buckets) { \ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ else x = i; \ } \ } \ } \ if (__ac_isempty(h->flags, x)) { \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; ++h->n_occupied; \ *ret = 1; \ } else if (__ac_isdel(h->flags, x)) { \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; \ *ret = 2; \ } else *ret = 0; \ return x; \ } \ static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ { \ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ __ac_set_isdel_true(h->flags, x); \ --h->size; \ } \ } /* --- BEGIN OF HASH FUNCTIONS --- */ /*! @function @abstract Integer hash function @param key The integer [uint32_t] @return The hash value [khint_t] */ #define kh_int_hash_func(key) (uint32_t)(key) /*! @function @abstract Integer comparison function */ #define kh_int_hash_equal(a, b) ((a) == (b)) /*! @function @abstract 64-bit integer hash function @param key The integer [uint64_t] @return The hash value [khint_t] */ #define kh_int64_hash_func(key) (uint32_t)((key)>>33^(key)^(key)<<11) /*! @function @abstract 64-bit integer comparison function */ #define kh_int64_hash_equal(a, b) ((a) == (b)) /*! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */ static inline khint_t __ac_X31_hash_string(const char *s) { khint_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } /*! @function @abstract Another interface to const char* hash function @param key Pointer to a null terminated string [const char*] @return The hash value [khint_t] */ #define kh_str_hash_func(key) __ac_X31_hash_string(key) /*! @function @abstract Const char* comparison function */ #define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) /* --- END OF HASH FUNCTIONS --- */ /* Other necessary macros... */ /*! @abstract Type of the hash table. @param name Name of the hash table [symbol] */ #define khash_t(name) kh_##name##_t /*! @function @abstract Initiate a hash table. @param name Name of the hash table [symbol] @return Pointer to the hash table [khash_t(name)*] */ #define kh_init(name) kh_init_##name() /*! @function @abstract Destroy a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_destroy(name, h) kh_destroy_##name(h) /*! @function @abstract Reset a hash table without deallocating memory. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_clear(name, h) kh_clear_##name(h) /*! @function @abstract Resize a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param s New size [khint_t] */ #define kh_resize(name, h, s) kh_resize_##name(h, s) /*! @function @abstract Insert a key to the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @param r Extra return code: 0 if the key is present in the hash table; 1 if the bucket is empty (never used); 2 if the element in the bucket has been deleted [int*] @return Iterator to the inserted element [khint_t] */ #define kh_put(name, h, k, r) kh_put_##name(h, k, r) /*! @function @abstract Retrieve a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t] */ #define kh_get(name, h, k) kh_get_##name(h, k) /*! @function @abstract Remove a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Iterator to the element to be deleted [khint_t] */ #define kh_del(name, h, k) kh_del_##name(h, k) /*! @function @abstract Test whether a bucket contains data. @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return 1 if containing data; 0 otherwise [int] */ #define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) /*! @function @abstract Get key given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Key [type of keys] */ #define kh_key(h, x) ((h)->keys[x]) /*! @function @abstract Get value given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Value [type of values] @discussion For hash sets, calling this results in segfault. */ #define kh_val(h, x) ((h)->vals[x]) /*! @function @abstract Alias of kh_val() */ #define kh_value(h, x) ((h)->vals[x]) /*! @function @abstract Get the start iterator @param h Pointer to the hash table [khash_t(name)*] @return The start iterator [khint_t] */ #define kh_begin(h) (khint_t)(0) /*! @function @abstract Get the end iterator @param h Pointer to the hash table [khash_t(name)*] @return The end iterator [khint_t] */ #define kh_end(h) ((h)->n_buckets) /*! @function @abstract Get the number of elements in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of elements in the hash table [khint_t] */ #define kh_size(h) ((h)->size) /*! @function @abstract Get the number of buckets in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of buckets in the hash table [khint_t] */ #define kh_n_buckets(h) ((h)->n_buckets) /* More conenient interfaces */ /*! @function @abstract Instantiate a hash set containing integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT(name) \ KHASH_INIT(name, uint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT(name, khval_t) \ KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT64(name) \ KHASH_INIT(name, uint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT64(name, khval_t) \ KHASH_INIT(name, uint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) typedef const char *kh_cstr_t; /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_STR(name) \ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_STR(name, khval_t) \ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) #endif /* __AC_KHASH_H */ pysam-0.7.7/tabix/tabix.h0000660000076400007650000001115012162637166015100 0ustar andreasandreas/* The MIT License Copyright (c) 2009 Genome Research Ltd (GRL), 2010 Broad Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ #ifndef __TABIDX_H #define __TABIDX_H #include #include "kstring.h" #include "bgzf.h" #define TI_PRESET_GENERIC 0 #define TI_PRESET_SAM 1 #define TI_PRESET_VCF 2 #define TI_FLAG_UCSC 0x10000 typedef int (*ti_fetch_f)(int l, const char *s, void *data); struct __ti_index_t; typedef struct __ti_index_t ti_index_t; struct __ti_iter_t; typedef struct __ti_iter_t *ti_iter_t; typedef struct { BGZF *fp; ti_index_t *idx; char *fn, *fnidx; } tabix_t; typedef struct { int32_t preset; int32_t sc, bc, ec; // seq col., beg col. and end col. int32_t meta_char, line_skip; } ti_conf_t; typedef struct { int beg, end; char *ss, *se; } ti_interval_t; extern ti_conf_t ti_conf_gff, ti_conf_bed, ti_conf_psltbl, ti_conf_vcf, ti_conf_sam; // preset #ifdef __cplusplus extern "C" { #endif /******************* * High-level APIs * *******************/ tabix_t *ti_open(const char *fn, const char *fnidx); int ti_lazy_index_load(tabix_t *t); void ti_close(tabix_t *t); ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end); ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end); ti_iter_t ti_querys(tabix_t *t, const char *reg); const char *ti_read(tabix_t *t, ti_iter_t iter, int *len); /* Destroy the iterator */ void ti_iter_destroy(ti_iter_t iter); /* Get the list of sequence names. Each "char*" pointer points to a * internal member of the index, so DO NOT modify the returned * pointer; otherwise the index will be corrupted. The returned * pointer should be freed by a single free() call by the routine * calling this function. The number of sequences is returned at *n. */ const char **ti_seqname(const ti_index_t *idx, int *n); /****************** * Low-level APIs * ******************/ /* Build the index for file . File .tbi will be generated * and overwrite the file of the same name. Return -1 on failure. */ int ti_index_build(const char *fn, const ti_conf_t *conf); /* Load the index from file .tbi. If is a URL and the index * file is not in the working directory, .tbi will be * downloaded. Return NULL on failure. */ ti_index_t *ti_index_load(const char *fn); ti_index_t *ti_index_load_local(const char *fnidx); /* Destroy the index */ void ti_index_destroy(ti_index_t *idx); /* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */ int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end); int ti_get_tid(const ti_index_t *idx, const char *name); /* Get the iterator pointing to the first record at the current file * position. If the file is just openned, the iterator points to the * first record in the file. */ ti_iter_t ti_iter_first(void); /* Get the iterator pointing to the first record in region tid:beg-end */ ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end); /* Get the data line pointed by the iterator and iterate to the next record. */ const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len); const ti_conf_t *ti_get_conf(ti_index_t *idx); int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv); /******************* * Deprecated APIs * *******************/ /* The callback version for random access */ int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func); /* Read one line. */ int ti_readline(BGZF *fp, kstring_t *str); #ifdef __cplusplus } #endif #endif pysam-0.7.7/tabix/kseq.h0000660000076400007650000001765412162637166014753 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* 2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*" */ /* Last Modified: 12APR2009 */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_MAX 1 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ unsigned char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { \ if (dret) *dret = 0; \ str->l = 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter > KS_SEP_MAX) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ if (str->m - str->l < i - ks->begin + 1) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (str->l == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } \ str->s[str->l] = '\0'; \ return str->l; \ } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #define __KSEQ_BASIC(type_t) \ static inline kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ static inline void kseq_rewind(kseq_t *ks) \ { \ ks->last_char = 0; \ ks->f->is_eof = ks->f->begin = ks->f->end = 0; \ } \ static inline void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string */ #define __KSEQ_READ \ static int kseq_read(kseq_t *seq) \ { \ int c; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ if (c == -1) return -1; /* end of file */ \ seq->last_char = c; \ } /* the first header char has been read */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; \ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; \ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ if (isgraph(c)) { /* printable non-space character */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l++] = (char)c; \ } \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate enough memory */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* we should not stop here */ \ while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l) \ if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c; \ seq->qual.s[seq->qual.l] = 0; /* null terminated string */ \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT(type_t, __read) \ KSTREAM_INIT(type_t, __read, 4096) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(type_t) \ __KSEQ_READ #endif pysam-0.7.7/tabix/bgzip.c0000660000076400007650000001341712162637166015107 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include "bgzf.h" static const int WINDOW_SIZE = 64 * 1024; static int bgzip_main_usage() { fprintf(stderr, "\n"); fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n"); fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n"); fprintf(stderr, " -d decompress\n"); fprintf(stderr, " -f overwrite files without asking\n"); fprintf(stderr, " -b INT decompress at virtual file pointer INT\n"); fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n"); fprintf(stderr, " -h give this help\n"); fprintf(stderr, "\n"); return 1; } static int write_open(const char *fn, int is_forced) { int fd = -1; char c; if (!is_forced) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) { fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn); scanf("%c", &c); if (c != 'Y' && c != 'y') { fprintf(stderr, "[bgzip] not overwritten\n"); exit(1); } } } if (fd < 0) { if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) { fprintf(stderr, "[bgzip] %s: Fail to write\n", fn); exit(1); } } return fd; } static void fail(BGZF* fp) { fprintf(stderr, "Error: %d\n", fp->errcode); exit(1); } int main(int argc, char **argv) { int c, compress, pstdout, is_forced; BGZF *fp; void *buffer; long start, end, size; compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){ switch(c){ case 'h': return bgzip_main_usage(); case 'd': compress = 0; break; case 'c': pstdout = 1; break; case 'b': start = atol(optarg); break; case 's': size = atol(optarg); break; case 'f': is_forced = 1; break; } } if (size >= 0) end = start + size; if (end >= 0 && end < start) { fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end); return 1; } if (compress == 1) { struct stat sbuf; int f_src = fileno(stdin); int f_dst = fileno(stdout); if ( argc>optind ) { if ( stat(argv[optind],&sbuf)<0 ) { fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } if ((f_src = open(argv[optind], O_RDONLY)) < 0) { fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } if (pstdout) f_dst = fileno(stdout); else { char *name = malloc(strlen(argv[optind]) + 5); strcpy(name, argv[optind]); strcat(name, ".gz"); f_dst = write_open(name, is_forced); if (f_dst < 0) return 1; free(name); } } else if (!pstdout && isatty(fileno((FILE *)stdout)) ) return bgzip_main_usage(); fp = bgzf_dopen(f_dst, "w"); buffer = malloc(WINDOW_SIZE); while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0) if (bgzf_write(fp, buffer, c) < 0) fail(fp); // f_dst will be closed here if (bgzf_close(fp) < 0) fail(fp); if (argc > optind && !pstdout) unlink(argv[optind]); free(buffer); close(f_src); return 0; } else { struct stat sbuf; int f_dst; if ( argc>optind ) { if ( stat(argv[optind],&sbuf)<0 ) { fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); return 1; } char *name; int len = strlen(argv[optind]); if ( strcmp(argv[optind]+len-3,".gz") ) { fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]); return 1; } fp = bgzf_open(argv[optind], "r"); if (fp == NULL) { fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]); return 1; } if (pstdout) { f_dst = fileno(stdout); } else { name = strdup(argv[optind]); name[strlen(name) - 3] = '\0'; f_dst = write_open(name, is_forced); free(name); } } else if (!pstdout && isatty(fileno((FILE *)stdin)) ) return bgzip_main_usage(); else { f_dst = fileno(stdout); fp = bgzf_dopen(fileno(stdin), "r"); if (fp == NULL) { fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno)); return 1; } } buffer = malloc(WINDOW_SIZE); if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp); while (1) { if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE); else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); if (c == 0) break; if (c < 0) fail(fp); start += c; write(f_dst, buffer, c); if (end >= 0 && start >= end) break; } free(buffer); if (bgzf_close(fp) < 0) fail(fp); if (!pstdout) unlink(argv[optind]); return 0; } } pysam-0.7.7/tabix/knetfile.c.pysam.c0000664000076400007650000004362512162637166017156 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* Probably I will not do socket programming in the next few years and therefore I decide to heavily annotate this file, for Linux and Windows as well. -lh3 */ #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #else #include #include #include #endif #include "knetfile.h" /* In winsock.h, the type of a socket is SOCKET, which is: "typedef * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed * integer -1. In knetfile.c, I use "int" for socket type * throughout. This should be improved to avoid confusion. * * In Linux/Mac, recv() and read() do almost the same thing. You can see * in the header file that netread() is simply an alias of read(). In * Windows, however, they are different and using recv() is mandatory. */ /* This function tests if the file handler is ready for reading (or * writing if is_read==0). */ static int socket_wait(int fd, int is_read) { fd_set fds, *fdr = 0, *fdw = 0; struct timeval tv; int ret; tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out FD_ZERO(&fds); FD_SET(fd, &fds); if (is_read) fdr = &fds; else fdw = &fds; ret = select(fd+1, fdr, fdw, 0, &tv); #ifndef _WIN32 if (ret == -1) perror("select"); #else if (ret == 0) fprintf(pysamerr, "select time-out\n"); else if (ret == SOCKET_ERROR) fprintf(pysamerr, "select: %d\n", WSAGetLastError()); #endif return ret; } #ifndef _WIN32 /* This function does not work with Windows due to the lack of * getaddrinfo() in winsock. It is addapted from an example in "Beej's * Guide to Network Programming" (http://beej.us/guide/bgnet/). */ static int socket_connect(const char *host, const char *port) { #define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0) int on = 1, fd; struct linger lng = { 0, 0 }; struct addrinfo hints, *res; memset(&hints, 0, sizeof(struct addrinfo)); hints.ai_family = AF_UNSPEC; hints.ai_socktype = SOCK_STREAM; /* In Unix/Mac, getaddrinfo() is the most convenient way to get * server information. */ if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo"); if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket"); /* The following two setsockopt() are used by ftplib * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they * necessary. */ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt"); if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect"); freeaddrinfo(res); return fd; } #else /* MinGW's printf has problem with "%lld" */ char *int64tostr(char *buf, int64_t x) { int cnt; int i = 0; do { buf[i++] = '0' + x % 10; x /= 10; } while (x); buf[i] = 0; for (cnt = i, i = 0; i < cnt/2; ++i) { int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c; } return buf; } int64_t strtoint64(const char *buf) { int64_t x; for (x = 0; *buf != '\0'; ++buf) x = x * 10 + ((int64_t) *buf - 48); return x; } /* In windows, the first thing is to establish the TCP connection. */ int knet_win32_init() { WSADATA wsaData; return WSAStartup(MAKEWORD(2, 2), &wsaData); } void knet_win32_destroy() { WSACleanup(); } /* A slightly modfied version of the following function also works on * Mac (and presummably Linux). However, this function is not stable on * my Mac. It sometimes works fine but sometimes does not. Therefore for * non-Windows OS, I do not use this one. */ static SOCKET socket_connect(const char *host, const char *port) { #define __err_connect(func) \ do { \ fprintf(pysamerr, "%s: %d\n", func, WSAGetLastError()); \ return -1; \ } while (0) int on = 1; SOCKET fd; struct linger lng = { 0, 0 }; struct sockaddr_in server; struct hostent *hp = 0; // open socket if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket"); if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt"); // get host info if (isalpha(host[0])) hp = gethostbyname(host); else { struct in_addr addr; addr.s_addr = inet_addr(host); hp = gethostbyaddr((char*)&addr, 4, AF_INET); } if (hp == 0) __err_connect("gethost"); // connect server.sin_addr.s_addr = *((unsigned long*)hp->h_addr); server.sin_family= AF_INET; server.sin_port = htons(atoi(port)); if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect"); // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!) return fd; } #endif static off_t my_netread(int fd, void *buf, off_t len) { off_t rest = len, curr, l = 0; /* recv() and read() may not read the required length of data with * one call. They have to be called repeatedly. */ while (rest) { if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading curr = netread(fd, buf + l, rest); /* According to the glibc manual, section 13.2, a zero returned * value indicates end-of-file (EOF), which should mean that * read() will not return zero if EOF has not been met but data * are not immediately available. */ if (curr == 0) break; l += curr; rest -= curr; } return l; } /************************* * FTP specific routines * *************************/ static int kftp_get_response(knetFile *ftp) { #ifndef _WIN32 unsigned char c; #else char c; #endif int n = 0; char *p; if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0; while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O //fputc(c, pysamerr); if (n >= ftp->max_response) { ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256; ftp->response = realloc(ftp->response, ftp->max_response); } ftp->response[n++] = c; if (c == '\n') { if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) && ftp->response[3] != '-') break; n = 0; continue; } } if (n < 2) return -1; ftp->response[n-2] = 0; return strtol(ftp->response, &p, 0); } static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get) { if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); return is_get? kftp_get_response(ftp) : 0; } static int kftp_pasv_prep(knetFile *ftp) { char *p; int v[6]; kftp_send_cmd(ftp, "PASV\r\n", 1); for (p = ftp->response; *p && *p != '('; ++p); if (*p != '(') return -1; ++p; sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]); memcpy(ftp->pasv_ip, v, 4 * sizeof(int)); ftp->pasv_port = (v[4]<<8&0xff00) + v[5]; return 0; } static int kftp_pasv_connect(knetFile *ftp) { char host[80], port[10]; if (ftp->pasv_port == 0) { fprintf(pysamerr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n"); return -1; } sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]); sprintf(port, "%d", ftp->pasv_port); ftp->fd = socket_connect(host, port); if (ftp->fd == -1) return -1; return 0; } int kftp_connect(knetFile *ftp) { ftp->ctrl_fd = socket_connect(ftp->host, ftp->port); if (ftp->ctrl_fd == -1) return -1; kftp_get_response(ftp); kftp_send_cmd(ftp, "USER anonymous\r\n", 1); kftp_send_cmd(ftp, "PASS kftp@\r\n", 1); kftp_send_cmd(ftp, "TYPE I\r\n", 1); return 0; } int kftp_reconnect(knetFile *ftp) { if (ftp->ctrl_fd != -1) { netclose(ftp->ctrl_fd); ftp->ctrl_fd = -1; } netclose(ftp->fd); ftp->fd = -1; return kftp_connect(ftp); } // initialize ->type, ->host, ->retr and ->size knetFile *kftp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p; int l; if (strstr(fn, "ftp://") != fn) return 0; for (p = (char*)fn + 6; *p && *p != '/'; ++p); if (*p != '/') return 0; l = p - fn - 6; fp = calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_FTP; fp->fd = -1; /* the Linux/Mac version of socket_connect() also recognizes a port * like "ftp", but the Windows version does not. */ fp->port = strdup("21"); fp->host = calloc(l + 1, 1); if (strchr(mode, 'c')) fp->no_reconnect = 1; strncpy(fp->host, fn + 6, l); fp->retr = calloc(strlen(p) + 8, 1); sprintf(fp->retr, "RETR %s\r\n", p); fp->size_cmd = calloc(strlen(p) + 8, 1); sprintf(fp->size_cmd, "SIZE %s\r\n", p); fp->seek_offset = 0; return fp; } // place ->fd at offset off int kftp_connect_file(knetFile *fp) { int ret; long long file_size; if (fp->fd != -1) { netclose(fp->fd); if (fp->no_reconnect) kftp_get_response(fp); } kftp_pasv_prep(fp); kftp_send_cmd(fp, fp->size_cmd, 1); #ifndef _WIN32 if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) { fprintf(pysamerr,"[kftp_connect_file] %s\n", fp->response); return -1; } #else const char *p = fp->response; while (*p != ' ') ++p; while (*p < '0' || *p > '9') ++p; file_size = strtoint64(p); #endif fp->file_size = file_size; if (fp->offset>=0) { char tmp[32]; #ifndef _WIN32 sprintf(tmp, "REST %lld\r\n", (long long)fp->offset); #else strcpy(tmp, "REST "); int64tostr(tmp + 5, fp->offset); strcat(tmp, "\r\n"); #endif kftp_send_cmd(fp, tmp, 1); } kftp_send_cmd(fp, fp->retr, 0); kftp_pasv_connect(fp); ret = kftp_get_response(fp); if (ret != 150) { fprintf(pysamerr, "[kftp_connect_file] %s\n", fp->response); netclose(fp->fd); fp->fd = -1; return -1; } fp->is_ready = 1; return 0; } /************************** * HTTP specific routines * **************************/ knetFile *khttp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p, *proxy, *q; int l; if (strstr(fn, "http://") != fn) return 0; // set ->http_host for (p = (char*)fn + 7; *p && *p != '/'; ++p); l = p - fn - 7; fp = calloc(1, sizeof(knetFile)); fp->http_host = calloc(l + 1, 1); strncpy(fp->http_host, fn + 7, l); fp->http_host[l] = 0; for (q = fp->http_host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; // get http_proxy proxy = getenv("http_proxy"); // set ->host, ->port and ->path if (proxy == 0) { fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name. fp->port = strdup(*q? q : "80"); fp->path = strdup(*p? p : "/"); } else { fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy); for (q = fp->host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; fp->port = strdup(*q? q : "80"); fp->path = strdup(fn); } fp->type = KNF_TYPE_HTTP; fp->ctrl_fd = fp->fd = -1; fp->seek_offset = 0; return fp; } int khttp_connect_file(knetFile *fp) { int ret, l = 0; char *buf, *p; if (fp->fd != -1) netclose(fp->fd); fp->fd = socket_connect(fp->host, fp->port); buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough. l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host); l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset); l += sprintf(buf + l, "\r\n"); netwrite(fp->fd, buf, l); l = 0; while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency if (buf[l] == '\n' && l >= 3) if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break; ++l; } buf[l] = 0; if (l < 14) { // prematured header netclose(fp->fd); fp->fd = -1; return -1; } ret = strtol(buf + 8, &p, 0); // HTTP return code if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file off_t rest = fp->offset; while (rest) { off_t l = rest < 0x10000? rest : 0x10000; rest -= my_netread(fp->fd, buf, l); } } else if (ret != 206 && ret != 200) { free(buf); fprintf(pysamerr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret); netclose(fp->fd); fp->fd = -1; return -1; } free(buf); fp->is_ready = 1; return 0; } /******************** * Generic routines * ********************/ knetFile *knet_open(const char *fn, const char *mode) { knetFile *fp = 0; if (mode[0] != 'r') { fprintf(pysamerr, "[kftp_open] only mode \"r\" is supported.\n"); return 0; } if (strstr(fn, "ftp://") == fn) { fp = kftp_parse_url(fn, mode); if (fp == 0) return 0; if (kftp_connect(fp) == -1) { knet_close(fp); return 0; } kftp_connect_file(fp); } else if (strstr(fn, "http://") == fn) { fp = khttp_parse_url(fn, mode); if (fp == 0) return 0; khttp_connect_file(fp); } else { // local file #ifdef _WIN32 /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may * be undefined on some systems, although it is defined on my * Mac and the Linux I have tested on. */ int fd = open(fn, O_RDONLY | O_BINARY); #else int fd = open(fn, O_RDONLY); #endif if (fd == -1) { perror("open"); return 0; } fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; fp->ctrl_fd = -1; } if (fp && fp->fd == -1) { knet_close(fp); return 0; } return fp; } knetFile *knet_dopen(int fd, const char *mode) { knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; return fp; } off_t knet_read(knetFile *fp, void *buf, off_t len) { off_t l = 0; if (fp->fd == -1) return 0; if (fp->type == KNF_TYPE_FTP) { if (fp->is_ready == 0) { if (!fp->no_reconnect) kftp_reconnect(fp); kftp_connect_file(fp); } } else if (fp->type == KNF_TYPE_HTTP) { if (fp->is_ready == 0) khttp_connect_file(fp); } if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX off_t rest = len, curr; while (rest) { curr = read(fp->fd, buf + l, rest); if (curr == 0) break; l += curr; rest -= curr; } } else l = my_netread(fp->fd, buf, len); fp->offset += l; return l; } off_t knet_seek(knetFile *fp, int64_t off, int whence) { if (whence == SEEK_SET && off == fp->offset) return 0; if (fp->type == KNF_TYPE_LOCAL) { /* Be aware that lseek() returns the offset after seeking, * while fseek() returns zero on success. */ off_t offset = lseek(fp->fd, off, whence); if (offset == -1) { // Be silent, it is OK for knet_seek to fail when the file is streamed // fprintf(pysamerr,"[knet_seek] %s\n", strerror(errno)); return -1; } fp->offset = offset; return 0; } else if (fp->type == KNF_TYPE_FTP) { if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; else if ( whence==SEEK_END) fp->offset = fp->file_size+off; fp->is_ready = 0; return 0; } else if (fp->type == KNF_TYPE_HTTP) { if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future? fprintf(pysamerr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n"); errno = ESPIPE; return -1; } if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; fp->is_ready = 0; return fp->offset; } errno = EINVAL; fprintf(pysamerr,"[knet_seek] %s\n", strerror(errno)); return -1; } int knet_close(knetFile *fp) { if (fp == 0) return 0; if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific if (fp->fd != -1) { /* On Linux/Mac, netclose() is an alias of close(), but on * Windows, it is an alias of closesocket(). */ if (fp->type == KNF_TYPE_LOCAL) close(fp->fd); else netclose(fp->fd); } free(fp->host); free(fp->port); free(fp->response); free(fp->retr); free(fp->size_cmd); // FTP specific free(fp->path); free(fp->http_host); // HTTP specific free(fp); return 0; } #ifdef KNETFILE_MAIN int main(void) { char *buf; knetFile *fp; int type = 4, l; #ifdef _WIN32 knet_win32_init(); #endif buf = calloc(0x100000, 1); if (type == 0) { fp = knet_open("knetfile.c", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 1) { // NCBI FTP, large file fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); knet_seek(fp, 2500000000ll, SEEK_SET); l = knet_read(fp, buf, 255); } else if (type == 2) { fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 3) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 4) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r"); knet_read(fp, buf, 10000); knet_seek(fp, 20000, SEEK_SET); knet_seek(fp, 10000, SEEK_SET); l = knet_read(fp, buf+10000, 10000000) + 10000; } if (type != 4 && type != 1) { knet_read(fp, buf, 255); buf[255] = 0; printf("%s\n", buf); } else write(fileno(stdout), buf, l); knet_close(fp); free(buf); return 0; } #endif pysam-0.7.7/tabix/pysam.h0000664000076400007650000000012212162637166015123 0ustar andreasandreas#ifndef PYSAM_H #define PYSAM_H #include "stdio.h" extern FILE * pysamerr; #endif pysam-0.7.7/tabix/bgzf.h0000660000076400007650000001316012162637166014724 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* The BGZF library was originally written by Bob Handsaker from the Broad * Institute. It was later improved by the SAMtools developers. */ #ifndef __BGZF_H #define __BGZF_H #include #include #include #define BGZF_BLOCK_SIZE 0x10000 // 64k #define BGZF_ERR_ZLIB 1 #define BGZF_ERR_HEADER 2 #define BGZF_ERR_IO 4 #define BGZF_ERR_MISUSE 8 typedef struct { int open_mode:8, compress_level:8, errcode:16; int cache_size; int block_length, block_offset; int64_t block_address; void *uncompressed_block, *compressed_block; void *cache; // a pointer to a hash table void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading } BGZF; #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifdef __cplusplus extern "C" { #endif /****************** * Basic routines * ******************/ /** * Open an existing file descriptor for reading or writing. * * @param fd file descriptor * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored. * @return BGZF file handler; 0 on error */ BGZF* bgzf_dopen(int fd, const char *mode); /** * Open the specified file for reading or writing. */ BGZF* bgzf_open(const char* path, const char *mode); /** * Close the BGZF and free all associated resources. * * @param fp BGZF file handler * @return 0 on success and -1 on error */ int bgzf_close(BGZF *fp); /** * Read up to _length_ bytes from the file storing into _data_. * * @param fp BGZF file handler * @param data data array to read into * @param length size of data to read * @return number of bytes actually read; 0 on end-of-file and -1 on error */ ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length); /** * Write _length_ bytes from _data_ to the file. * * @param fp BGZF file handler * @param data data array to write * @param length size of data to write * @return number of bytes actually written; -1 on error */ ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length); /** * Write the data in the buffer to the file. */ int bgzf_flush(BGZF *fp); /** * Return a virtual file pointer to the current location in the file. * No interpetation of the value should be made, other than a subsequent * call to bgzf_seek can be used to position the file at the same point. * Return value is non-negative on success. */ #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF)) /** * Set the file to read from the location specified by _pos_. * * @param fp BGZF file handler * @param pos virtual file offset returned by bgzf_tell() * @param whence must be SEEK_SET * @return 0 on success and -1 on error */ int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence); /** * Check if the BGZF end-of-file (EOF) marker is present * * @param fp BGZF file handler opened for reading * @return 1 if EOF is present; 0 if not or on I/O error */ int bgzf_check_EOF(BGZF *fp); /** * Check if a file is in the BGZF format * * @param fn file name * @return 1 if _fn_ is BGZF; 0 if not or on I/O error */ int bgzf_is_bgzf(const char *fn); /********************* * Advanced routines * *********************/ /** * Set the cache size. Only effective when compiled with -DBGZF_CACHE. * * @param fp BGZF file handler * @param size size of cache in bytes; 0 to disable caching (default) */ void bgzf_set_cache_size(BGZF *fp, int size); /** * Flush the file if the remaining buffer size is smaller than _size_ */ int bgzf_flush_try(BGZF *fp, ssize_t size); /** * Read one byte from a BGZF file. It is faster than bgzf_read() * @param fp BGZF file handler * @return byte read; -1 on end-of-file or error */ int bgzf_getc(BGZF *fp); /** * Read one line from a BGZF file. It is faster than bgzf_getc() * * @param fp BGZF file handler * @param delim delimitor * @param str string to write to; must be initialized * @return length of the string; 0 on end-of-file; negative on error */ int bgzf_getline(BGZF *fp, int delim, kstring_t *str); /** * Read the next BGZF block. */ int bgzf_read_block(BGZF *fp); #ifdef __cplusplus } #endif #endif pysam-0.7.7/tabix/kstring.c0000660000076400007650000000765112162637166015460 0ustar andreasandreas#include #include #include #include #include #include "kstring.h" int ksprintf(kstring_t *s, const char *fmt, ...) { va_list ap; int l; va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'. va_end(ap); if (l + 1 > s->m - s->l) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); } va_end(ap); s->l += l; return l; } // s MUST BE a null terminated string; l = strlen(s) int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) { int i, n, max, last_char, last_start, *offsets, l; n = 0; max = *_max; offsets = *_offsets; l = strlen(s); #define __ksplit_aux do { \ if (_offsets) { \ s[i] = 0; \ if (n == max) { \ max = max? max<<1 : 2; \ offsets = (int*)realloc(offsets, sizeof(int) * max); \ } \ offsets[n++] = last_start; \ } else ++n; \ } while (0) for (i = 0, last_char = last_start = 0; i <= l; ++i) { if (delimiter == 0) { if (isspace(s[i]) || s[i] == 0) { if (isgraph(last_char)) __ksplit_aux; // the end of a field } else { if (isspace(last_char) || last_char == 0) last_start = i; } } else { if (s[i] == delimiter || s[i] == 0) { if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field } else { if (last_char == delimiter || last_char == 0) last_start = i; } } last_char = s[i]; } *_max = max; *_offsets = offsets; return n; } /********************** * Boyer-Moore search * **********************/ // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html int *ksBM_prep(const uint8_t *pat, int m) { int i, *suff, *prep, *bmGs, *bmBc; prep = calloc(m + 256, 1); bmGs = prep; bmBc = prep + m; { // preBmBc() for (i = 0; i < 256; ++i) bmBc[i] = m; for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; } suff = calloc(m, sizeof(int)); { // suffixes() int f = 0, g; suff[m - 1] = m; g = m - 1; for (i = m - 2; i >= 0; --i) { if (i > g && suff[i + m - 1 - f] < i - g) suff[i] = suff[i + m - 1 - f]; else { if (i < g) g = i; f = i; while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; suff[i] = f - g; } } } { // preBmGs() int j = 0; for (i = 0; i < m; ++i) bmGs[i] = m; for (i = m - 1; i >= 0; --i) if (suff[i] == i + 1) for (; j < m - 1 - i; ++j) if (bmGs[j] == m) bmGs[j] = m - 1 - i; for (i = 0; i <= m - 2; ++i) bmGs[m - 1 - suff[i]] = m - 1 - i; } free(suff); return prep; } int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches) { int i, j, *prep, *bmGs, *bmBc; int *matches = 0, mm = 0, nm = 0; prep = _prep? _prep : ksBM_prep(pat, m); bmGs = prep; bmBc = prep + m; j = 0; while (j <= n - m) { for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); if (i < 0) { if (nm == mm) { mm = mm? mm<<1 : 1; matches = realloc(matches, mm * sizeof(int)); } matches[nm++] = j; j += bmGs[0]; } else { int max = bmBc[str[i+j]] - m + 1 + i; if (max < bmGs[i]) max = bmGs[i]; j += max; } } *n_matches = nm; if (_prep == 0) free(prep); return matches; } #ifdef KSTRING_MAIN #include int main() { kstring_t *s; int *fields, n, i; s = (kstring_t*)calloc(1, sizeof(kstring_t)); // test ksprintf() ksprintf(s, " abcdefg: %d ", 100); printf("'%s'\n", s->s); // test ksplit() fields = ksplit(s, 0, &n); for (i = 0; i < n; ++i) printf("field[%d] = '%s'\n", i, s->s + fields[i]); free(s); { static char *str = "abcdefgcdg"; static char *pat = "cd"; int n, *matches; matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n); printf("%d: \n", n); for (i = 0; i < n; ++i) printf("- %d\n", matches[i]); free(matches); } return 0; } #endif pysam-0.7.7/tabix/knetfile.h0000660000076400007650000000311312162637166015572 0ustar andreasandreas#ifndef KNETFILE_H #define KNETFILE_H #include #include #ifndef _WIN32 #define netread(fd, ptr, len) read(fd, ptr, len) #define netwrite(fd, ptr, len) write(fd, ptr, len) #define netclose(fd) close(fd) #else #include #define netread(fd, ptr, len) recv(fd, ptr, len, 0) #define netwrite(fd, ptr, len) send(fd, ptr, len, 0) #define netclose(fd) closesocket(fd) #endif // FIXME: currently I/O is unbuffered #define KNF_TYPE_LOCAL 1 #define KNF_TYPE_FTP 2 #define KNF_TYPE_HTTP 3 typedef struct knetFile_s { int type, fd; int64_t offset; char *host, *port; // the following are for FTP only int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; char *response, *retr, *size_cmd; int64_t seek_offset; // for lazy seek int64_t file_size; // the following are for HTTP only char *path, *http_host; } knetFile; #define knet_tell(fp) ((fp)->offset) #define knet_fileno(fp) ((fp)->fd) #ifdef __cplusplus extern "C" { #endif #ifdef _WIN32 int knet_win32_init(); void knet_win32_destroy(); #endif knetFile *knet_open(const char *fn, const char *mode); /* This only works with local files. */ knetFile *knet_dopen(int fd, const char *mode); /* If ->is_ready==0, this routine updates ->fd; otherwise, it simply reads from ->fd. */ off_t knet_read(knetFile *fp, void *buf, off_t len); /* This routine only sets ->offset and ->is_ready=0. It does not communicate with the FTP server. */ off_t knet_seek(knetFile *fp, int64_t off, int whence); int knet_close(knetFile *fp); #ifdef __cplusplus } #endif #endif pysam-0.7.7/tabix/bgzf.c0000660000076400007650000004125312162637166014723 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bgzf.h" #ifdef _USE_KNETFILE #include "knetfile.h" typedef knetFile *_bgzf_file_t; #define _bgzf_open(fn, mode) knet_open(fn, mode) #define _bgzf_dopen(fp, mode) knet_dopen(fp, mode) #define _bgzf_close(fp) knet_close(fp) #define _bgzf_fileno(fp) ((fp)->fd) #define _bgzf_tell(fp) knet_tell(fp) #define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence) #define _bgzf_read(fp, buf, len) knet_read(fp, buf, len) #define _bgzf_write(fp, buf, len) knet_write(fp, buf, len) #else // ~defined(_USE_KNETFILE) #if defined(_WIN32) || defined(_MSC_VER) #define ftello(fp) ftell(fp) #define fseeko(fp, offset, whence) fseek(fp, offset, whence) #else // ~defined(_WIN32) extern off_t ftello(FILE *stream); extern int fseeko(FILE *stream, off_t offset, int whence); #endif // ~defined(_WIN32) typedef FILE *_bgzf_file_t; #define _bgzf_open(fn, mode) fopen(fn, mode) #define _bgzf_dopen(fp, mode) fdopen(fp, mode) #define _bgzf_close(fp) fclose(fp) #define _bgzf_fileno(fp) fileno(fp) #define _bgzf_tell(fp) ftello(fp) #define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence) #define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp) #define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp) #endif // ~define(_USE_KNETFILE) #define BLOCK_HEADER_LENGTH 18 #define BLOCK_FOOTER_LENGTH 8 /* BGZF/GZIP header (speciallized from RFC 1952; little endian): +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ */ static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; #ifdef BGZF_CACHE typedef struct { int size; uint8_t *block; int64_t end_offset; } cache_t; #include "khash.h" KHASH_MAP_INIT_INT64(cache, cache_t) #endif static inline void packInt16(uint8_t *buffer, uint16_t value) { buffer[0] = value; buffer[1] = value >> 8; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static inline void packInt32(uint8_t *buffer, uint32_t value) { buffer[0] = value; buffer[1] = value >> 8; buffer[2] = value >> 16; buffer[3] = value >> 24; } static BGZF *bgzf_read_init() { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->open_mode = 'r'; fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_BLOCK_SIZE); #ifdef BGZF_CACHE fp->cache = kh_init(cache); #endif return fp; } static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->open_mode = 'w'; fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_BLOCK_SIZE); fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; return fp; } // get the compress level from the mode string static int mode2level(const char *__restrict mode) { int i, compress_level = -1; for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; if (mode[i]) compress_level = (int)mode[i] - '0'; if (strchr(mode, 'u')) compress_level = 0; return compress_level; } BGZF *bgzf_open(const char *path, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_open(path, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fopen(path, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } BGZF *bgzf_dopen(int fd, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fdopen(fd, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } // Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. static int deflate_block(BGZF *fp, int block_length) { uint8_t *buffer = fp->compressed_block; int buffer_size = BGZF_BLOCK_SIZE; int input_length = block_length; int compressed_length = 0; int remaining; uint32_t crc; assert(block_length <= BGZF_BLOCK_SIZE); // guaranteed by the caller memcpy(buffer, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block while (1) { // loop to retry for blocks that do not compress enough int status; z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = fp->uncompressed_block; zs.avail_in = input_length; zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH]; zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer if (status != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } status = deflate(&zs, Z_FINISH); if (status != Z_STREAM_END) { // not compressed enough deflateEnd(&zs); // reset the stream if (status == Z_OK) { // reduce the size and recompress input_length -= 1024; assert(input_length > 0); // logically, this should not happen continue; } fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (deflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } compressed_length = zs.total_out; compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; assert(compressed_length <= BGZF_BLOCK_SIZE); break; } assert(compressed_length > 0); packInt16((uint8_t*)&buffer[16], compressed_length - 1); // write the compressed_length; -1 to fit 2 bytes crc = crc32(0L, NULL, 0L); crc = crc32(crc, fp->uncompressed_block, input_length); packInt32((uint8_t*)&buffer[compressed_length-8], crc); packInt32((uint8_t*)&buffer[compressed_length-4], input_length); remaining = block_length - input_length; if (remaining > 0) { assert(remaining <= input_length); memcpy(fp->uncompressed_block, fp->uncompressed_block + input_length, remaining); } fp->block_offset = remaining; return compressed_length; } // Inflate the block in fp->compressed_block into fp->uncompressed_block static int inflate_block(BGZF* fp, int block_length) { z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = fp->compressed_block + 18; zs.avail_in = block_length - 16; zs.next_out = fp->uncompressed_block; zs.avail_out = BGZF_BLOCK_SIZE; if (inflateInit2(&zs, -15) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { inflateEnd(&zs); fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } return zs.total_out; } static int check_header(const uint8_t *header) { return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2); } #ifdef BGZF_CACHE static void free_cache(BGZF *fp) { khint_t k; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (fp->open_mode != 'r') return; for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) free(kh_val(h, k).block); kh_destroy(cache, h); } static int load_block_from_cache(BGZF *fp, int64_t block_address) { khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; k = kh_get(cache, h, block_address); if (k == kh_end(h)) return 0; p = &kh_val(h, k); if (fp->block_length != 0) fp->block_offset = 0; fp->block_address = block_address; fp->block_length = p->size; memcpy(fp->uncompressed_block, p->block, BGZF_BLOCK_SIZE); _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET); return p->size; } static void cache_block(BGZF *fp, int size) { int ret; khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (BGZF_BLOCK_SIZE >= fp->cache_size) return; if ((kh_size(h) + 1) * BGZF_BLOCK_SIZE > fp->cache_size) { /* A better way would be to remove the oldest block in the * cache, but here we remove a random one for simplicity. This * should not have a big impact on performance. */ for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) break; if (k < kh_end(h)) { free(kh_val(h, k).block); kh_del(cache, h, k); } } k = kh_put(cache, h, fp->block_address, &ret); if (ret == 0) return; // if this happens, a bug! p = &kh_val(h, k); p->size = fp->block_length; p->end_offset = fp->block_address + size; p->block = malloc(BGZF_BLOCK_SIZE); memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_BLOCK_SIZE); } #else static void free_cache(BGZF *fp) {} static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} static void cache_block(BGZF *fp, int size) {} #endif int bgzf_read_block(BGZF *fp) { uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, size = 0, block_length, remaining; int64_t block_address; block_address = _bgzf_tell((_bgzf_file_t)fp->fp); if (load_block_from_cache(fp, block_address)) return 0; count = _bgzf_read(fp->fp, header, sizeof(header)); if (count == 0) { // no data read fp->block_length = 0; return 0; } if (count != sizeof(header) || !check_header(header)) { fp->errcode |= BGZF_ERR_HEADER; return -1; } size = count; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" compressed_block = (uint8_t*)fp->compressed_block; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { fp->errcode |= BGZF_ERR_IO; return -1; } size += count; if ((count = inflate_block(fp, block_length)) < 0) return -1; if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. fp->block_address = block_address; fp->block_length = count; cache_block(fp, size); return 0; } ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length) { ssize_t bytes_read = 0; uint8_t *output = data; if (length <= 0) return 0; assert(fp->open_mode == 'r'); while (bytes_read < length) { int copy_length, available = fp->block_length - fp->block_offset; uint8_t *buffer; if (available <= 0) { if (bgzf_read_block(fp) != 0) return -1; available = fp->block_length - fp->block_offset; if (available <= 0) break; } copy_length = length - bytes_read < available? length - bytes_read : available; buffer = fp->uncompressed_block; memcpy(output, buffer + fp->block_offset, copy_length); fp->block_offset += copy_length; output += copy_length; bytes_read += copy_length; } if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = fp->block_length = 0; } return bytes_read; } int bgzf_flush(BGZF *fp) { assert(fp->open_mode == 'w'); while (fp->block_offset > 0) { int block_length; block_length = deflate_block(fp, fp->block_offset); if (block_length < 0) return -1; if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { fp->errcode |= BGZF_ERR_IO; // possibly truncated file return -1; } fp->block_address += block_length; } return 0; } int bgzf_flush_try(BGZF *fp, ssize_t size) { if (fp->block_offset + size > BGZF_BLOCK_SIZE) return bgzf_flush(fp); return -1; } ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; int block_length = BGZF_BLOCK_SIZE, bytes_written; assert(fp->open_mode == 'w'); input = data; bytes_written = 0; while (bytes_written < length) { uint8_t* buffer = fp->uncompressed_block; int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written; memcpy(buffer + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; bytes_written += copy_length; if (fp->block_offset == block_length && bgzf_flush(fp)) break; } return bytes_written; } int bgzf_close(BGZF* fp) { int ret, count, block_length; if (fp == 0) return -1; if (fp->open_mode == 'w') { if (bgzf_flush(fp) != 0) return -1; block_length = deflate_block(fp, 0); // write an empty block count = fwrite(fp->compressed_block, 1, block_length, fp->fp); if (fflush(fp->fp) != 0) { fp->errcode |= BGZF_ERR_IO; return -1; } } ret = fp->open_mode == 'w'? fclose(fp->fp) : _bgzf_close(fp->fp); if (ret != 0) return -1; free(fp->uncompressed_block); free(fp->compressed_block); free_cache(fp); free(fp); return 0; } void bgzf_set_cache_size(BGZF *fp, int cache_size) { if (fp) fp->cache_size = cache_size; } int bgzf_check_EOF(BGZF *fp) { static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; uint8_t buf[28]; off_t offset; offset = _bgzf_tell((_bgzf_file_t)fp->fp); if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0; _bgzf_read(fp->fp, buf, 28); _bgzf_seek(fp->fp, offset, SEEK_SET); return (memcmp(magic, buf, 28) == 0)? 1 : 0; } int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) { int block_offset; int64_t block_address; if (fp->open_mode != 'r' || where != SEEK_SET) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } block_offset = pos & 0xFFFF; block_address = pos >> 16; if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; return 0; } int bgzf_is_bgzf(const char *fn) { uint8_t buf[16]; int n; _bgzf_file_t fp; if ((fp = _bgzf_open(fn, "r")) == 0) return 0; n = _bgzf_read(fp, buf, 16); _bgzf_close(fp); if (n != 16) return 0; return memcmp(g_magic, buf, 16) == 0? 1 : 0; } int bgzf_getc(BGZF *fp) { int c; if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) return -2; /* error */ if (fp->block_length == 0) return -1; /* end-of-file */ } c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } return c; } #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif int bgzf_getline(BGZF *fp, int delim, kstring_t *str) { int l, state = 0; unsigned char *buf = (unsigned char*)fp->uncompressed_block; str->l = 0; do { if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) { state = -2; break; } if (fp->block_length == 0) { state = -1; break; } } for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); if (l < fp->block_length) state = 1; l -= fp->block_offset; if (str->l + l + 1 >= str->m) { str->m = str->l + l + 2; kroundup32(str->m); str->s = (char*)realloc(str->s, str->m); } memcpy(str->s + str->l, buf + fp->block_offset, l); str->l += l; fp->block_offset += l + 1; if (fp->block_offset >= fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } } while (state == 0); if (str->l == 0 && state < 0) return state; str->s[str->l] = 0; return str->l; } pysam-0.7.7/tabix/bgzf.c.pysam.c0000664000076400007650000004127712162637166016306 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include "bgzf.h" #ifdef _USE_KNETFILE #include "knetfile.h" typedef knetFile *_bgzf_file_t; #define _bgzf_open(fn, mode) knet_open(fn, mode) #define _bgzf_dopen(fp, mode) knet_dopen(fp, mode) #define _bgzf_close(fp) knet_close(fp) #define _bgzf_fileno(fp) ((fp)->fd) #define _bgzf_tell(fp) knet_tell(fp) #define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence) #define _bgzf_read(fp, buf, len) knet_read(fp, buf, len) #define _bgzf_write(fp, buf, len) knet_write(fp, buf, len) #else // ~defined(_USE_KNETFILE) #if defined(_WIN32) || defined(_MSC_VER) #define ftello(fp) ftell(fp) #define fseeko(fp, offset, whence) fseek(fp, offset, whence) #else // ~defined(_WIN32) extern off_t ftello(FILE *stream); extern int fseeko(FILE *stream, off_t offset, int whence); #endif // ~defined(_WIN32) typedef FILE *_bgzf_file_t; #define _bgzf_open(fn, mode) fopen(fn, mode) #define _bgzf_dopen(fp, mode) fdopen(fp, mode) #define _bgzf_close(fp) fclose(fp) #define _bgzf_fileno(fp) fileno(fp) #define _bgzf_tell(fp) ftello(fp) #define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence) #define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp) #define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp) #endif // ~define(_USE_KNETFILE) #define BLOCK_HEADER_LENGTH 18 #define BLOCK_FOOTER_LENGTH 8 /* BGZF/GZIP header (speciallized from RFC 1952; little endian): +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ */ static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; #ifdef BGZF_CACHE typedef struct { int size; uint8_t *block; int64_t end_offset; } cache_t; #include "khash.h" KHASH_MAP_INIT_INT64(cache, cache_t) #endif static inline void packInt16(uint8_t *buffer, uint16_t value) { buffer[0] = value; buffer[1] = value >> 8; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static inline void packInt32(uint8_t *buffer, uint32_t value) { buffer[0] = value; buffer[1] = value >> 8; buffer[2] = value >> 16; buffer[3] = value >> 24; } static BGZF *bgzf_read_init() { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->open_mode = 'r'; fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_BLOCK_SIZE); #ifdef BGZF_CACHE fp->cache = kh_init(cache); #endif return fp; } static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->open_mode = 'w'; fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_BLOCK_SIZE); fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; return fp; } // get the compress level from the mode string static int mode2level(const char *__restrict mode) { int i, compress_level = -1; for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; if (mode[i]) compress_level = (int)mode[i] - '0'; if (strchr(mode, 'u')) compress_level = 0; return compress_level; } BGZF *bgzf_open(const char *path, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_open(path, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fopen(path, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } BGZF *bgzf_dopen(int fd, const char *mode) { BGZF *fp = 0; if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fdopen(fd, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } // Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. static int deflate_block(BGZF *fp, int block_length) { uint8_t *buffer = fp->compressed_block; int buffer_size = BGZF_BLOCK_SIZE; int input_length = block_length; int compressed_length = 0; int remaining; uint32_t crc; assert(block_length <= BGZF_BLOCK_SIZE); // guaranteed by the caller memcpy(buffer, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block while (1) { // loop to retry for blocks that do not compress enough int status; z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = fp->uncompressed_block; zs.avail_in = input_length; zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH]; zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer if (status != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } status = deflate(&zs, Z_FINISH); if (status != Z_STREAM_END) { // not compressed enough deflateEnd(&zs); // reset the stream if (status == Z_OK) { // reduce the size and recompress input_length -= 1024; assert(input_length > 0); // logically, this should not happen continue; } fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (deflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } compressed_length = zs.total_out; compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; assert(compressed_length <= BGZF_BLOCK_SIZE); break; } assert(compressed_length > 0); packInt16((uint8_t*)&buffer[16], compressed_length - 1); // write the compressed_length; -1 to fit 2 bytes crc = crc32(0L, NULL, 0L); crc = crc32(crc, fp->uncompressed_block, input_length); packInt32((uint8_t*)&buffer[compressed_length-8], crc); packInt32((uint8_t*)&buffer[compressed_length-4], input_length); remaining = block_length - input_length; if (remaining > 0) { assert(remaining <= input_length); memcpy(fp->uncompressed_block, fp->uncompressed_block + input_length, remaining); } fp->block_offset = remaining; return compressed_length; } // Inflate the block in fp->compressed_block into fp->uncompressed_block static int inflate_block(BGZF* fp, int block_length) { z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = fp->compressed_block + 18; zs.avail_in = block_length - 16; zs.next_out = fp->uncompressed_block; zs.avail_out = BGZF_BLOCK_SIZE; if (inflateInit2(&zs, -15) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { inflateEnd(&zs); fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } return zs.total_out; } static int check_header(const uint8_t *header) { return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2); } #ifdef BGZF_CACHE static void free_cache(BGZF *fp) { khint_t k; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (fp->open_mode != 'r') return; for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) free(kh_val(h, k).block); kh_destroy(cache, h); } static int load_block_from_cache(BGZF *fp, int64_t block_address) { khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; k = kh_get(cache, h, block_address); if (k == kh_end(h)) return 0; p = &kh_val(h, k); if (fp->block_length != 0) fp->block_offset = 0; fp->block_address = block_address; fp->block_length = p->size; memcpy(fp->uncompressed_block, p->block, BGZF_BLOCK_SIZE); _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET); return p->size; } static void cache_block(BGZF *fp, int size) { int ret; khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (BGZF_BLOCK_SIZE >= fp->cache_size) return; if ((kh_size(h) + 1) * BGZF_BLOCK_SIZE > fp->cache_size) { /* A better way would be to remove the oldest block in the * cache, but here we remove a random one for simplicity. This * should not have a big impact on performance. */ for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) break; if (k < kh_end(h)) { free(kh_val(h, k).block); kh_del(cache, h, k); } } k = kh_put(cache, h, fp->block_address, &ret); if (ret == 0) return; // if this happens, a bug! p = &kh_val(h, k); p->size = fp->block_length; p->end_offset = fp->block_address + size; p->block = malloc(BGZF_BLOCK_SIZE); memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_BLOCK_SIZE); } #else static void free_cache(BGZF *fp) {} static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} static void cache_block(BGZF *fp, int size) {} #endif int bgzf_read_block(BGZF *fp) { uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, size = 0, block_length, remaining; int64_t block_address; block_address = _bgzf_tell((_bgzf_file_t)fp->fp); if (load_block_from_cache(fp, block_address)) return 0; count = _bgzf_read(fp->fp, header, sizeof(header)); if (count == 0) { // no data read fp->block_length = 0; return 0; } if (count != sizeof(header) || !check_header(header)) { fp->errcode |= BGZF_ERR_HEADER; return -1; } size = count; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" compressed_block = (uint8_t*)fp->compressed_block; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { fp->errcode |= BGZF_ERR_IO; return -1; } size += count; if ((count = inflate_block(fp, block_length)) < 0) return -1; if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. fp->block_address = block_address; fp->block_length = count; cache_block(fp, size); return 0; } ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length) { ssize_t bytes_read = 0; uint8_t *output = data; if (length <= 0) return 0; assert(fp->open_mode == 'r'); while (bytes_read < length) { int copy_length, available = fp->block_length - fp->block_offset; uint8_t *buffer; if (available <= 0) { if (bgzf_read_block(fp) != 0) return -1; available = fp->block_length - fp->block_offset; if (available <= 0) break; } copy_length = length - bytes_read < available? length - bytes_read : available; buffer = fp->uncompressed_block; memcpy(output, buffer + fp->block_offset, copy_length); fp->block_offset += copy_length; output += copy_length; bytes_read += copy_length; } if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = fp->block_length = 0; } return bytes_read; } int bgzf_flush(BGZF *fp) { assert(fp->open_mode == 'w'); while (fp->block_offset > 0) { int block_length; block_length = deflate_block(fp, fp->block_offset); if (block_length < 0) return -1; if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { fp->errcode |= BGZF_ERR_IO; // possibly truncated file return -1; } fp->block_address += block_length; } return 0; } int bgzf_flush_try(BGZF *fp, ssize_t size) { if (fp->block_offset + size > BGZF_BLOCK_SIZE) return bgzf_flush(fp); return -1; } ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; int block_length = BGZF_BLOCK_SIZE, bytes_written; assert(fp->open_mode == 'w'); input = data; bytes_written = 0; while (bytes_written < length) { uint8_t* buffer = fp->uncompressed_block; int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written; memcpy(buffer + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; bytes_written += copy_length; if (fp->block_offset == block_length && bgzf_flush(fp)) break; } return bytes_written; } int bgzf_close(BGZF* fp) { int ret, count, block_length; if (fp == 0) return -1; if (fp->open_mode == 'w') { if (bgzf_flush(fp) != 0) return -1; block_length = deflate_block(fp, 0); // write an empty block count = fwrite(fp->compressed_block, 1, block_length, fp->fp); if (fflush(fp->fp) != 0) { fp->errcode |= BGZF_ERR_IO; return -1; } } ret = fp->open_mode == 'w'? fclose(fp->fp) : _bgzf_close(fp->fp); if (ret != 0) return -1; free(fp->uncompressed_block); free(fp->compressed_block); free_cache(fp); free(fp); return 0; } void bgzf_set_cache_size(BGZF *fp, int cache_size) { if (fp) fp->cache_size = cache_size; } int bgzf_check_EOF(BGZF *fp) { static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; uint8_t buf[28]; off_t offset; offset = _bgzf_tell((_bgzf_file_t)fp->fp); if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0; _bgzf_read(fp->fp, buf, 28); _bgzf_seek(fp->fp, offset, SEEK_SET); return (memcmp(magic, buf, 28) == 0)? 1 : 0; } int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) { int block_offset; int64_t block_address; if (fp->open_mode != 'r' || where != SEEK_SET) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } block_offset = pos & 0xFFFF; block_address = pos >> 16; if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; return 0; } int bgzf_is_bgzf(const char *fn) { uint8_t buf[16]; int n; _bgzf_file_t fp; if ((fp = _bgzf_open(fn, "r")) == 0) return 0; n = _bgzf_read(fp, buf, 16); _bgzf_close(fp); if (n != 16) return 0; return memcmp(g_magic, buf, 16) == 0? 1 : 0; } int bgzf_getc(BGZF *fp) { int c; if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) return -2; /* error */ if (fp->block_length == 0) return -1; /* end-of-file */ } c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } return c; } #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif int bgzf_getline(BGZF *fp, int delim, kstring_t *str) { int l, state = 0; unsigned char *buf = (unsigned char*)fp->uncompressed_block; str->l = 0; do { if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) { state = -2; break; } if (fp->block_length == 0) { state = -1; break; } } for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); if (l < fp->block_length) state = 1; l -= fp->block_offset; if (str->l + l + 1 >= str->m) { str->m = str->l + l + 2; kroundup32(str->m); str->s = (char*)realloc(str->s, str->m); } memcpy(str->s + str->l, buf + fp->block_offset, l); str->l += l; fp->block_offset += l + 1; if (fp->block_offset >= fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } } while (state == 0); if (str->l == 0 && state < 0) return state; str->s[str->l] = 0; return str->l; } pysam-0.7.7/tabix/bedidx.c.pysam.c0000664000076400007650000000732212162637166016606 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "ksort.h" KSORT_INIT_GENERIC(uint64_t) #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 8192) typedef struct { int n, m; uint64_t *a; int *idx; } bed_reglist_t; #include "khash.h" KHASH_MAP_INIT_STR(reg, bed_reglist_t) #define LIDX_SHIFT 13 typedef kh_reg_t reghash_t; int *bed_index_core(int n, uint64_t *a, int *n_idx) { int i, j, m, *idx; m = *n_idx = 0; idx = 0; for (i = 0; i < n; ++i) { int beg, end; beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT; if (m < end + 1) { int oldm = m; m = end + 1; kroundup32(m); idx = realloc(idx, m * sizeof(int)); for (j = oldm; j < m; ++j) idx[j] = -1; } if (beg == end) { if (idx[beg] < 0) idx[beg] = i; } else { for (j = beg; j <= end; ++j) if (idx[j] < 0) idx[j] = i; } *n_idx = end + 1; } return idx; } void bed_index(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { bed_reglist_t *p = &kh_val(h, k); if (p->idx) free(p->idx); ks_introsort(uint64_t, p->n, p->a); p->idx = bed_index_core(p->n, p->a, &p->m); } } } int bed_overlap_core(const bed_reglist_t *p, int beg, int end) { int i, min_off; if (p->n == 0) return 0; min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT]; if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here int n = beg>>LIDX_SHIFT; if (n > p->n) n = p->n; for (i = n - 1; i >= 0; --i) if (p->idx[i] >= 0) break; min_off = i >= 0? p->idx[i] : 0; } for (i = min_off; i < p->n; ++i) { if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end) return 1; // find the overlap; return } return 0; } int bed_overlap(const void *_h, const char *chr, int beg, int end) { const reghash_t *h = (const reghash_t*)_h; khint_t k; if (!h) return 0; k = kh_get(reg, h, chr); if (k == kh_end(h)) return 0; return bed_overlap_core(&kh_val(h, k), beg, end); } void *bed_read(const char *fn) { reghash_t *h = kh_init(reg); gzFile fp; kstream_t *ks; int dret; kstring_t *str; // read the list fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) return 0; str = calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name int beg = -1, end = -1; bed_reglist_t *p; khint_t k = kh_get(reg, h, str->s); if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(str->s); k = kh_put(reg, h, s, &ret); memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); if (dret != '\n') { // if the lines has other characters if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) { beg = atoi(str->s); // begin if (dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) end = atoi(str->s); // end } } } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column if (beg >= 0 && end > beg) { if (p->n == p->m) { p->m = p->m? p->m<<1 : 4; p->a = realloc(p->a, p->m * 8); } p->a[p->n++] = (uint64_t)beg<<32 | end; } } ks_destroy(ks); gzclose(fp); free(str->s); free(str); bed_index(h); return h; } void bed_destroy(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); free(kh_val(h, k).idx); free((char*)kh_key(h, k)); } } kh_destroy(reg, h); } pysam-0.7.7/tabix/knetfile.c0000660000076400007650000004355112162637166015577 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* Probably I will not do socket programming in the next few years and therefore I decide to heavily annotate this file, for Linux and Windows as well. -lh3 */ #include #include #include #include #include #include #include #include #ifdef _WIN32 #include #else #include #include #include #endif #include "knetfile.h" /* In winsock.h, the type of a socket is SOCKET, which is: "typedef * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed * integer -1. In knetfile.c, I use "int" for socket type * throughout. This should be improved to avoid confusion. * * In Linux/Mac, recv() and read() do almost the same thing. You can see * in the header file that netread() is simply an alias of read(). In * Windows, however, they are different and using recv() is mandatory. */ /* This function tests if the file handler is ready for reading (or * writing if is_read==0). */ static int socket_wait(int fd, int is_read) { fd_set fds, *fdr = 0, *fdw = 0; struct timeval tv; int ret; tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out FD_ZERO(&fds); FD_SET(fd, &fds); if (is_read) fdr = &fds; else fdw = &fds; ret = select(fd+1, fdr, fdw, 0, &tv); #ifndef _WIN32 if (ret == -1) perror("select"); #else if (ret == 0) fprintf(stderr, "select time-out\n"); else if (ret == SOCKET_ERROR) fprintf(stderr, "select: %d\n", WSAGetLastError()); #endif return ret; } #ifndef _WIN32 /* This function does not work with Windows due to the lack of * getaddrinfo() in winsock. It is addapted from an example in "Beej's * Guide to Network Programming" (http://beej.us/guide/bgnet/). */ static int socket_connect(const char *host, const char *port) { #define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0) int on = 1, fd; struct linger lng = { 0, 0 }; struct addrinfo hints, *res; memset(&hints, 0, sizeof(struct addrinfo)); hints.ai_family = AF_UNSPEC; hints.ai_socktype = SOCK_STREAM; /* In Unix/Mac, getaddrinfo() is the most convenient way to get * server information. */ if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo"); if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket"); /* The following two setsockopt() are used by ftplib * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they * necessary. */ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt"); if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect"); freeaddrinfo(res); return fd; } #else /* MinGW's printf has problem with "%lld" */ char *int64tostr(char *buf, int64_t x) { int cnt; int i = 0; do { buf[i++] = '0' + x % 10; x /= 10; } while (x); buf[i] = 0; for (cnt = i, i = 0; i < cnt/2; ++i) { int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c; } return buf; } int64_t strtoint64(const char *buf) { int64_t x; for (x = 0; *buf != '\0'; ++buf) x = x * 10 + ((int64_t) *buf - 48); return x; } /* In windows, the first thing is to establish the TCP connection. */ int knet_win32_init() { WSADATA wsaData; return WSAStartup(MAKEWORD(2, 2), &wsaData); } void knet_win32_destroy() { WSACleanup(); } /* A slightly modfied version of the following function also works on * Mac (and presummably Linux). However, this function is not stable on * my Mac. It sometimes works fine but sometimes does not. Therefore for * non-Windows OS, I do not use this one. */ static SOCKET socket_connect(const char *host, const char *port) { #define __err_connect(func) \ do { \ fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \ return -1; \ } while (0) int on = 1; SOCKET fd; struct linger lng = { 0, 0 }; struct sockaddr_in server; struct hostent *hp = 0; // open socket if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket"); if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt"); // get host info if (isalpha(host[0])) hp = gethostbyname(host); else { struct in_addr addr; addr.s_addr = inet_addr(host); hp = gethostbyaddr((char*)&addr, 4, AF_INET); } if (hp == 0) __err_connect("gethost"); // connect server.sin_addr.s_addr = *((unsigned long*)hp->h_addr); server.sin_family= AF_INET; server.sin_port = htons(atoi(port)); if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect"); // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!) return fd; } #endif static off_t my_netread(int fd, void *buf, off_t len) { off_t rest = len, curr, l = 0; /* recv() and read() may not read the required length of data with * one call. They have to be called repeatedly. */ while (rest) { if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading curr = netread(fd, buf + l, rest); /* According to the glibc manual, section 13.2, a zero returned * value indicates end-of-file (EOF), which should mean that * read() will not return zero if EOF has not been met but data * are not immediately available. */ if (curr == 0) break; l += curr; rest -= curr; } return l; } /************************* * FTP specific routines * *************************/ static int kftp_get_response(knetFile *ftp) { #ifndef _WIN32 unsigned char c; #else char c; #endif int n = 0; char *p; if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0; while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O //fputc(c, stderr); if (n >= ftp->max_response) { ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256; ftp->response = realloc(ftp->response, ftp->max_response); } ftp->response[n++] = c; if (c == '\n') { if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) && ftp->response[3] != '-') break; n = 0; continue; } } if (n < 2) return -1; ftp->response[n-2] = 0; return strtol(ftp->response, &p, 0); } static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get) { if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); return is_get? kftp_get_response(ftp) : 0; } static int kftp_pasv_prep(knetFile *ftp) { char *p; int v[6]; kftp_send_cmd(ftp, "PASV\r\n", 1); for (p = ftp->response; *p && *p != '('; ++p); if (*p != '(') return -1; ++p; sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]); memcpy(ftp->pasv_ip, v, 4 * sizeof(int)); ftp->pasv_port = (v[4]<<8&0xff00) + v[5]; return 0; } static int kftp_pasv_connect(knetFile *ftp) { char host[80], port[10]; if (ftp->pasv_port == 0) { fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n"); return -1; } sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]); sprintf(port, "%d", ftp->pasv_port); ftp->fd = socket_connect(host, port); if (ftp->fd == -1) return -1; return 0; } int kftp_connect(knetFile *ftp) { ftp->ctrl_fd = socket_connect(ftp->host, ftp->port); if (ftp->ctrl_fd == -1) return -1; kftp_get_response(ftp); kftp_send_cmd(ftp, "USER anonymous\r\n", 1); kftp_send_cmd(ftp, "PASS kftp@\r\n", 1); kftp_send_cmd(ftp, "TYPE I\r\n", 1); return 0; } int kftp_reconnect(knetFile *ftp) { if (ftp->ctrl_fd != -1) { netclose(ftp->ctrl_fd); ftp->ctrl_fd = -1; } netclose(ftp->fd); ftp->fd = -1; return kftp_connect(ftp); } // initialize ->type, ->host, ->retr and ->size knetFile *kftp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p; int l; if (strstr(fn, "ftp://") != fn) return 0; for (p = (char*)fn + 6; *p && *p != '/'; ++p); if (*p != '/') return 0; l = p - fn - 6; fp = calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_FTP; fp->fd = -1; /* the Linux/Mac version of socket_connect() also recognizes a port * like "ftp", but the Windows version does not. */ fp->port = strdup("21"); fp->host = calloc(l + 1, 1); if (strchr(mode, 'c')) fp->no_reconnect = 1; strncpy(fp->host, fn + 6, l); fp->retr = calloc(strlen(p) + 8, 1); sprintf(fp->retr, "RETR %s\r\n", p); fp->size_cmd = calloc(strlen(p) + 8, 1); sprintf(fp->size_cmd, "SIZE %s\r\n", p); fp->seek_offset = 0; return fp; } // place ->fd at offset off int kftp_connect_file(knetFile *fp) { int ret; long long file_size; if (fp->fd != -1) { netclose(fp->fd); if (fp->no_reconnect) kftp_get_response(fp); } kftp_pasv_prep(fp); kftp_send_cmd(fp, fp->size_cmd, 1); #ifndef _WIN32 if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) { fprintf(stderr,"[kftp_connect_file] %s\n", fp->response); return -1; } #else const char *p = fp->response; while (*p != ' ') ++p; while (*p < '0' || *p > '9') ++p; file_size = strtoint64(p); #endif fp->file_size = file_size; if (fp->offset>=0) { char tmp[32]; #ifndef _WIN32 sprintf(tmp, "REST %lld\r\n", (long long)fp->offset); #else strcpy(tmp, "REST "); int64tostr(tmp + 5, fp->offset); strcat(tmp, "\r\n"); #endif kftp_send_cmd(fp, tmp, 1); } kftp_send_cmd(fp, fp->retr, 0); kftp_pasv_connect(fp); ret = kftp_get_response(fp); if (ret != 150) { fprintf(stderr, "[kftp_connect_file] %s\n", fp->response); netclose(fp->fd); fp->fd = -1; return -1; } fp->is_ready = 1; return 0; } /************************** * HTTP specific routines * **************************/ knetFile *khttp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p, *proxy, *q; int l; if (strstr(fn, "http://") != fn) return 0; // set ->http_host for (p = (char*)fn + 7; *p && *p != '/'; ++p); l = p - fn - 7; fp = calloc(1, sizeof(knetFile)); fp->http_host = calloc(l + 1, 1); strncpy(fp->http_host, fn + 7, l); fp->http_host[l] = 0; for (q = fp->http_host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; // get http_proxy proxy = getenv("http_proxy"); // set ->host, ->port and ->path if (proxy == 0) { fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name. fp->port = strdup(*q? q : "80"); fp->path = strdup(*p? p : "/"); } else { fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy); for (q = fp->host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; fp->port = strdup(*q? q : "80"); fp->path = strdup(fn); } fp->type = KNF_TYPE_HTTP; fp->ctrl_fd = fp->fd = -1; fp->seek_offset = 0; return fp; } int khttp_connect_file(knetFile *fp) { int ret, l = 0; char *buf, *p; if (fp->fd != -1) netclose(fp->fd); fp->fd = socket_connect(fp->host, fp->port); buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough. l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host); l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset); l += sprintf(buf + l, "\r\n"); netwrite(fp->fd, buf, l); l = 0; while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency if (buf[l] == '\n' && l >= 3) if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break; ++l; } buf[l] = 0; if (l < 14) { // prematured header netclose(fp->fd); fp->fd = -1; return -1; } ret = strtol(buf + 8, &p, 0); // HTTP return code if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file off_t rest = fp->offset; while (rest) { off_t l = rest < 0x10000? rest : 0x10000; rest -= my_netread(fp->fd, buf, l); } } else if (ret != 206 && ret != 200) { free(buf); fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret); netclose(fp->fd); fp->fd = -1; return -1; } free(buf); fp->is_ready = 1; return 0; } /******************** * Generic routines * ********************/ knetFile *knet_open(const char *fn, const char *mode) { knetFile *fp = 0; if (mode[0] != 'r') { fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n"); return 0; } if (strstr(fn, "ftp://") == fn) { fp = kftp_parse_url(fn, mode); if (fp == 0) return 0; if (kftp_connect(fp) == -1) { knet_close(fp); return 0; } kftp_connect_file(fp); } else if (strstr(fn, "http://") == fn) { fp = khttp_parse_url(fn, mode); if (fp == 0) return 0; khttp_connect_file(fp); } else { // local file #ifdef _WIN32 /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may * be undefined on some systems, although it is defined on my * Mac and the Linux I have tested on. */ int fd = open(fn, O_RDONLY | O_BINARY); #else int fd = open(fn, O_RDONLY); #endif if (fd == -1) { perror("open"); return 0; } fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; fp->ctrl_fd = -1; } if (fp && fp->fd == -1) { knet_close(fp); return 0; } return fp; } knetFile *knet_dopen(int fd, const char *mode) { knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; return fp; } off_t knet_read(knetFile *fp, void *buf, off_t len) { off_t l = 0; if (fp->fd == -1) return 0; if (fp->type == KNF_TYPE_FTP) { if (fp->is_ready == 0) { if (!fp->no_reconnect) kftp_reconnect(fp); kftp_connect_file(fp); } } else if (fp->type == KNF_TYPE_HTTP) { if (fp->is_ready == 0) khttp_connect_file(fp); } if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX off_t rest = len, curr; while (rest) { curr = read(fp->fd, buf + l, rest); if (curr == 0) break; l += curr; rest -= curr; } } else l = my_netread(fp->fd, buf, len); fp->offset += l; return l; } off_t knet_seek(knetFile *fp, int64_t off, int whence) { if (whence == SEEK_SET && off == fp->offset) return 0; if (fp->type == KNF_TYPE_LOCAL) { /* Be aware that lseek() returns the offset after seeking, * while fseek() returns zero on success. */ off_t offset = lseek(fp->fd, off, whence); if (offset == -1) { // Be silent, it is OK for knet_seek to fail when the file is streamed // fprintf(stderr,"[knet_seek] %s\n", strerror(errno)); return -1; } fp->offset = offset; return 0; } else if (fp->type == KNF_TYPE_FTP) { if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; else if ( whence==SEEK_END) fp->offset = fp->file_size+off; fp->is_ready = 0; return 0; } else if (fp->type == KNF_TYPE_HTTP) { if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future? fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n"); errno = ESPIPE; return -1; } if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; fp->is_ready = 0; return fp->offset; } errno = EINVAL; fprintf(stderr,"[knet_seek] %s\n", strerror(errno)); return -1; } int knet_close(knetFile *fp) { if (fp == 0) return 0; if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific if (fp->fd != -1) { /* On Linux/Mac, netclose() is an alias of close(), but on * Windows, it is an alias of closesocket(). */ if (fp->type == KNF_TYPE_LOCAL) close(fp->fd); else netclose(fp->fd); } free(fp->host); free(fp->port); free(fp->response); free(fp->retr); free(fp->size_cmd); // FTP specific free(fp->path); free(fp->http_host); // HTTP specific free(fp); return 0; } #ifdef KNETFILE_MAIN int main(void) { char *buf; knetFile *fp; int type = 4, l; #ifdef _WIN32 knet_win32_init(); #endif buf = calloc(0x100000, 1); if (type == 0) { fp = knet_open("knetfile.c", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 1) { // NCBI FTP, large file fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); knet_seek(fp, 2500000000ll, SEEK_SET); l = knet_read(fp, buf, 255); } else if (type == 2) { fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 3) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 4) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r"); knet_read(fp, buf, 10000); knet_seek(fp, 20000, SEEK_SET); knet_seek(fp, 10000, SEEK_SET); l = knet_read(fp, buf+10000, 10000000) + 10000; } if (type != 4 && type != 1) { knet_read(fp, buf, 255); buf[255] = 0; printf("%s\n", buf); } else write(fileno(stdout), buf, l); knet_close(fp); free(buf); return 0; } #endif pysam-0.7.7/tabix/__init__.py0000664000076400007650000000000012162643063015716 0ustar andreasandreaspysam-0.7.7/tabix/bam_endian.h0000660000076400007650000000205012162637166016045 0ustar andreasandreas#ifndef BAM_ENDIAN_H #define BAM_ENDIAN_H #include static inline int bam_is_big_endian() { long one= 1; return !(*((char *)(&one))); } static inline uint16_t bam_swap_endian_2(uint16_t v) { return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); } static inline void *bam_swap_endian_2p(void *x) { *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x); return x; } static inline uint32_t bam_swap_endian_4(uint32_t v) { v = ((v & 0x0000FFFFU) << 16) | (v >> 16); return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); } static inline void *bam_swap_endian_4p(void *x) { *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x); return x; } static inline uint64_t bam_swap_endian_8(uint64_t v) { v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); } static inline void *bam_swap_endian_8p(void *x) { *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x); return x; } #endif pysam-0.7.7/tabix/kstring.c.pysam.c0000664000076400007650000000767512162637166017043 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "kstring.h" int ksprintf(kstring_t *s, const char *fmt, ...) { va_list ap; int l; va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'. va_end(ap); if (l + 1 > s->m - s->l) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); } va_end(ap); s->l += l; return l; } // s MUST BE a null terminated string; l = strlen(s) int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) { int i, n, max, last_char, last_start, *offsets, l; n = 0; max = *_max; offsets = *_offsets; l = strlen(s); #define __ksplit_aux do { \ if (_offsets) { \ s[i] = 0; \ if (n == max) { \ max = max? max<<1 : 2; \ offsets = (int*)realloc(offsets, sizeof(int) * max); \ } \ offsets[n++] = last_start; \ } else ++n; \ } while (0) for (i = 0, last_char = last_start = 0; i <= l; ++i) { if (delimiter == 0) { if (isspace(s[i]) || s[i] == 0) { if (isgraph(last_char)) __ksplit_aux; // the end of a field } else { if (isspace(last_char) || last_char == 0) last_start = i; } } else { if (s[i] == delimiter || s[i] == 0) { if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field } else { if (last_char == delimiter || last_char == 0) last_start = i; } } last_char = s[i]; } *_max = max; *_offsets = offsets; return n; } /********************** * Boyer-Moore search * **********************/ // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html int *ksBM_prep(const uint8_t *pat, int m) { int i, *suff, *prep, *bmGs, *bmBc; prep = calloc(m + 256, 1); bmGs = prep; bmBc = prep + m; { // preBmBc() for (i = 0; i < 256; ++i) bmBc[i] = m; for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; } suff = calloc(m, sizeof(int)); { // suffixes() int f = 0, g; suff[m - 1] = m; g = m - 1; for (i = m - 2; i >= 0; --i) { if (i > g && suff[i + m - 1 - f] < i - g) suff[i] = suff[i + m - 1 - f]; else { if (i < g) g = i; f = i; while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; suff[i] = f - g; } } } { // preBmGs() int j = 0; for (i = 0; i < m; ++i) bmGs[i] = m; for (i = m - 1; i >= 0; --i) if (suff[i] == i + 1) for (; j < m - 1 - i; ++j) if (bmGs[j] == m) bmGs[j] = m - 1 - i; for (i = 0; i <= m - 2; ++i) bmGs[m - 1 - suff[i]] = m - 1 - i; } free(suff); return prep; } int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches) { int i, j, *prep, *bmGs, *bmBc; int *matches = 0, mm = 0, nm = 0; prep = _prep? _prep : ksBM_prep(pat, m); bmGs = prep; bmBc = prep + m; j = 0; while (j <= n - m) { for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); if (i < 0) { if (nm == mm) { mm = mm? mm<<1 : 1; matches = realloc(matches, mm * sizeof(int)); } matches[nm++] = j; j += bmGs[0]; } else { int max = bmBc[str[i+j]] - m + 1 + i; if (max < bmGs[i]) max = bmGs[i]; j += max; } } *n_matches = nm; if (_prep == 0) free(prep); return matches; } #ifdef KSTRING_MAIN #include int main() { kstring_t *s; int *fields, n, i; s = (kstring_t*)calloc(1, sizeof(kstring_t)); // test ksprintf() ksprintf(s, " abcdefg: %d ", 100); printf("'%s'\n", s->s); // test ksplit() fields = ksplit(s, 0, &n); for (i = 0; i < n; ++i) printf("field[%d] = '%s'\n", i, s->s + fields[i]); free(s); { static char *str = "abcdefgcdg"; static char *pat = "cd"; int n, *matches; matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n); printf("%d: \n", n); for (i = 0; i < n; ++i) printf("- %d\n", matches[i]); free(matches); } return 0; } #endif pysam-0.7.7/tabix/ksort.h0000660000076400007650000002271012162637166015137 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* 2008-11-16 (0.1.4): * Fixed a bug in introsort() that happens in rare cases. 2008-11-05 (0.1.3): * Fixed a bug in introsort() for complex comparisons. * Fixed a bug in mergesort(). The previous version is not stable. 2008-09-15 (0.1.2): * Accelerated introsort. On my Mac (not on another Linux machine), my implementation is as fast as std::sort on random input. * Added combsort and in introsort, switch to combsort if the recursion is too deep. 2008-09-13 (0.1.1): * Added k-small algorithm 2008-09-05 (0.1.0): * Initial version */ #ifndef AC_KSORT_H #define AC_KSORT_H #include #include typedef struct { void *left, *right; int depth; } ks_isort_stack_t; #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } #define KSORT_INIT(name, type_t, __sort_lt) \ void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \ { \ type_t *a2[2], *a, *b; \ int curr, shift; \ \ a2[0] = array; \ a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \ for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i) \ ks_heapadjust_##name(i, lsize, l); \ } \ void ks_heapsort_##name(size_t lsize, type_t l[]) \ { \ size_t i; \ for (i = lsize - 1; i > 0; --i) { \ type_t tmp; \ tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \ } \ } \ inline void __ks_insertsort_##name(type_t *s, type_t *t) \ { \ type_t *i, *j, swap_tmp; \ for (i = s + 1; i < t; ++i) \ for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \ } \ } \ void ks_combsort_##name(size_t n, type_t a[]) \ { \ const double shrink_factor = 1.2473309501039786540366528676643; \ int do_swap; \ size_t gap = n; \ type_t tmp, *i, *j; \ do { \ if (gap > 2) { \ gap = (size_t)(gap / shrink_factor); \ if (gap == 9 || gap == 10) gap = 11; \ } \ do_swap = 0; \ for (i = a; i < a + n - gap; ++i) { \ j = i + gap; \ if (__sort_lt(*j, *i)) { \ tmp = *i; *i = *j; *j = tmp; \ do_swap = 1; \ } \ } \ } while (do_swap || gap > 2); \ if (gap != 1) __ks_insertsort_##name(a, a + n); \ } \ void ks_introsort_##name(size_t n, type_t a[]) \ { \ int d; \ ks_isort_stack_t *top, *stack; \ type_t rp, swap_tmp; \ type_t *s, *t, *i, *j, *k; \ \ if (n < 1) return; \ else if (n == 2) { \ if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \ return; \ } \ for (d = 2; 1ul<>1) + 1; \ if (__sort_lt(*k, *i)) { \ if (__sort_lt(*k, *j)) k = j; \ } else k = __sort_lt(*j, *i)? i : j; \ rp = *k; \ if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \ for (;;) { \ do ++i; while (__sort_lt(*i, rp)); \ do --j; while (i <= j && __sort_lt(rp, *j)); \ if (j <= i) break; \ swap_tmp = *i; *i = *j; *j = swap_tmp; \ } \ swap_tmp = *i; *i = *t; *t = swap_tmp; \ if (i-s > t-i) { \ if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \ s = t-i > 16? i+1 : t; \ } else { \ if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \ t = i-s > 16? i-1 : s; \ } \ } else { \ if (top == stack) { \ free(stack); \ __ks_insertsort_##name(a, a+n); \ return; \ } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \ } \ } \ } \ /* This function is adapted from: http://ndevilla.free.fr/median/ */ \ /* 0 <= kk < n */ \ type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \ { \ type_t *low, *high, *k, *ll, *hh, *mid; \ low = arr; high = arr + n - 1; k = arr + kk; \ for (;;) { \ if (high <= low) return *k; \ if (high == low + 1) { \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ return *k; \ } \ mid = low + (high - low) / 2; \ if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ KSORT_SWAP(type_t, *mid, *(low+1)); \ ll = low + 1; hh = high; \ for (;;) { \ do ++ll; while (__sort_lt(*ll, *low)); \ do --hh; while (__sort_lt(*low, *hh)); \ if (hh < ll) break; \ KSORT_SWAP(type_t, *ll, *hh); \ } \ KSORT_SWAP(type_t, *low, *hh); \ if (hh <= k) low = ll; \ if (hh >= k) high = hh - 1; \ } \ } #define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t) #define ks_introsort(name, n, a) ks_introsort_##name(n, a) #define ks_combsort(name, n, a) ks_combsort_##name(n, a) #define ks_heapsort(name, n, a) ks_heapsort_##name(n, a) #define ks_heapmake(name, n, a) ks_heapmake_##name(n, a) #define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a) #define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k) #define ks_lt_generic(a, b) ((a) < (b)) #define ks_lt_str(a, b) (strcmp((a), (b)) < 0) typedef const char *ksstr_t; #define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic) #define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str) #endif pysam-0.7.7/tabix/kstring.h0000660000076400007650000000306312162637166015456 0ustar andreasandreas#ifndef KSTRING_H #define KSTRING_H #include #include #include #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif int ksprintf(kstring_t *s, const char *fmt, ...); int ksplit_core(char *s, int delimiter, int *_max, int **_offsets); // calculate the auxiliary array, allocated by calloc() int *ksBM_prep(const uint8_t *pat, int m); /* Search pat in str and returned the list of matches. The size of the * list is returned as n_matches. _prep is the array returned by * ksBM_prep(). If it is a NULL pointer, ksBM_prep() will be called. */ int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches); static inline int kputsn(const char *p, int l, kstring_t *s) { if (s->l + l + 1 >= s->m) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } strncpy(s->s + s->l, p, l); s->l += l; s->s[s->l] = 0; return l; } static inline int kputs(const char *p, kstring_t *s) { return kputsn(p, strlen(p), s); } static inline int kputc(int c, kstring_t *s) { if (s->l + 1 >= s->m) { s->m = s->l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } s->s[s->l++] = c; s->s[s->l] = 0; return c; } static inline int *ksplit(kstring_t *s, int delimiter, int *n) { int max = 0, *offsets = 0; *n = ksplit_core(s->s, delimiter, &max, &offsets); return offsets; } #endif pysam-0.7.7/setup.py0000664000076400007650000002100112216376174014222 0ustar andreasandreas#!/usr/bin/python ''' pysam ***** ''' import os, sys, glob, shutil, hashlib, re, fnmatch import platform name = "pysam" IS_PYTHON3 = sys.version_info[0] >= 3 # collect pysam version sys.path.insert( 0, "pysam") import version version = version.__version__ samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c", "main.c", "calDepth.c", "bam2bed.c", "wgsim.c", "md5fa.c", "maq2sam.c", "bamcheck.c", "chk_indel.c" ) samtools_dest = os.path.abspath( "samtools" ) tabix_exclude = ( "main.c", ) tabix_dest = os.path.abspath( "tabix" ) def locate(pattern, root=os.curdir): '''Locate all files matching supplied filename pattern in and below supplied root directory.''' for path, dirs, files in os.walk(os.path.abspath(root)): for filename in fnmatch.filter(files, pattern): yield os.path.join(path, filename) def _update_pysam_files(cf, destdir): '''update pysam files applying redirection of ouput''' for filename in cf: if not filename: continue dest = filename + ".pysam.c" with open( filename ) as infile: with open( dest, "w" ) as outfile: outfile.write( '#include "pysam.h"\n\n' ) outfile.write( re.sub( "stderr", "pysamerr", "".join(infile.readlines()) ) ) with open( os.path.join( destdir, "pysam.h" ), "w" )as outfile: outfile.write ("""#ifndef PYSAM_H #define PYSAM_H #include "stdio.h" extern FILE * pysamerr; #endif """) # copy samtools source if len(sys.argv) >= 2 and sys.argv[1] == "import": if len(sys.argv) < 3: raise ValueError("missing PATH to samtools source directory") if len(sys.argv) < 4: raise ValueError("missing PATH to tabix source directory") for destdir, srcdir, exclude in zip( (samtools_dest, tabix_dest), sys.argv[2:4], (samtools_exclude, tabix_exclude)): srcdir = os.path.abspath( srcdir ) if not os.path.exists( srcdir ): raise IOError( "samtools src dir `%s` does not exist." % srcdir ) cfiles = locate( "*.c", srcdir ) hfiles = locate( "*.h", srcdir ) ncopied = 0 def _compareAndCopy( src, srcdir, destdir, exclude ): d, f = os.path.split(src) if f in exclude: return None common_prefix = os.path.commonprefix( (d, srcdir ) ) subdir = re.sub( common_prefix, "", d )[1:] targetdir = os.path.join( destdir, subdir ) if not os.path.exists( targetdir ): os.makedirs( targetdir ) old_file = os.path.join( targetdir, f ) if os.path.exists( old_file ): md5_old = hashlib.md5("".join(open(old_file,"r").readlines())).digest() md5_new = hashlib.md5("".join(open(src,"r").readlines())).digest() if md5_old != md5_new: raise ValueError( "incompatible files for %s and %s" % (old_file, src )) shutil.copy( src, targetdir ) return old_file for src_file in hfiles: _compareAndCopy( src_file, srcdir,destdir, exclude ) ncopied += 1 cf = [] for src_file in cfiles: cf.append( _compareAndCopy( src_file, srcdir, destdir, exclude ) ) ncopied += 1 sys.stdout.write("installed latest source code from %s: %i files copied" % (srcdir, ncopied)) # redirect stderr to pysamerr and replace bam.h with a stub. sys.stdout.write("applying stderr redirection") _update_pysam_files(cf, destdir) sys.exit(0) if len(sys.argv) >= 2 and sys.argv[1] == "refresh": sys.stdout.write("refreshing latest source code from .c to .pysam.c") # redirect stderr to pysamerr and replace bam.h with a stub. sys.stdout.write("applying stderr redirection") for destdir in ('samtools', 'tabix'): pysamcfiles = locate( "*.pysam.c", destdir ) for f in pysamcfiles: os.remove(f) cfiles = locate( "*.c", destdir ) _update_pysam_files(cfiles, destdir) sys.exit(0) ################### # populate headers # mkdir pysam/include pysam/include/win32 # touch pysam/include/__init__.py pysam/include/win32/__init__.py # cp samtools/*.h pysam/*.h pysam/include # cp samtools/win32/*.h pysam/include/win32 try: from setuptools import Extension, setup, find_packages except ImportError: from ez_setup import use_setuptools use_setuptools() from setuptools import Extension, setup, find_packages ####################################################### ####################################################### try: from Cython.Distutils import build_ext except ImportError: # no Cython available - use existing C code cmdclass = { } csamtools_sources = [ "pysam/csamtools.c" ] tabix_sources = [ "pysam/ctabix.c" ] tabproxies_sources = ["pysam/TabProxies.c" ] cvcf_sources = ["pysam/cvcf.c" ] else: # remove existing files to recompute # necessary to be both compatible for python 2.7 and 3.3 if IS_PYTHON3: for f in ( "pysam/csamtools.c", "pysam/ctabix.c", "pysam/TabProxies.c", "pysam/cvcf.c" ): try: os.unlink( f ) except: pass cmdclass = { 'build_ext' : build_ext } csamtools_sources = [ "pysam/csamtools.pyx" ] tabix_sources = [ "pysam/ctabix.pyx" ] tabproxies_sources = ["pysam/TabProxies.pyx" ] cvcf_sources = ["pysam/cvcf.pyx" ] ####################################################### classifiers = """ Development Status :: 2 - Alpha Operating System :: MacOS :: MacOS X Operating System :: Microsoft :: Windows :: Windows NT/2000 Operating System :: OS Independent Operating System :: POSIX Operating System :: POSIX :: Linux Operating System :: Unix Programming Language :: Python Topic :: Scientific/Engineering Topic :: Scientific/Engineering :: Bioinformatics """ ####################################################### ## Windows compatibility if platform.system()=='Windows': include_os = ['win32'] os_c_files = ['win32/getopt.c'] else: include_os = [] os_c_files = [] ####################################################### samtools = Extension( "pysam.csamtools", csamtools_sources +\ [ "pysam/%s" % x for x in ( "pysam_util.c", )] +\ glob.glob( os.path.join( "samtools", "*.pysam.c" )) +\ os_c_files + \ glob.glob( os.path.join( "samtools", "*", "*.pysam.c" ) ), library_dirs=[], include_dirs=[ "samtools", "pysam" ] + include_os, libraries=[ "z", ], language="c", define_macros = [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')], ) tabix = Extension( "pysam.ctabix", tabix_sources +\ [ "pysam/%s" % x for x in ( "tabix_util.c", )] +\ os_c_files + \ glob.glob( os.path.join( "tabix", "*.pysam.c" ) ), library_dirs=[], include_dirs=[ "tabix", "pysam" ] + include_os, libraries=[ "z", ], language="c", define_macros = [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')], ) tabproxies = Extension( "pysam.TabProxies", tabproxies_sources + os_c_files, library_dirs=[], include_dirs= include_os, libraries=[ "z", ], language="c", ) cvcf = Extension( "pysam.cvcf", cvcf_sources + os_c_files, library_dirs=[], include_dirs= ["tabix",] + include_os, libraries=[ "z", ], language="c", ) metadata = { 'name': name, 'version': version, 'description': "pysam", 'long_description': __doc__, 'author': "Andreas Heger", 'author_email': "andreas.heger@gmail.com", 'license': "MIT", 'platforms': "ALL", 'url': "http://code.google.com/p/pysam/", 'packages' : ['pysam', 'pysam.include', 'pysam.include.samtools', 'pysam.include.samtools.bcftools', 'pysam.include.samtools.win32', 'pysam.include.tabix'], 'requires' : ['cython (>=0.17)'], 'ext_modules': [samtools, tabix, tabproxies, cvcf ], 'cmdclass' : cmdclass, 'install_requires' : ['cython>=0.17',], 'package_dir' : { 'pysam' : 'pysam', 'pysam.include.samtools' : 'samtools', 'pysam.include.tabix' : 'tabix' }, 'package_data' : { '' : ['*.pxd', '*.h'], }, # do not pack in order to permit linking to csamtools.so 'zip_safe' :False, 'use_2to3': True, } if __name__=='__main__': dist = setup(**metadata) pysam-0.7.7/pysam.egg-info/0000775000076400007650000000000012241575073015336 5ustar andreasandreaspysam-0.7.7/pysam.egg-info/dependency_links.txt0000664000076400007650000000000112241575073021404 0ustar andreasandreas pysam-0.7.7/pysam.egg-info/PKG-INFO0000664000076400007650000000044112241575073016432 0ustar andreasandreasMetadata-Version: 1.1 Name: pysam Version: 0.7.7 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger Author-email: andreas.heger@gmail.com License: MIT Description: pysam ***** Platform: ALL Requires: cython (>=0.17) pysam-0.7.7/pysam.egg-info/top_level.txt0000664000076400007650000000000612241575073020064 0ustar andreasandreaspysam pysam-0.7.7/pysam.egg-info/not-zip-safe0000664000076400007650000000000111705373166017567 0ustar andreasandreas pysam-0.7.7/pysam.egg-info/SOURCES.txt0000664000076400007650000001060112241575073017220 0ustar andreasandreasCOPYING INSTALL KNOWN_BUGS MANIFEST.in THANKS pysam.py setup.cfg setup.py doc/Makefile doc/api.rst doc/conf.py doc/contents.rst doc/developer.rst doc/faq.rst doc/glossary.rst doc/make.bat doc/release.rst doc/usage.rst pysam/Pileup.py pysam/TabProxies.c pysam/TabProxies.pxd pysam/TabProxies.pyx pysam/__init__.py pysam/csamtools.c pysam/csamtools.pxd pysam/csamtools.pyx pysam/ctabix.c pysam/ctabix.pxd pysam/ctabix.pyx pysam/cvcf.c pysam/cvcf.pxd pysam/cvcf.pyx pysam/namedtuple.py pysam/pysam_util.c pysam/pysam_util.h pysam/tabix_util.c pysam/tabix_util.h pysam/version.py pysam.egg-info/PKG-INFO pysam.egg-info/SOURCES.txt pysam.egg-info/dependency_links.txt pysam.egg-info/not-zip-safe pysam.egg-info/requires.txt pysam.egg-info/top_level.txt pysam/include/__init__.py samtools/__init__.py samtools/bam.c.pysam.c samtools/bam.h samtools/bam2bcf.c.pysam.c samtools/bam2bcf.h samtools/bam2bcf_indel.c.pysam.c samtools/bam2depth.c.pysam.c samtools/bam_aux.c.pysam.c samtools/bam_cat.c.pysam.c samtools/bam_color.c.pysam.c samtools/bam_endian.h samtools/bam_import.c.pysam.c samtools/bam_index.c.pysam.c samtools/bam_lpileup.c.pysam.c samtools/bam_mate.c.pysam.c samtools/bam_md.c.pysam.c samtools/bam_pileup.c.pysam.c samtools/bam_plcmd.c.pysam.c samtools/bam_reheader.c.pysam.c samtools/bam_rmdup.c.pysam.c samtools/bam_rmdupse.c.pysam.c samtools/bam_sort.c.pysam.c samtools/bam_stat.c.pysam.c samtools/bam_tview.c.pysam.c samtools/bam_tview.h samtools/bam_tview_curses.c.pysam.c samtools/bam_tview_html.c.pysam.c samtools/bamshuf.c.pysam.c samtools/bedcov.c.pysam.c samtools/bedidx.c.pysam.c samtools/bgzf.c.pysam.c samtools/bgzf.h samtools/cut_target.c.pysam.c samtools/errmod.c.pysam.c samtools/errmod.h samtools/faidx.c.pysam.c samtools/faidx.h samtools/kaln.c.pysam.c samtools/kaln.h samtools/khash.h samtools/klist.h samtools/knetfile.c.pysam.c samtools/knetfile.h samtools/kprobaln.c.pysam.c samtools/kprobaln.h samtools/kseq.h samtools/ksort.h samtools/kstring.c.pysam.c samtools/kstring.h samtools/padding.c.pysam.c samtools/phase.c.pysam.c samtools/pysam.h samtools/razf.c.pysam.c samtools/razf.h samtools/sam.c.pysam.c samtools/sam.h samtools/sam_header.c.pysam.c samtools/sam_header.h samtools/sam_view.c.pysam.c samtools/sample.c.pysam.c samtools/sample.h samtools/bcftools/__init__.py samtools/bcftools/bcf.c.pysam.c samtools/bcftools/bcf.h samtools/bcftools/bcf2qcall.c.pysam.c samtools/bcftools/bcfutils.c.pysam.c samtools/bcftools/call1.c.pysam.c samtools/bcftools/em.c.pysam.c samtools/bcftools/fet.c.pysam.c samtools/bcftools/index.c.pysam.c samtools/bcftools/kfunc.c.pysam.c samtools/bcftools/kmin.c.pysam.c samtools/bcftools/kmin.h samtools/bcftools/mut.c.pysam.c samtools/bcftools/prob1.c.pysam.c samtools/bcftools/prob1.h samtools/bcftools/vcf.c.pysam.c samtools/misc/ace2sam.c.pysam.c samtools/misc/md5.c.pysam.c samtools/misc/md5.h samtools/win32/__init__.py samtools/win32/xcurses.h samtools/win32/zconf.h samtools/win32/zlib.h tabix/__init__.py tabix/bam_endian.h tabix/bedidx.c tabix/bedidx.c.pysam.c tabix/bgzf.c tabix/bgzf.c.pysam.c tabix/bgzf.h tabix/bgzip.c tabix/bgzip.c.pysam.c tabix/index.c tabix/index.c.pysam.c tabix/khash.h tabix/knetfile.c tabix/knetfile.c.pysam.c tabix/knetfile.h tabix/kseq.h tabix/ksort.h tabix/kstring.c tabix/kstring.c.pysam.c tabix/kstring.h tabix/pysam.h tabix/tabix.h tests/00README.txt tests/Makefile tests/ex1.fa tests/ex1.sam.gz tests/ex10.sam tests/ex3.sam tests/ex4.sam tests/ex5.sam tests/ex6.sam tests/ex7.sam tests/ex8.sam tests/ex9_fail.bam tests/ex9_nofail.bam tests/example.bed.gz tests/example.bed.gz.tbi tests/example.gtf.gz tests/example.gtf.gz.tbi tests/example.py tests/example.vcf40 tests/example_btag.bam tests/example_btag.sam tests/example_empty_header.bam tests/example_unmapped_reads_no_sq.sam tests/example_user_header.sam tests/issue100.bam tests/pysam_test.py tests/segfault_tests.py tests/tabix_test.py tests/tag_bug.bam tests/test_unaligned.bam tests/vcf-examples/10.vcf tests/vcf-examples/11.vcf tests/vcf-examples/12.vcf tests/vcf-examples/13.vcf tests/vcf-examples/15.vcf tests/vcf-examples/16.vcf tests/vcf-examples/18.vcf tests/vcf-examples/2.vcf tests/vcf-examples/20.vcf tests/vcf-examples/21.vcf tests/vcf-examples/22.vcf tests/vcf-examples/23.vcf tests/vcf-examples/24.vcf tests/vcf-examples/3.vcf tests/vcf-examples/4.vcf tests/vcf-examples/5.vcf tests/vcf-examples/6.vcf tests/vcf-examples/7.vcf tests/vcf-examples/8.vcf tests/vcf-examples/9.vcf tests/vcf-examples/issue85.vcfpysam-0.7.7/pysam.egg-info/requires.txt0000664000076400007650000000001412241575073017731 0ustar andreasandreascython>=0.17pysam-0.7.7/MANIFEST.in0000664000076400007650000000320012163223270014234 0ustar andreasandreas# # Use .add_data_files and .add_data_dir methods in a appropriate # setup.py files to include non-python files such as documentation, # data, etc files to distribution. Avoid using MANIFEST.in for that. # include MANIFEST.in include COPYING include INSTALL include KNOWN_BUGS include THANKS include distribute_setup.py include pysam/csamtools.pxd include pysam/csamtools.pyx include pysam/csamtools.c include pysam/ctabix.pxd include pysam/ctabix.c include pysam/ctabix.pyx include pysam/TabProxies.c include pysam/TabProxies.pyx include pysam/TabProxies.pxd include pysam/cvcf.pyx include pysam/cvcf.pxd include pysam/cvcf.c include pysam/*.c include pysam/*.h include pysam/pysam_util.h include pysam/tabix_util.h include samtools/*.h include samtools/*/*.h include tabix/*.c include tabix/*.h include pysam.py # pysam tests include tests/00README.txt include tests/Makefile include tests/ex1.fa include tests/ex1.sam.gz include tests/ex3.sam include tests/ex4.sam include tests/ex5.sam include tests/ex6.sam include tests/ex7.sam include tests/ex8.sam include tests/ex9_fail.bam include tests/ex9_nofail.bam include tests/ex10.sam include tests/example.py include tests/pysam_test.py include tests/segfault_tests.py include tests/example_*.sam include tests/example_btag.bam include tests/tag_bug.bam include tests/example.vcf40 include tests/example_empty_header.bam include tests/test_unaligned.bam include tests/issue100.bam # tabix tests include tests/tabix_test.py include tests/example.gtf.gz include tests/example.gtf.gz.tbi include tests/example.bed.gz include tests/example.bed.gz.tbi include tests/vcf-examples/*.vcf # documentation include doc/* pysam-0.7.7/pysam/0000775000076400007650000000000012241575073013644 5ustar andreasandreaspysam-0.7.7/pysam/TabProxies.pyx0000664000076400007650000005137212216376103016471 0ustar andreasandreasimport types, sys from cpython.version cimport PY_MAJOR_VERSION from cpython cimport PyErr_SetString, PyBytes_Check, PyUnicode_Check, PyBytes_FromStringAndSize cdef from_string_and_size(char* s, size_t length): if PY_MAJOR_VERSION < 3: return s[:length] else: return s[:length].decode("ascii") # filename encoding (copied from lxml.etree.pyx) cdef str _FILENAME_ENCODING _FILENAME_ENCODING = sys.getfilesystemencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = sys.getdefaultencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = 'ascii' cdef bytes _my_encodeFilename(object filename): u"""Make sure a filename is 8-bit encoded (or None). """ if filename is None: return None elif PyBytes_Check(filename): return filename elif PyUnicode_Check(filename): return filename.encode(_FILENAME_ENCODING) else: raise TypeError, u"Argument must be string or unicode." cdef bytes _force_bytes(object s): u"""convert string or unicode object to bytes, assuming ascii encoding. """ if PY_MAJOR_VERSION < 3: return s elif s is None: return None elif PyBytes_Check(s): return s elif PyUnicode_Check(s): return s.encode('ascii') else: raise TypeError, u"Argument must be string, bytes or unicode." cdef inline bytes _force_cmdline_bytes(object s): return _force_bytes(s) cdef _charptr_to_str(char* s): if PY_MAJOR_VERSION < 3: return s else: return s.decode("ascii") cdef _force_str(object s): """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" if s is None: return None if PY_MAJOR_VERSION < 3: return s elif PyBytes_Check(s): return s.decode('ascii') else: # assume unicode return s cdef char * nextItem( char * buffer ): cdef char * pos pos = strchr( buffer, '\t' ) if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer ) pos[0] = '\0' pos += 1 return pos cdef char *StrOrEmpty( char * buffer ): if buffer == NULL: return "" else: return buffer cdef int isNew( char * p, char * buffer, size_t nbytes ): if p == NULL: return 0 return not (buffer <= p < buffer + nbytes ) cdef class TupleProxy: '''Proxy class for access to parsed row as a tuple. This class represents a table row for fast read-access. Access to individual fields is via the [] operator. Only read-only access is implemented. ''' def __cinit__(self ): self.data = NULL self.fields = NULL self.index = 0 self.nbytes = 0 self.is_modified = 0 self.nfields = 0 # start counting at field offset self.offset = 0 def __dealloc__(self): cdef int x if self.is_modified: for x from 0 <= x < self.nfields: if isNew( self.fields[x], self.data, self.nbytes ): free( self.fields[x] ) self.fields[x] = NULL if self.data != NULL: free(self.data) if self.fields != NULL: free( self.fields ) cdef take( self, char * buffer, size_t nbytes ): '''start presenting buffer. Take ownership of the pointer. ''' self.data = buffer self.nbytes = nbytes self.update( buffer, nbytes ) cdef present( self, char * buffer, size_t nbytes ): '''start presenting buffer. Do not take ownership of the pointer. ''' self.update( buffer, nbytes ) cdef copy( self, char * buffer, size_t nbytes ): '''start presenting buffer of size *nbytes*. Buffer is a '\0'-terminated string without the '\n'. Take a copy of buffer. ''' cdef int s # +1 for '\0' s = sizeof(char) * (nbytes + 1) self.data = malloc( s ) if self.data == NULL: raise ValueError("out of memory" ) self.nbytes = nbytes memcpy( self.data, buffer, s ) self.update( self.data, nbytes ) cdef int getMaxFields( self, size_t nbytes ): '''initialize fields.''' return nbytes / 2 cdef update( self, char * buffer, size_t nbytes ): '''update internal data. *buffer* is a \0 terminated string. *nbytes* is the number of bytes in buffer (excluding the \0) Update starts work in buffer, thus can be used to collect any number of fields until nbytes is exhausted. If max_fields is set, the number of fields is initialized to max_fields. ''' cdef char * pos cdef char * old_pos cdef int field cdef int max_fields, x assert strlen(buffer) == nbytes if buffer[nbytes] != 0: raise ValueError( "incomplete line at %s" % buffer ) ################################# # remove line breaks and feeds and update number of bytes x = nbytes - 1 while x > 0 and (buffer[x] == '\n' or buffer[x] == '\r'): buffer[x] = '\0' x -= 1 self.nbytes = x + 1 ################################# # clear data if self.fields != NULL: free(self.fields) for field from 0 <= field < self.nfields: if isNew( self.fields[field], self.data, self.nbytes ): free( self.fields[field] ) self.is_modified = self.nfields = 0 ################################# # allocate new max_fields = self.getMaxFields( nbytes ) self.fields = calloc( max_fields, sizeof(char *) ) if self.fields == NULL: raise ValueError("out of memory" ) ################################# # start filling field = 0 self.fields[field] = pos = buffer field += 1 old_pos = pos while 1: pos = memchr( pos, '\t', nbytes ) if pos == NULL: break pos[0] = '\0' pos += 1 self.fields[field] = pos field += 1 if field > max_fields: raise ValueError("row too large - more than %i fields" % max_fields ) nbytes -= pos - old_pos if nbytes < 0: break old_pos = pos self.nfields = field def _getindex( self, int index ): '''return item at idx index''' cdef int i = index if i < 0: i += self.nfields if i < 0: raise IndexError( "list index out of range" ) i += self.offset if i >= self.nfields: raise IndexError( "list index out of range %i >= %i" % (i, self.nfields )) return self.fields[i] def __getitem__( self, key ): if type(key) == int: return self._getindex( key ) # slice object start, end, step = key.indices( self.nfields ) result = [] for index in range( start, end, step ): result.append( self._getindex( index ) ) return result def _setindex( self, index, value ): '''set item at idx index.''' cdef int idx = index if idx < 0: raise IndexError( "list index out of range" ) if idx >= self.nfields: raise IndexError( "list index out of range" ) if isNew( self.fields[idx], self.data, self.nbytes ): free( self.fields[idx] ) self.is_modified = 1 if value == None: self.fields[idx] = NULL return # conversion with error checking value = _force_bytes(value) cdef char * tmp = value self.fields[idx] = malloc( (strlen( tmp ) + 1) * sizeof(char) ) if self.fields[idx] == NULL: raise ValueError("out of memory" ) strcpy( self.fields[idx], tmp ) def __setitem__(self, index, value ): '''set item at *index* to *value*''' cdef int i = index if i < 0: i += self.nfields i += self.offset self._setindex( i, value ) def __len__(self): return self.nfields def __iter__(self): self.index = 0 return self def __next__(self): """python version of next(). """ if self.index >= self.nfields: raise StopIteration cdef char * retval = self.fields[self.index] self.index += 1 if retval == NULL: return None else: return retval def __str__(self): '''return original data''' # copy and replace \0 bytes with \t characters if self.is_modified: # todo: treat NULL values result = [] for x in xrange( 0, self.nfields ): result.append( StrOrEmpty( self.fields[x]).decode('ascii') ) return "\t".join( result ) else: cpy = calloc( sizeof(char), self.nbytes+1 ) if cpy == NULL: raise ValueError("out of memory" ) memcpy( cpy, self.data, self.nbytes+1) for x from 0 <= x < self.nbytes: if cpy[x] == '\0': cpy[x] = '\t' result = cpy[:self.nbytes] free(cpy) return result.decode('ascii') def toDot( v ): '''convert value to '.' if None''' if v == None: return "." else: return str(v) def quote( v ): '''return a quoted attribute.''' if type(v) in types.StringTypes: return '"%s"' % v else: return str(v) cdef class GTFProxy( TupleProxy ): '''Proxy class for access to GTF fields. This class represents a GTF entry for fast read-access. Write-access has been added as well, though some care must be taken. If any of the string fields (contig, source, ...) are set, the new value is tied to the lifetime of the argument that was supplied. The only exception is the attributes field when set from a dictionary - this field will manage its own memory. ''' def __cinit__(self ): # automatically calls TupleProxy.__cinit__ self.hasOwnAttributes = False self._attributes = NULL def __dealloc__(self): # automatically calls TupleProxy.__dealloc__ if self.hasOwnAttributes: free(self._attributes) cdef int getMaxFields( self, size_t nbytes ): '''return max number of fields.''' return 9 property contig: '''contig of feature.''' def __get__( self ): return self._getindex( 0 ) def __set__( self, value ): self._setindex( 0, value ) property source: '''feature source.''' def __get__( self ): return self._getindex( 1 ) def __set__( self, value ): self._setindex( 1, value ) property feature: '''feature name.''' def __get__( self ): return self._getindex( 2 ) def __set__( self, value ): self._setindex( 2, value ) property start: '''feature start (in 0-based open/closed coordinates).''' def __get__( self ): return int( self._getindex( 3 )) - 1 def __set__( self, value ): self._setindex( 3, str(value+1) ) property end: '''feature end (in 0-based open/closed coordinates).''' def __get__( self ): return int( self._getindex( 4 ) ) def __set__( self, value ): self._setindex( 4, str(value) ) property score: '''feature score.''' def __get__( self ): v = self._getindex(5) if v == "" or v[0] == '.': return None else: return float(v) def __set__( self, value ): self._setindex( 5, value ) property strand: '''feature strand.''' def __get__( self ): return self._getindex( 6 ) def __set__( self, value ): self._setindex( 6, value ) property frame: '''feature frame.''' def __get__( self ): return self._getindex( 7 ) def __set__( self, value ): self._setindex( 7, value ) property attributes: '''feature attributes (as a string).''' def __get__( self ): if self.hasOwnAttributes: return self._attributes else: return self._getindex( 8 ) def __set__( self, value ): if self.hasOwnAttributes: free(self._attributes) self._attributes = NULL self.hasOwnAttributes = False self._setindex(8, value ) cdef char * getAttributes( self ): '''return pointer to attributes.''' if self.hasOwnAttributes: return self._attributes else: return self.fields[ 8 ] def asDict( self ): """parse attributes - return as dict """ # remove comments attributes = self.attributes # separate into fields fields = [ x.strip() for x in attributes.split(";")[:-1]] result = {} for f in fields: d = [ x.strip() for x in f.split(" ")] n,v = d[0], d[1] if len(d) > 2: v = d[1:] if v[0] == '"' and v[-1] == '"': v = v[1:-1] else: ## try to convert to a value try: v = float( v ) v = int( v ) except ValueError: pass except TypeError: pass result[n] = v return result def fromDict( self, d ): '''set attributes from a dictionary.''' cdef char * p cdef int l # clean up if this field is set twice if self.hasOwnAttributes: free(self._attributes) aa = [] for k,v in d.items(): if type(v) in types.StringTypes: aa.append( '%s "%s"' % (k,v) ) else: aa.append( '%s %s' % (k,str(v)) ) a = "; ".join( aa ) + ";" p = a l = len(a) self._attributes = calloc( l + 1, sizeof(char) ) if self._attributes == NULL: raise ValueError("out of memory" ) memcpy( self._attributes, p, l ) self.hasOwnAttributes = True self.is_modified = True def __str__(self): cdef char * cpy cdef int x if self.is_modified: return "\t".join( (self.contig, self.source, self.feature, str(self.start+1), str(self.end), toDot(self.score), self.strand, self.frame, self.attributes ) ) else: return TupleProxy.__str__(self) def invert( self, int lcontig ): '''invert coordinates to negative strand coordinates This method will only act if the feature is on the negative strand.''' if self.strand[0] == '-': start = min(self.start, self.end) end = max(self.start, self.end) self.start, self.end = lcontig - end, lcontig - start def keys( self ): '''return a list of attributes defined in this entry.''' r = self.attributes return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ] def __getitem__(self, key): return self.__getattr__( key ) def __getattr__(self, item ): """Generic lookup of attribute from GFF/GTF attributes Only called if there *isn't* an attribute with this name """ cdef char * start cdef char * query cdef char * cpy cdef char * end cdef int l # # important to use the getAttributes function. # Using the self.attributes property to access # the attributes caused a hard-to-trace bug # in which fields in the attribute string were # set to 0. # Running through valgrind complained that # memory was accessed in the memory field # that has been released. It is not clear # why this happened and might be a cython bug # (Version 0.16). The valgrind warnings # disappeard after accessing the C data structures # directly and so did the bug. cdef char * attributes = self.getAttributes() r = _force_bytes(item) query = r start = strstr( attributes, query) if start == NULL: raise AttributeError("'GTFProxy' has no attribute '%s'" % item ) start += strlen(query) + 1 # skip gaps before while start[0] == ' ': start += 1 if start[0] == '"': start += 1 end = start while end[0] != '\0' and end[0] != '"': end += 1 l = end - start result = _force_str( PyBytes_FromStringAndSize( start, l ) ) return result else: return _force_str( start ) def setAttribute( self, name, value ): '''convenience method to set an attribute.''' r = self.asDict() r[name] = value self.fromDict( r ) cdef class NamedTupleProxy( TupleProxy ): map_key2field = {} def __setattr__(self, key, value ): '''set attribute.''' cdef int idx idx, f = self.map_key2field[key] if self.nfields < idx: raise KeyError( "field %s not set" % key ) TupleProxy.__setitem__(self, idx, str(value) ) def __getattr__(self, key ): cdef int idx idx, f = self.map_key2field[key] if self.nfields < idx: raise KeyError( "field %s not set" % key ) return f( self.fields[idx] ) cdef class BedProxy( NamedTupleProxy ): '''Proxy class for access to Bed fields. This class represents a GTF entry for fast read-access. ''' map_key2field = { 'contig' : (0, bytes), 'start' : (1, int), 'end' : (2, int), 'name' : (3, bytes), 'score' : (4, float), 'strand' : (5, bytes), 'thickStart' : (6, int ), 'thickEnd' : (7, int), 'itemRGB' : (8, bytes), 'blockCount': (9, int), 'blockSizes': (10, bytes), 'blockStarts': (11, bytes), } cdef int getMaxFields( self, size_t nbytes ): '''return max number of fields.''' return 12 cdef update( self, char * buffer, size_t nbytes ): '''update internal data. nbytes does not include the terminal '\0'. ''' TupleProxy.update( self, buffer, nbytes ) if self.nfields < 3: raise ValueError( "bed format requires at least three columns" ) # determines bed format self.bedfields = self.nfields # do automatic conversion self.contig = self.fields[0] self.start = atoi( self.fields[1] ) self.end = atoi( self.fields[2] ) # __setattr__ in base class seems to take precedence # hence implement setters in __setattr__ #property start: # def __get__( self ): return self.start #property end: # def __get__( self ): return self.end def __str__(self): cdef int save_fields = self.nfields # ensure fields to use correct format self.nfields = self.bedfields retval = TupleProxy.__str__( self ) self.nfields = save_fields return retval def __setattr__(self, key, value ): '''set attribute.''' if key == "start": self.start = value elif key == "end": self.end = value cdef int idx idx, f = self.map_key2field[key] TupleProxy._setindex(self, idx, str(value) ) cdef class VCFProxy( NamedTupleProxy ): '''Proxy class for access to VCF fields. The genotypes are accessed via index. ''' map_key2field = { 'contig' : (0, bytes), 'pos' : (1, int), 'id' : (2, bytes), 'ref' : (3, bytes), 'alt' : (4, bytes), 'qual' : (5, bytes), 'filter' : (6, bytes), 'info' : (7, bytes), 'format' : (8, bytes) } def __cinit__(self ): # automatically calls TupleProxy.__cinit__ # start indexed access at genotypes self.offset = 9 cdef update( self, char * buffer, size_t nbytes ): '''update internal data. nbytes does not include the terminal '\0'. ''' TupleProxy.update( self, buffer, nbytes ) self.contig = self.fields[0] # vcf counts from 1 - correct here self.pos = atoi( self.fields[1] ) - 1 def __len__(self): '''return number of genotype fields.''' return max(0, self.nfields - 9) property pos: '''feature end (in 0-based open/closed coordinates).''' def __get__( self ): return self.pos def __setattr__(self, key, value ): '''set attribute.''' if key == "pos": self.pos = value value += 1 cdef int idx idx, f = self.map_key2field[key] TupleProxy._setindex(self, idx, str(value) ) pysam-0.7.7/pysam/cvcf.c0000664000076400007650000573344612241546221014750 0ustar andreasandreas/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? 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(Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? 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struct __pyx_obj_5pysam_10TabProxies_TupleProxy; struct __pyx_obj_5pysam_4cvcf_VCFRecord; struct __pyx_obj_5pysam_6ctabix_asGTF; struct __pyx_obj_5pysam_10TabProxies_GTFProxy; struct __pyx_obj_5pysam_6ctabix_asTuple; struct __pyx_obj_5pysam_6ctabix_asBed; struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data; struct __pyx_obj_5pysam_4cvcf_asVCFRecord; struct __pyx_obj_5pysam_6ctabix_Tabixfile; struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; struct __pyx_obj_5pysam_10TabProxies_BedProxy; struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr; struct __pyx_obj_5pysam_6ctabix_asVCF; struct __pyx_obj_5pysam_6ctabix_TabixIterator; struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator; struct __pyx_obj_5pysam_10TabProxies_VCFProxy; struct __pyx_defaults; typedef struct __pyx_defaults __pyx_defaults; struct __pyx_defaults1; typedef struct __pyx_defaults1 __pyx_defaults1; struct __pyx_defaults2; 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}; /* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; int index; int nbytes; int offset; int is_modified; }; /* "pysam/cvcf.pyx":95 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< * '''vcf record. * */ struct __pyx_obj_5pysam_4cvcf_VCFRecord { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; PyObject *vcf; char *contig; uint32_t pos; }; /* "ctabix.pxd":239 * * * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asGTF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_GTFProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; char *_attributes; int hasOwnAttributes; }; /* "ctabix.pxd":235 * cdef parse( self, char * buffer, int len ) * * cdef class asTuple(Parser): # <<<<<<<<<<<<<< * cdef parse( self, char * buffer, int len ) * */ struct __pyx_obj_5pysam_6ctabix_asTuple { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "ctabix.pxd":242 * pass * * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asBed { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "ctabix.pxd":201 * int ks_getuntil( kstream_t *, int, kstring_t *, int * ) * * cdef class tabix_file_iterator: # <<<<<<<<<<<<<< * cdef gzFile fh * cdef kstream_t * ks */ struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator { PyObject_HEAD struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab; gzFile fh; kstream_t *ks; kstring_t buffer; size_t size; struct __pyx_obj_5pysam_6ctabix_Parser *parser; int fd; PyObject *infile; }; /* "pysam/cvcf.pyx":650 * return False * * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<< * cols = line.split('\t') * if len(cols) != len(self._samples)+9: */ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data { PyObject_HEAD PyObject *__pyx_v_alt; }; /* "pysam/cvcf.pyx":229 * * * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a VCF record.''' * cdef vcffile */ struct __pyx_obj_5pysam_4cvcf_asVCFRecord { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; PyObject *vcffile; }; /* "ctabix.pxd":212 * cdef __cnext__(self) * * cdef class Tabixfile: # <<<<<<<<<<<<<< * * # pointer to tabixfile */ struct __pyx_obj_5pysam_6ctabix_Tabixfile { PyObject_HEAD tabix_t *tabixfile; int isremote; char *_filename; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; /* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_BedProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; int bedfields; }; /* "ctabix.pxd":248 * pass * * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "pysam/cvcf.pyx":793 * if alt: * for i in range(1,min(len(ref),min(map(len,alt)))): * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<< * break * ref, alt = ref[:-1], [allele[:-1] for allele in alt] */ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr { PyObject_HEAD struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope; PyObject *__pyx_v_allele; PyObject *__pyx_t_0; Py_ssize_t __pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "ctabix.pxd":245 * pass * * cdef class asVCF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asVCF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "ctabix.pxd":224 * cdef Parser parser * * cdef class TabixIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "ctabix.pxd":228 * cdef tabix_t * tabixfile * * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_VCFProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t pos; }; /* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy { int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t); PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); }; static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; /* "pysam/cvcf.pyx":95 * ########################################################################################################### * * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<< * '''vcf record. * */ struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord; /* "TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy; /* "ctabix.pxd":232 * cdef tabix_t * tabixfile * * cdef class Parser: # <<<<<<<<<<<<<< * cdef parse( self, char * buffer, int len ) * */ struct __pyx_vtabstruct_5pysam_6ctabix_Parser { PyObject *(*parse)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int); }; static struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtabptr_5pysam_6ctabix_Parser; /* "ctabix.pxd":242 * pass * * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_vtabstruct_5pysam_6ctabix_asBed { struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base; 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/*proto*/ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyObject_AsDouble(obj) \ (likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \ likely(PyInt_CheckExact(obj)) ? \ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj)) #else #define __Pyx_PyObject_AsDouble(obj) \ ((likely(PyFloat_CheckExact(obj))) ? \ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) PyErr_SetObject(PyExc_KeyError, key); return NULL; } Py_INCREF(value); return value; } #else #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { int result = PyDict_Contains(dict, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); Py_SIZE(list) = len+1; return 0; } return PyList_Append(list, x); } #else #define __Pyx_PyList_Append(L,x) PyList_Append(L,x) #endif static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (unlikely(PyList_Append(L, x) < 0)) return NULL; Py_INCREF(Py_None); return Py_None; /* this is just to have an accurate signature */ } else { PyObject *r, *m; m = __Pyx_GetAttrString(L, "append"); if (!m) return NULL; r = PyObject_CallFunctionObjArgs(m, x, NULL); Py_DECREF(m); return r; } } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/ static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2, int is_tuple, int has_known_size, int decref_tuple); static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_is_dict); static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict); #define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_SetItemInt_Fast(o, i, v) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v)) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { int r; if (!j) return -1; r = PyObject_SetItem(o, j, v); Py_DECREF(j); return r; } static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) { #if CYTHON_COMPILING_IN_CPYTHON if (PyList_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { PyObject* old = PyList_GET_ITEM(o, n); Py_INCREF(v); PyList_SET_ITEM(o, n, v); Py_DECREF(old); return 1; } } else { /* inlined PySequence_SetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_ass_item)) { if (unlikely(i < 0) && likely(m->sq_length)) { Py_ssize_t l = m->sq_length(o); if (unlikely(l < 0)) return -1; i += l; } return m->sq_ass_item(o, i, v); } } #else #if CYTHON_COMPILING_IN_PYPY if (PySequence_Check(o) && !PyDict_Check(o)) { #else if (PySequence_Check(o)) { #endif return PySequence_SetItem(o, i, v); } #endif return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); } static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname); #if PY_VERSION_HEX < 0x02050000 #ifndef PyAnySet_CheckExact #define PyAnySet_CheckExact(ob) \ ((ob)->ob_type == &PySet_Type || \ (ob)->ob_type == &PyFrozenSet_Type) #define PySet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL) #define Pyx_PyFrozenSet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL) #define PySet_Size(anyset) \ PyObject_Size((anyset)) #define PySet_Contains(anyset, key) \ PySequence_Contains((anyset), (key)) #define PySet_Pop(set) \ PyObject_CallMethod(set, (char *)"pop", NULL) static CYTHON_INLINE int PySet_Clear(PyObject *set) { PyObject *ret = PyObject_CallMethod(set, (char *)"clear", NULL); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"discard", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char *)"add", (char *)"O", key); if (!ret) return -1; Py_DECREF(ret); return 0; } #endif /* PyAnySet_CheckExact (<= Py2.4) */ #endif /* < Py2.5 */ static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc); static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name); static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *qualname, PyObject *modname); /*proto*/ #define __Pyx_CyFunction_USED 1 #include #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 #define __Pyx_CYFUNCTION_CCLASS 0x04 #define __Pyx_CyFunction_GetClosure(f) \ (((__pyx_CyFunctionObject *) (f))->func_closure) #define __Pyx_CyFunction_GetClassObj(f) \ (((__pyx_CyFunctionObject *) (f))->func_classobj) #define __Pyx_CyFunction_Defaults(type, f) \ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) #define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; int flags; PyObject *func_dict; PyObject *func_weakreflist; PyObject *func_name; PyObject *func_qualname; PyObject *func_doc; PyObject *func_code; PyObject *func_closure; PyObject *func_classobj; /* No-args super() class cell */ void *defaults; int defaults_pyobjects; PyObject *defaults_tuple; /* Const defaults tuple */ PyObject *(*defaults_getter)(PyObject *); } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; #define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, code) \ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *self, PyObject *module, PyObject* code); static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, size_t size, int pyobjects); static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, PyObject *tuple); static int __Pyx_CyFunction_init(void); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ #define __Pyx_Generator_USED #include #include typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD __pyx_generator_body_t body; PyObject *closure; PyObject *exc_type; PyObject *exc_value; PyObject *exc_traceback; PyObject *gi_weakreflist; PyObject *classobj; PyObject *yieldfrom; int resume_label; char is_running; // using T_BOOL for property below requires char value } __pyx_GeneratorObject; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure); static int __pyx_Generator_init(void); static int __Pyx_Generator_clear(PyObject* self); #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue); #else #define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue) #endif static int __Pyx_check_binary_version(void); #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static void* __Pyx_GetVtable(PyObject *dict); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'pysam.ctabix' */ static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0; /* Module declarations from 'pysam.TabProxies' */ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0; /* Module declarations from 'pysam.cvcf' */ static PyTypeObject *__pyx_ptype_5pysam_4cvcf_VCFRecord = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf_asVCFRecord = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = 0; static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = 0; #define __Pyx_MODULE_NAME "pysam.cvcf" int __pyx_module_is_main_pysam__cvcf = 0; /* Implementation of 'pysam.cvcf' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_min; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */ static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */ static char __pyx_k_1[] = ""; static char __pyx_k_2[] = ","; static char __pyx_k_4[] = ":"; static char __pyx_k_6[] = "-"; static char __pyx_k_8[] = "Don't understand region string '%s'"; static char __pyx_k_9[] = "."; static char __pyx_k_11[] = ";"; static char __pyx_k_14[] = "="; static char __pyx_k_18[] = "BAD_NUMBER_OF_VALUES"; static char __pyx_k_19[] = "(found %s values in element %s; expected %s)"; static char __pyx_k_20[] = "BAD_NUMBER_OF_PARAMETERS"; static char __pyx_k_21[] = "id=%s, expected %s parameters, got %s"; static char __pyx_k_24[] = " in line %s: '%s'\n%s %s: %s\n"; static char __pyx_k_25[] = "<"; static char __pyx_k_27[] = "V40_MISSING_ANGLE_BRACKETS"; static char __pyx_k_28[] = ">"; static char __pyx_k_32[] = "\""; static char __pyx_k_36[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS"; static char __pyx_k_37[] = "BADLY_FORMATTED_FORMAT_STRING"; static char __pyx_k_38[] = "ID="; static char __pyx_k_39[] = "Number="; static char __pyx_k_40[] = "Type="; static char __pyx_k_41[] = "Description="; static char __pyx_k_50[] = "FORMAT_MISSING_QUOTES"; static char __pyx_k_53[] = "#alleles"; static char __pyx_k_54[] = "#nonref_alleles"; static char __pyx_k_55[] = "#genotypes"; static char __pyx_k_56[] = "#phased_genotypes"; static char __pyx_k_57[] = "ZERO_FOR_NON_FLAG_FIELD"; static char __pyx_k_58[] = "Unknown number type encountered: %s"; static char __pyx_k_59[] = "%s=%s"; static char __pyx_k_60[] = "(Undefined tag)"; static char __pyx_k_61[] = "(output)"; static char __pyx_k_64[] = "Read depth at this position for this sample"; static char __pyx_k_65[] = "Sample Genotype Filter"; static char __pyx_k_66[] = "Genotype likelihoods"; static char __pyx_k_67[] = "Genotype Quality"; static char __pyx_k_68[] = "Phred-scaled genotype likelihoods"; static char __pyx_k_69[] = "Genotype posterior probabilities"; static char __pyx_k_70[] = "Conditional genotype quality"; static char __pyx_k_71[] = "Haplotype Quality"; static char __pyx_k_72[] = "Phase set"; static char __pyx_k_73[] = "Phasing quality"; static char __pyx_k_74[] = "Expected alternate allel counts"; static char __pyx_k_75[] = "RMS mapping quality"; static char __pyx_k_76[] = "##"; static char __pyx_k_79[] = "VCFv3.3"; static char __pyx_k_80[] = "VCFv4.0"; static char __pyx_k_81[] = "VCFv4.1"; static char __pyx_k_82[] = "UNKNOWN_FORMAT_STRING"; static char __pyx_k_83[] = "##fileformat=VCFv%s.%s\n"; static char __pyx_k_84[] = "##%s=%s\n"; static char __pyx_k_85[] = "#"; static char __pyx_k_88[] = "\t"; static char __pyx_k_90[] = "HEADING_NOT_SEPARATED_BY_TABS"; static char __pyx_k_91[] = "(%sth entry not found)"; static char __pyx_k_92[] = "(found %s, expected %s)"; static char __pyx_k_93[] = "BADLY_FORMATTED_HEADING"; static char __pyx_k_94[] = "\n"; static char __pyx_k_95[] = "|"; static char __pyx_k_96[] = "ERROR_FLAG_HAS_VALUE"; static char __pyx_k__0[] = "0"; static char __pyx_k__A[] = "A"; static char __pyx_k__D[] = "D"; static char __pyx_k__G[] = "G"; static char __pyx_k__I[] = "I"; static char __pyx_k__N[] = "N"; static char __pyx_k__a[] = "a"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; static char __pyx_k__f[] = "f"; static char __pyx_k__i[] = "i"; static char __pyx_k__k[] = "k"; static char __pyx_k__l[] = "l"; static char __pyx_k__n[] = "n"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__t[] = "t"; static char __pyx_k__v[] = "v"; static char __pyx_k__x[] = "x"; static char __pyx_k__y[] = "y"; static char __pyx_k_100[] = "ERROR_FORMAT_NOT_INTEGER"; static char __pyx_k_101[] = "ERROR_FORMAT_NOT_CHAR"; static char __pyx_k_102[] = "ERROR_FORMAT_NOT_NUMERICAL"; static char __pyx_k_104[] = "BAD_NUMBER_OF_COLUMNS"; static char __pyx_k_105[] = "expected %s for %s samples (%s), got %s"; static char __pyx_k_106[] = "(reference is %s, VCF says %s)"; static char __pyx_k_114[] = "V33_UNMATCHED_DELETION"; static char __pyx_k_115[] = "(deletion is %s, reference is %s)"; static char __pyx_k_116[] = "MISSING_INDEL_ALLELE_REF_BASE"; static char __pyx_k_118[] = "Required key %s not found in data"; static char __pyx_k_121[] = "enter_default_format"; static char __pyx_k_123[] = "Can only handle v3.3 and v4.0 VCF files"; static char __pyx_k_125[] = "Invalid error string: %s"; static char __pyx_k_126[] = "needs to be checked"; static char __pyx_k_128[] = "[|/\\\\]"; static char __pyx_k_130[] = "^[ACGTN]+$"; static char __pyx_k_134[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx"; static char __pyx_k_135[] = "pysam.cvcf"; static char __pyx_k_138[] = "id numbertype number type description missingvalue"; static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier"; static char __pyx_k_141[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string"; static char __pyx_k_142[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s"; static char __pyx_k_143[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)"; static char __pyx_k_144[] = "POS_NOT_NUMERICAL:Position column is not numerical"; static char __pyx_k_145[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field"; static char __pyx_k_146[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF"; static char __pyx_k_147[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF"; static char __pyx_k_148[] = "POS_NOT_POSITIVE:Position field must be >0"; static char __pyx_k_149[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'"; static char __pyx_k_150[] = "ERROR_INFO_STRING:Error while parsing info field"; static char __pyx_k_151[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)"; static char __pyx_k_152[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s"; static char __pyx_k_153[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string"; static char __pyx_k_154[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header"; static char __pyx_k_155[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header"; static char __pyx_k_156[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)"; static char __pyx_k_157[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)"; static char __pyx_k_158[] = "BAD_GENOTYPE:Cannot parse genotype (%s)"; static char __pyx_k_159[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)"; static char __pyx_k_160[] = "MISSING_REF:Reference allele missing"; static char __pyx_k_161[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)"; static char __pyx_k_162[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets"; static char __pyx_k_163[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes"; static char __pyx_k_164[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields"; static char __pyx_k_165[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs"; static char __pyx_k_166[] = "WRONG_REF:Wrong reference %s"; static char __pyx_k_167[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data"; static char __pyx_k_168[] = "BAD_CHR_TAG:Error calculating chr tag for %s"; static char __pyx_k_169[] = "ZERO_LENGTH_ALLELE:Found zero-length allele"; static char __pyx_k_170[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"; static char __pyx_k_171[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'"; static char __pyx_k_172[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s"; static char __pyx_k_173[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value"; static char __pyx_k_176[] = "VCF.__init__"; static char __pyx_k_180[] = "VCF.error"; static char __pyx_k_183[] = "VCF.parse_format"; static char __pyx_k_186[] = "VCF.format_format"; static char __pyx_k_189[] = "VCF.get_expected"; static char __pyx_k_192[] = "VCF._add_definition"; static char __pyx_k_195[] = "VCF.format_formatdata"; static char __pyx_k_198[] = "VCF.enter_default_format"; static char __pyx_k_201[] = "VCF.parse_header"; static char __pyx_k_204[] = "VCF.write_header"; static char __pyx_k_207[] = "VCF.parse_heading"; static char __pyx_k_210[] = "VCF.write_heading"; static char __pyx_k_213[] = "VCF.convertGT"; static char __pyx_k_216[] = "VCF.convertGTback"; static char __pyx_k_219[] = "VCF.parse_formatdata"; static char __pyx_k_222[] = "VCF.inregion"; static char __pyx_k_225[] = "VCF.parse_data"; static char __pyx_k_228[] = "VCF.write_data"; static char __pyx_k_231[] = "VCF._parse_header"; static char __pyx_k_234[] = "VCF._parse"; static char __pyx_k_237[] = "VCF.getsamples"; static char __pyx_k_240[] = "VCF.setsamples"; static char __pyx_k_243[] = "VCF.getheader"; static char __pyx_k_246[] = "VCF.setheader"; static char __pyx_k_249[] = "VCF.getinfo"; static char __pyx_k_252[] = "VCF.setinfo"; static char __pyx_k_255[] = "VCF.getformat"; static char __pyx_k_258[] = "VCF.setformat"; static char __pyx_k_261[] = "VCF.getfilter"; static char __pyx_k_264[] = "VCF.setfilter"; static char __pyx_k_267[] = "VCF.setversion"; static char __pyx_k_270[] = "VCF.setregions"; static char __pyx_k_273[] = "VCF.setreference"; static char __pyx_k_276[] = "VCF.ignoreerror"; static char __pyx_k_279[] = "VCF.warnerror"; static char __pyx_k_282[] = "VCF.parse"; static char __pyx_k_285[] = "VCF.write"; static char __pyx_k_288[] = "VCF.writeheader"; static char __pyx_k_291[] = "VCF.compare_calls"; static char __pyx_k_294[] = "VCF.connect"; static char __pyx_k_298[] = "VCF.fetch"; static char __pyx_k_301[] = "VCF.validate"; static char __pyx_k__DP[] = "DP"; static char __pyx_k__EC[] = "EC"; static char __pyx_k__FT[] = "FT"; static char __pyx_k__GL[] = "GL"; static char __pyx_k__GP[] = "GP"; static char __pyx_k__GQ[] = "GQ"; static char __pyx_k__GT[] = "GT"; static char __pyx_k__HQ[] = "HQ"; static char __pyx_k__ID[] = "ID"; static char __pyx_k__MQ[] = "MQ"; static char __pyx_k__PL[] = "PL"; static char __pyx_k__PQ[] = "PQ"; static char __pyx_k__PS[] = "PS"; static char __pyx_k__fa[] = "fa"; static char __pyx_k__id[] = "id"; static char __pyx_k__na[] = "na"; static char __pyx_k__re[] = "re"; static char __pyx_k__ALT[] = "ALT"; static char __pyx_k__GLE[] = "GLE"; static char __pyx_k__POS[] = "POS"; static char __pyx_k__REF[] = "REF"; static char __pyx_k__VCF[] = "VCF"; static char __pyx_k__add[] = "add"; static char __pyx_k__alt[] = "alt"; static char __pyx_k__end[] = "end"; static char __pyx_k__err[] = "err"; static char __pyx_k__fmt[] = "fmt"; static char __pyx_k__get[] = "get"; static char __pyx_k__gts[] = "gts"; static char __pyx_k__idx[] = "idx"; static char __pyx_k__key[] = "key"; static char __pyx_k__len[] = "len"; static char __pyx_k__map[] = "map"; static char __pyx_k__min[] = "min"; static char __pyx_k__nmb[] = "nmb"; static char __pyx_k__opt[] = "opt"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__ref[] = "ref"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__var[] = "var"; static char __pyx_k__vcf[] = "vcf"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__Flag[] = "Flag"; static char __pyx_k__INFO[] = "INFO"; static char __pyx_k__PASS[] = "PASS"; static char __pyx_k__QUAL[] = "QUAL"; static char __pyx_k__Type[] = "Type"; static char __pyx_k__addn[] = "addn"; static char __pyx_k__alt1[] = "alt1"; static char __pyx_k__alt2[] = "alt2"; static char __pyx_k__cols[] = "cols"; static char __pyx_k__copy[] = "copy"; static char __pyx_k__data[] = "data"; static char __pyx_k__dict[] = "dict"; static char __pyx_k__elts[] = "elts"; static char __pyx_k__find[] = "find"; static char __pyx_k__info[] = "info"; static char __pyx_k__join[] = "join"; static char __pyx_k__keys[] = "keys"; static char __pyx_k__last[] = "last"; static char __pyx_k__left[] = "left"; static char __pyx_k__line[] = "line"; static char __pyx_k__pos1[] = "pos1"; static char __pyx_k__pos2[] = "pos2"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__ref1[] = "ref1"; static char __pyx_k__ref2[] = "ref2"; static char __pyx_k__rest[] = "rest"; static char __pyx_k__self[] = "self"; static char __pyx_k__type[] = "type"; static char __pyx_k__ACGTN[] = "ACGTN"; static char __pyx_k__CHROM[] = "CHROM"; static char __pyx_k__Error[] = "Error"; static char __pyx_k__Float[] = "Float"; static char __pyx_k___copy[] = "_copy"; static char __pyx_k___info[] = "_info"; static char __pyx_k___line[] = "_line"; static char __pyx_k__addns[] = "addns"; static char __pyx_k__blurp[] = "blurp"; static char __pyx_k__chrom[] = "chrom"; static char __pyx_k__descr[] = "descr"; static char __pyx_k__error[] = "error"; static char __pyx_k__faref[] = "faref"; static char __pyx_k__fetch[] = "fetch"; static char __pyx_k__first[] = "first"; static char __pyx_k__ielts[] = "ielts"; static char __pyx_k__label[] = "label"; static char __pyx_k__lines[] = "lines"; static char __pyx_k__match[] = "match"; static char __pyx_k__parse[] = "parse"; static char __pyx_k__pysam[] = "pysam"; static char __pyx_k__range[] = "range"; static char __pyx_k__sdata[] = "sdata"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__upper[] = "upper"; static char __pyx_k__value[] = "value"; static char __pyx_k__write[] = "write"; static char __pyx_k__FILTER[] = "FILTER"; static char __pyx_k__FORMAT[] = "FORMAT"; static char __pyx_k__GTdata[] = "GTdata"; static char __pyx_k__Number[] = "Number"; static char __pyx_k__String[] = "String"; static char __pyx_k___lines[] = "_lines"; static char __pyx_k___parse[] = "_parse"; static char __pyx_k__allele[] = "allele"; static char __pyx_k__bisect[] = "bisect"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__filter[] = "filter"; static char __pyx_k__format[] = "format"; static char __pyx_k__header[] = "header"; static char __pyx_k__number[] = "number"; static char __pyx_k__object[] = "object"; static char __pyx_k__output[] = "output"; static char __pyx_k__parser[] = "parser"; static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; static char __pyx_k__result[] = "result"; static char __pyx_k__sample[] = "sample"; static char __pyx_k__stream[] = "stream"; static char __pyx_k__string[] = "string"; static char __pyx_k__values[] = "values"; static char __pyx_k__Integer[] = "Integer"; static char __pyx_k__Warning[] = "Warning"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k___errors[] = "_errors"; static char __pyx_k___filter[] = "_filter"; static char __pyx_k___format[] = "_format"; static char __pyx_k___header[] = "_header"; static char __pyx_k___lineno[] = "_lineno"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__connect[] = "connect"; static char __pyx_k__errwarn[] = "errwarn"; static char __pyx_k__genexpr[] = "genexpr"; static char __pyx_k__getinfo[] = "getinfo"; static char __pyx_k__longest[] = "longest"; static char __pyx_k__missing[] = "missing"; static char __pyx_k__movable[] = "movable"; static char __pyx_k__newalts[] = "newalts"; static char __pyx_k__regions[] = "regions"; static char __pyx_k__replace[] = "replace"; static char __pyx_k__samples[] = "samples"; static char __pyx_k__setinfo[] = "setinfo"; static char __pyx_k__vcffile[] = "vcffile"; static char __pyx_k__version[] = "version"; static char __pyx_k__GTstring[] = "GTstring"; static char __pyx_k__Genotype[] = "Genotype"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k____dict__[] = "__dict__"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k___regions[] = "_regions"; static char __pyx_k___samples[] = "_samples"; static char __pyx_k___version[] = "_version"; static char __pyx_k__deepcopy[] = "deepcopy"; static char __pyx_k__endswith[] = "endswith"; static char __pyx_k__expected[] = "expected"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__gtsRegEx[] = "gtsRegEx"; static char __pyx_k__headings[] = "headings"; static char __pyx_k__inregion[] = "inregion"; static char __pyx_k__operator[] = "operator"; static char __pyx_k__required[] = "required"; static char __pyx_k__sequence[] = "sequence"; static char __pyx_k__shortest[] = "shortest"; static char __pyx_k__validate[] = "validate"; static char __pyx_k__Character[] = "Character"; static char __pyx_k__NT_NUMBER[] = "NT_NUMBER"; static char __pyx_k__Tabixfile[] = "Tabixfile"; static char __pyx_k__VCFRecord[] = "VCFRecord"; static char __pyx_k__WRONG_REF[] = "WRONG_REF"; static char __pyx_k___required[] = "_required"; static char __pyx_k__convertGT[] = "convertGT"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__getfilter[] = "getfilter"; static char __pyx_k__getformat[] = "getformat"; static char __pyx_k__getheader[] = "getheader"; static char __pyx_k__last_line[] = "last_line"; static char __pyx_k__leftalign[] = "leftalign"; static char __pyx_k__lineparse[] = "lineparse"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__separator[] = "separator"; static char __pyx_k__setfilter[] = "setfilter"; static char __pyx_k__setformat[] = "setformat"; static char __pyx_k__setheader[] = "setheader"; static char __pyx_k__tabixfile[] = "tabixfile"; static char __pyx_k__warnerror[] = "warnerror"; static char __pyx_k__NT_ALLELES[] = "NT_ALLELES"; static char __pyx_k__NT_UNKNOWN[] = "NT_UNKNOWN"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___leftalign[] = "_leftalign"; static char __pyx_k___reference[] = "_reference"; static char __pyx_k__errorlabel[] = "errorlabel"; static char __pyx_k__fileformat[] = "fileformat"; static char __pyx_k__formatdict[] = "formatdict"; static char __pyx_k__getsamples[] = "getsamples"; static char __pyx_k__itemgetter[] = "itemgetter"; static char __pyx_k__itervalues[] = "itervalues"; static char __pyx_k__namedtuple[] = "namedtuple"; static char __pyx_k__numbertype[] = "numbertype"; static char __pyx_k__parse_data[] = "parse_data"; static char __pyx_k__setregions[] = "setregions"; static char __pyx_k__setsamples[] = "setsamples"; static char __pyx_k__setversion[] = "setversion"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__write_data[] = "write_data"; static char __pyx_k__Description[] = "Description"; static char __pyx_k__MISSING_REF[] = "MISSING_REF"; static char __pyx_k__V33_BAD_REF[] = "V33_BAD_REF"; static char __pyx_k__alleleRegEx[] = "alleleRegEx"; static char __pyx_k__collections[] = "collections"; static char __pyx_k__defaultdict[] = "defaultdict"; static char __pyx_k__description[] = "description"; static char __pyx_k__errorstring[] = "errorstring"; static char __pyx_k__ignoreerror[] = "ignoreerror"; static char __pyx_k__writeheader[] = "writeheader"; static char __pyx_k__BAD_GENOTYPE[] = "BAD_GENOTYPE"; static char __pyx_k__NT_GENOTYPES[] = "NT_GENOTYPES"; static char __pyx_k___warn_errors[] = "_warn_errors"; static char __pyx_k__get_expected[] = "get_expected"; static char __pyx_k__get_sequence[] = "get_sequence"; static char __pyx_k__missingvalue[] = "missingvalue"; static char __pyx_k__parse_format[] = "parse_format"; static char __pyx_k__parse_header[] = "parse_header"; static char __pyx_k__setreference[] = "setreference"; static char __pyx_k__write_header[] = "write_header"; static char __pyx_k__NT_NR_ALLELES[] = "NT_NR_ALLELES"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k___parse_header[] = "_parse_header"; static char __pyx_k__compare_calls[] = "compare_calls"; static char __pyx_k__convertGTback[] = "convertGTback"; static char __pyx_k__datagenerator[] = "datagenerator"; static char __pyx_k__format_format[] = "format_format"; static char __pyx_k__parse_heading[] = "parse_heading"; static char __pyx_k__parse_regions[] = "parse_regions"; static char __pyx_k__write_heading[] = "write_heading"; static char __pyx_k__V33_BAD_ALLELE[] = "V33_BAD_ALLELE"; static char __pyx_k__V40_BAD_ALLELE[] = "V40_BAD_ALLELE"; static char __pyx_k___sample2column[] = "_sample2column"; static char __pyx_k__have_deletions[] = "have_deletions"; static char __pyx_k___add_definition[] = "_add_definition"; static char __pyx_k___ignored_errors[] = "_ignored_errors"; static char __pyx_k__faref_leftflank[] = "faref_leftflank"; static char __pyx_k__POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE"; static char __pyx_k__parse_formatdata[] = "parse_formatdata"; static char __pyx_k__ERROR_INFO_STRING[] = "ERROR_INFO_STRING"; static char __pyx_k__ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY"; static char __pyx_k__POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL"; static char __pyx_k__format_formatdata[] = "format_formatdata"; static char __pyx_k__FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED"; static char __pyx_k__FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED"; static char __pyx_k__QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL"; static char __pyx_k__ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE"; static char __pyx_k__ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA"; static char __pyx_k__NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF"; static PyObject *__pyx_kp_s_1; 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static PyObject *__pyx_n_s__GTstring; static PyObject *__pyx_n_s__Genotype; static PyObject *__pyx_n_s__HQ; static PyObject *__pyx_n_s__I; static PyObject *__pyx_n_s__ID; static PyObject *__pyx_n_s__INFO; static PyObject *__pyx_n_s__Integer; static PyObject *__pyx_n_s__KeyError; static PyObject *__pyx_n_s__MISSING_REF; static PyObject *__pyx_n_s__MQ; static PyObject *__pyx_n_s__N; static PyObject *__pyx_n_s__NT_ALLELES; static PyObject *__pyx_n_s__NT_GENOTYPES; static PyObject *__pyx_n_s__NT_NR_ALLELES; static PyObject *__pyx_n_s__NT_NUMBER; static PyObject *__pyx_n_s__NT_PHASED_GENOTYPES; static PyObject *__pyx_n_s__NT_UNKNOWN; static PyObject *__pyx_n_s__NotImplementedError; static PyObject *__pyx_n_s__Number; static PyObject *__pyx_n_b__PASS; static PyObject *__pyx_n_s__PASS; static PyObject *__pyx_n_s__PL; static PyObject *__pyx_n_s__POS; static PyObject *__pyx_n_s__POS_NOT_NUMERICAL; static PyObject *__pyx_n_s__POS_NOT_POSITIVE; static PyObject *__pyx_n_s__PQ; static PyObject *__pyx_n_s__PS; static PyObject *__pyx_n_s__QUAL; static PyObject *__pyx_n_s__QUAL_NOT_NUMERICAL; static PyObject *__pyx_n_s__REF; static PyObject *__pyx_n_s__StopIteration; static PyObject *__pyx_n_s__String; static PyObject *__pyx_n_s__Tabixfile; static PyObject *__pyx_n_s__Type; static PyObject *__pyx_n_s__UNKNOWN_CHAR_IN_REF; static PyObject *__pyx_n_s__V33_BAD_ALLELE; static PyObject *__pyx_n_s__V33_BAD_REF; static PyObject *__pyx_n_s__V40_BAD_ALLELE; static PyObject *__pyx_n_s__VCF; static PyObject *__pyx_n_s__VCFRecord; static PyObject *__pyx_n_s__ValueError; static PyObject *__pyx_n_s__WRONG_REF; static PyObject *__pyx_n_s__Warning; static PyObject *__pyx_n_s__ZERO_LENGTH_ALLELE; static PyObject *__pyx_n_s____all__; static PyObject *__pyx_n_s____dict__; static PyObject *__pyx_n_s____init__; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___add_definition; static PyObject *__pyx_n_s___copy; static PyObject *__pyx_n_s___errors; static PyObject *__pyx_n_s___filter; 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static PyObject *__pyx_n_s__blurp; static PyObject *__pyx_n_s__buffer; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__chrom; static PyObject *__pyx_n_s__collections; static PyObject *__pyx_n_s__cols; static PyObject *__pyx_n_s__compare_calls; static PyObject *__pyx_n_s__compile; static PyObject *__pyx_n_s__connect; static PyObject *__pyx_n_s__convertGT; static PyObject *__pyx_n_s__convertGTback; static PyObject *__pyx_n_s__copy; static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data; static PyObject *__pyx_n_s__datagenerator; static PyObject *__pyx_n_s__deepcopy; static PyObject *__pyx_n_s__defaultdict; static PyObject *__pyx_n_s__descr; static PyObject *__pyx_n_s__description; static PyObject *__pyx_n_s__dict; static PyObject *__pyx_n_s__elts; static PyObject *__pyx_n_s__end; static PyObject *__pyx_n_s__endswith; static PyObject *__pyx_n_s__enumerate; static PyObject *__pyx_n_s__err; static PyObject *__pyx_n_s__error; static PyObject *__pyx_n_s__errorlabel; static PyObject *__pyx_n_s__errorstring; 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static PyObject *__pyx_n_s__gtsRegEx; static PyObject *__pyx_n_s__have_deletions; static PyObject *__pyx_n_s__header; static PyObject *__pyx_n_s__headings; static PyObject *__pyx_n_s__i; static PyObject *__pyx_n_s__id; static PyObject *__pyx_n_s__idx; static PyObject *__pyx_n_s__ielts; static PyObject *__pyx_n_s__ignoreerror; static PyObject *__pyx_n_s__info; static PyObject *__pyx_n_s__inregion; static PyObject *__pyx_n_s__itemgetter; static PyObject *__pyx_n_s__itervalues; static PyObject *__pyx_n_s__join; static PyObject *__pyx_n_s__k; static PyObject *__pyx_n_s__key; static PyObject *__pyx_n_s__keys; static PyObject *__pyx_n_s__l; static PyObject *__pyx_n_s__label; static PyObject *__pyx_n_s__last; static PyObject *__pyx_n_s__last_line; static PyObject *__pyx_n_s__left; static PyObject *__pyx_n_s__leftalign; static PyObject *__pyx_n_s__len; static PyObject *__pyx_n_s__line; static PyObject *__pyx_n_s__lineparse; static PyObject *__pyx_n_s__lines; static PyObject *__pyx_n_s__longest; 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static PyObject *__pyx_n_s__setregions; static PyObject *__pyx_n_s__setsamples; static PyObject *__pyx_n_s__setversion; static PyObject *__pyx_n_s__shortest; static PyObject *__pyx_n_s__split; static PyObject *__pyx_n_s__start; static PyObject *__pyx_n_s__startswith; static PyObject *__pyx_n_s__stream; static PyObject *__pyx_n_s__string; static PyObject *__pyx_n_s__strip; static PyObject *__pyx_n_s__sys; static PyObject *__pyx_n_s__t; static PyObject *__pyx_n_s__tabixfile; static PyObject *__pyx_n_s__type; static PyObject *__pyx_n_s__upper; static PyObject *__pyx_n_s__v; static PyObject *__pyx_n_s__validate; static PyObject *__pyx_n_s__value; static PyObject *__pyx_n_s__values; static PyObject *__pyx_n_s__var; static PyObject *__pyx_n_s__vcf; static PyObject *__pyx_n_s__vcffile; static PyObject *__pyx_n_s__version; static PyObject *__pyx_n_s__warnerror; static PyObject *__pyx_n_s__write; static PyObject *__pyx_n_s__write_data; static PyObject *__pyx_n_s__write_header; static PyObject *__pyx_n_s__write_heading; 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static PyObject *__pyx_k_codeobj_266; static PyObject *__pyx_k_codeobj_269; static PyObject *__pyx_k_codeobj_272; static PyObject *__pyx_k_codeobj_275; static PyObject *__pyx_k_codeobj_278; static PyObject *__pyx_k_codeobj_281; static PyObject *__pyx_k_codeobj_284; static PyObject *__pyx_k_codeobj_287; static PyObject *__pyx_k_codeobj_290; static PyObject *__pyx_k_codeobj_293; static PyObject *__pyx_k_codeobj_296; static PyObject *__pyx_k_codeobj_300; /* Python wrapper */ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyMethodDef __pyx_mdef_5pysam_4cvcf_1get_sequence = {__Pyx_NAMESTR("get_sequence"), (PyCFunction)__pyx_pw_5pysam_4cvcf_1get_sequence, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}; static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_chrom = 0; PyObject *__pyx_v_start = 0; PyObject *__pyx_v_end = 0; 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return __pyx_r; } static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord __pyx_vtable_5pysam_4cvcf_VCFRecord; static PyObject *__pyx_tp_new_5pysam_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_4cvcf_VCFRecord *p; PyObject *o = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_new(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_4cvcf_VCFRecord; p->vcf = Py_None; Py_INCREF(Py_None); if (__pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->vcf); PyObject_GC_Track(o); if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord); } static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; e = ((likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) ? ((__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) ? __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_VCFRecord)); if (e) return e; if (p->vcf) { e = (*v)(p->vcf, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o; PyObject* tmp; if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) { if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_VCFRecord); tmp = ((PyObject*)p->vcf); p->vcf = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_sq_item_5pysam_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); Py_DECREF(x); return r; } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o); } static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_4cvcf_VCFRecord[] = { {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_5pysam_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_9VCFRecord_4error)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_4cvcf_VCFRecord[] = { {(char *)"contig", __pyx_getprop_5pysam_4cvcf_9VCFRecord_contig, 0, 0, 0}, {(char *)"pos", __pyx_getprop_5pysam_4cvcf_9VCFRecord_pos, 0, 0, 0}, {(char *)"id", __pyx_getprop_5pysam_4cvcf_9VCFRecord_id, 0, 0, 0}, {(char *)"ref", __pyx_getprop_5pysam_4cvcf_9VCFRecord_ref, 0, 0, 0}, {(char *)"alt", __pyx_getprop_5pysam_4cvcf_9VCFRecord_alt, 0, 0, 0}, {(char *)"qual", __pyx_getprop_5pysam_4cvcf_9VCFRecord_qual, 0, 0, 0}, {(char *)"filter", __pyx_getprop_5pysam_4cvcf_9VCFRecord_filter, 0, 0, 0}, {(char *)"info", __pyx_getprop_5pysam_4cvcf_9VCFRecord_info, 0, 0, 0}, {(char *)"format", __pyx_getprop_5pysam_4cvcf_9VCFRecord_format, 0, 0, 0}, {(char *)"samples", __pyx_getprop_5pysam_4cvcf_9VCFRecord_samples, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_VCFRecord = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = { __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5pysam_4cvcf_VCFRecord, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = { __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*mp_length*/ __pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf_VCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.VCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf_VCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_VCFRecord, /*tp_as_number*/ &__pyx_tp_as_sequence_VCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_VCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("vcf record.\n\n initialized from data and vcf meta \n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf_VCFRecord, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf_VCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf_VCFRecord, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_4cvcf_VCFRecord, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf_VCFRecord, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_4cvcf_asVCFRecord __pyx_vtable_5pysam_4cvcf_asVCFRecord; static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p; PyObject *o = __pyx_ptype_5pysam_6ctabix_Parser->tp_new(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_4cvcf_asVCFRecord; p->vcffile = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->vcffile); PyObject_GC_Track(o); if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord); } static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e; if (p->vcffile) { e = (*v)(p->vcffile, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) { struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o; PyObject* tmp; if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord); tmp = ((PyObject*)p->vcffile); p->vcffile = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf_asVCFRecord[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asVCFRecord = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asVCFRecord = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asVCFRecord = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.asVCFRecord"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf_asVCFRecord), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_asVCFRecord, /*tp_as_number*/ &__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf_asVCFRecord, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf_asVCFRecord, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf_asVCFRecord, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o); p->__pyx_v_alt = 0; return o; } static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->__pyx_v_alt); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; if (p->__pyx_v_alt) { e = (*v)(p->__pyx_v_alt, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_v_alt); p->__pyx_v_alt = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct__parse_data = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct__parse_data = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct__parse_data = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__parse_data = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct__parse_data"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number___pyx_scope_struct__parse_data, /*tp_as_number*/ &__pyx_tp_as_sequence___pyx_scope_struct__parse_data, /*tp_as_sequence*/ &__pyx_tp_as_mapping___pyx_scope_struct__parse_data, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer___pyx_scope_struct__parse_data, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o); p->__pyx_outer_scope = 0; p->__pyx_v_allele = 0; p->__pyx_t_0 = 0; return o; } static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->__pyx_outer_scope); Py_CLEAR(p->__pyx_v_allele); Py_CLEAR(p->__pyx_t_0); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; if (p->__pyx_outer_scope) { e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e; } if (p->__pyx_v_allele) { e = (*v)(p->__pyx_v_allele, a); if (e) return e; } if (p->__pyx_t_0) { e = (*v)(p->__pyx_t_0, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_outer_scope); p->__pyx_outer_scope = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_v_allele); p->__pyx_v_allele = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_t_0); p->__pyx_t_0 = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_1_genexpr = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_1_genexpr = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping___pyx_scope_struct_1_genexpr = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct_1_genexpr"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number___pyx_scope_struct_1_genexpr, /*tp_as_number*/ &__pyx_tp_as_sequence___pyx_scope_struct_1_genexpr, /*tp_as_sequence*/ &__pyx_tp_as_mapping___pyx_scope_struct_1_genexpr, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ 0, /*tp_doc*/ __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_traverse*/ __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o); p->__pyx_v_d = 0; p->__pyx_v_line = 0; p->__pyx_v_self = 0; p->__pyx_v_stream = 0; p->__pyx_t_1 = 0; return o; } static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->__pyx_v_d); Py_CLEAR(p->__pyx_v_line); Py_CLEAR(p->__pyx_v_self); Py_CLEAR(p->__pyx_v_stream); Py_CLEAR(p->__pyx_t_1); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; if (p->__pyx_v_d) { e = (*v)(p->__pyx_v_d, a); if (e) return e; } if (p->__pyx_v_line) { e = (*v)(p->__pyx_v_line, a); if (e) return e; } if (p->__pyx_v_self) { e = (*v)(p->__pyx_v_self, a); if (e) return e; } if (p->__pyx_v_stream) { e = (*v)(p->__pyx_v_stream, a); if (e) return e; } if (p->__pyx_t_1) { e = (*v)(p->__pyx_t_1, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) { struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o; PyObject* tmp; tmp = ((PyObject*)p->__pyx_v_d); p->__pyx_v_d = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_v_line); p->__pyx_v_line = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_v_self); p->__pyx_v_self = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_v_stream); p->__pyx_v_stream = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->__pyx_t_1); p->__pyx_t_1 = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_2__parse[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number___pyx_scope_struct_2__parse = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence___pyx_scope_struct_2__parse = { 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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46)); __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_47); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47)); /* "pysam/cvcf.pyx":368 * elif first.startswith('Number='): data['number'] = first.split('=')[1] * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): # <<<<<<<<<<<<<< * elts = format.split('"') * if len(elts)<3: */ __pyx_k_tuple_48 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_41)); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_48); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48)); /* "pysam/cvcf.pyx":369 * elif first.startswith('Type='): data['type'] = first.split('=')[1] * elif first.startswith('Description='): * elts = format.split('"') # <<<<<<<<<<<<<< * if len(elts)<3: * self.error(line,self.FORMAT_MISSING_QUOTES) */ __pyx_k_tuple_49 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); 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__pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_289); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_289)); __pyx_k_codeobj_290 = (PyObject*)__Pyx_PyCode_New(7, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_289, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__compare_calls, 997, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_290)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pysam/cvcf.pyx":1019 * ########################################################################################################### * * def connect( self, filename ): # <<<<<<<<<<<<<< * '''connect to tabix file.''' * self.tabixfile = pysam.Tabixfile( filename ) */ __pyx_k_tuple_292 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename)); if (unlikely(!__pyx_k_tuple_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; 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if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; #if CYTHON_COMPILING_IN_PYPY float_value = PyNumber_Float(obj); #else if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) { return PyFloat_AsDouble(obj); } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) { #if PY_MAJOR_VERSION >= 3 float_value = PyFloat_FromString(obj); #else float_value = PyFloat_FromString(obj, 0); #endif } else { PyObject* args = PyTuple_New(1); if (unlikely(!args)) goto bad; PyTuple_SET_ITEM(args, 0, obj); float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0); PyTuple_SET_ITEM(args, 0, 0); Py_DECREF(args); } #endif if (likely(float_value)) { double value = PyFloat_AS_DOUBLE(float_value); Py_DECREF(float_value); return value; } bad: return (double)-1; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) { if (t == Py_None) { __Pyx_RaiseNoneNotIterableError(); } else if (PyTuple_GET_SIZE(t) < index) { __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t)); } else { __Pyx_RaiseTooManyValuesError(index); } } static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2, int is_tuple, int has_known_size, int decref_tuple) { Py_ssize_t index; PyObject *value1 = NULL, *value2 = NULL, *iter = NULL; if (!is_tuple && unlikely(!PyTuple_Check(tuple))) { iternextfunc iternext; iter = PyObject_GetIter(tuple); if (unlikely(!iter)) goto bad; if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; } iternext = Py_TYPE(iter)->tp_iternext; value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; } value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; } if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad; Py_DECREF(iter); } else { if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) { __Pyx_UnpackTupleError(tuple, 2); goto bad; } #if CYTHON_COMPILING_IN_PYPY value1 = PySequence_ITEM(tuple, 0); if (unlikely(!value1)) goto bad; value2 = PySequence_ITEM(tuple, 1); if (unlikely(!value2)) goto bad; #else value1 = PyTuple_GET_ITEM(tuple, 0); value2 = PyTuple_GET_ITEM(tuple, 1); Py_INCREF(value1); Py_INCREF(value2); #endif if (decref_tuple) { Py_DECREF(tuple); } } *pvalue1 = value1; *pvalue2 = value2; return 0; unpacking_failed: if (!has_known_size && __Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); bad: Py_XDECREF(iter); Py_XDECREF(value1); Py_XDECREF(value2); if (decref_tuple) { Py_XDECREF(tuple); } return -1; } static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name, Py_ssize_t* p_orig_length, int* p_source_is_dict) { is_dict = is_dict || likely(PyDict_CheckExact(iterable)); *p_source_is_dict = is_dict; #if !CYTHON_COMPILING_IN_PYPY if (is_dict) { *p_orig_length = PyDict_Size(iterable); Py_INCREF(iterable); return iterable; } #endif *p_orig_length = 0; if (method_name) { PyObject* iter; iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL); if (!iterable) return NULL; #if !CYTHON_COMPILING_IN_PYPY if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable)) return iterable; #endif iter = PyObject_GetIter(iterable); Py_DECREF(iterable); return iter; } return PyObject_GetIter(iterable); } static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos, PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) { PyObject* next_item; #if !CYTHON_COMPILING_IN_PYPY if (source_is_dict) { PyObject *key, *value; if (unlikely(orig_length != PyDict_Size(iter_obj))) { PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration"); return -1; } if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) { return 0; } if (pitem) { PyObject* tuple = PyTuple_New(2); if (unlikely(!tuple)) { return -1; } Py_INCREF(key); Py_INCREF(value); PyTuple_SET_ITEM(tuple, 0, key); PyTuple_SET_ITEM(tuple, 1, value); *pitem = tuple; } else { if (pkey) { Py_INCREF(key); *pkey = key; } if (pvalue) { Py_INCREF(value); *pvalue = value; } } return 1; } else if (PyTuple_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyTuple_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else if (PyList_CheckExact(iter_obj)) { Py_ssize_t pos = *ppos; if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0; *ppos = pos + 1; next_item = PyList_GET_ITEM(iter_obj, pos); Py_INCREF(next_item); } else #endif { next_item = PyIter_Next(iter_obj); if (unlikely(!next_item)) { return __Pyx_IterFinish(); } } if (pitem) { *pitem = next_item; } else if (pkey && pvalue) { if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1)) return -1; } else if (pkey) { *pkey = next_item; } else { *pvalue = next_item; } return 1; } static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_dealloc != current_tp_dealloc) type = type->tp_base; while (type && type->tp_dealloc == current_tp_dealloc) type = type->tp_base; if (type) type->tp_dealloc(obj); } static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_traverse != current_tp_traverse) type = type->tp_base; while (type && type->tp_traverse == current_tp_traverse) type = type->tp_base; if (type && type->tp_traverse) return type->tp_traverse(obj, v, a); return 0; } static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_clear != current_tp_clear) type = type->tp_base; while (type && type->tp_clear == current_tp_clear) type = type->tp_base; if (type && type->tp_clear) type->tp_clear(obj); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) { #if PY_MAJOR_VERSION < 3 PyErr_Format(PyExc_ImportError, "cannot import name %.230s", PyString_AsString(name)); #else PyErr_Format(PyExc_ImportError, "cannot import name %S", name); #endif } static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = PyObject_GetAttrString(base, (char *)"__class__"); if (!metaclass) { PyErr_Clear(); metaclass = (PyObject*) Py_TYPE(base); } } else { metaclass = (PyObject *) &PyClass_Type; } #else if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = (PyObject*) Py_TYPE(base); } else { metaclass = (PyObject *) &PyType_Type; } #endif Py_INCREF(metaclass); return metaclass; } static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *qualname, PyObject *modname) { PyObject *result; PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0) return NULL; metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); } else { metaclass = __Pyx_FindPy2Metaclass(bases); } result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); Py_DECREF(metaclass); return result; } static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { if (op->func.m_ml->ml_doc) { #if PY_MAJOR_VERSION >= 3 op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); #else op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); #endif if (unlikely(op->func_doc == NULL)) return NULL; } else { Py_INCREF(Py_None); return Py_None; } } Py_INCREF(op->func_doc); return op->func_doc; } static int __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp = op->func_doc; if (value == NULL) value = Py_None; /* Mark as deleted */ Py_INCREF(value); op->func_doc = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) { if (unlikely(op->func_name == NULL)) { #if PY_MAJOR_VERSION >= 3 op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); #else op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); #endif if (unlikely(op->func_name == NULL)) return NULL; } Py_INCREF(op->func_name); return op->func_name; } static int __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__name__ must be set to a string object"); return -1; } tmp = op->func_name; Py_INCREF(value); op->func_name = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op) { Py_INCREF(op->func_qualname); return op->func_qualname; } static int __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__qualname__ must be set to a string object"); return -1; } tmp = op->func_qualname; Py_INCREF(value); op->func_qualname = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) { PyObject *self; self = m->func_closure; if (self == NULL) self = Py_None; Py_INCREF(self); return self; } static PyObject * __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) { if (unlikely(op->func_dict == NULL)) { op->func_dict = PyDict_New(); if (unlikely(op->func_dict == NULL)) return NULL; } Py_INCREF(op->func_dict); return op->func_dict; } static int __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; if (unlikely(value == NULL)) { PyErr_SetString(PyExc_TypeError, "function's dictionary may not be deleted"); return -1; } if (unlikely(!PyDict_Check(value))) { PyErr_SetString(PyExc_TypeError, "setting function's dictionary to a non-dict"); return -1; } tmp = op->func_dict; Py_INCREF(value); op->func_dict = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) { PyObject* dict = PyModule_GetDict(__pyx_m); Py_XINCREF(dict); return dict; } static PyObject * __Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) { Py_INCREF(Py_None); return Py_None; } static PyObject * __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) { PyObject* result = (op->func_code) ? op->func_code : Py_None; Py_INCREF(result); return result; } static PyObject * __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { if (op->defaults_tuple) { Py_INCREF(op->defaults_tuple); return op->defaults_tuple; } if (op->defaults_getter) { PyObject *res = op->defaults_getter((PyObject *) op); if (likely(res)) { Py_INCREF(res); op->defaults_tuple = res; } return res; } Py_INCREF(Py_None); return Py_None; } static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {0, 0, 0, 0, 0} }; #ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ #define PY_WRITE_RESTRICTED WRITE_RESTRICTED #endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} }; static PyObject * __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromString(m->func.m_ml->ml_name); #else return PyString_FromString(m->func.m_ml->ml_name); #endif } static PyMethodDef __pyx_CyFunction_methods[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, {0, 0, 0, 0} }; static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *closure, PyObject *module, PyObject* code) { __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; op->flags = flags; op->func_weakreflist = NULL; op->func.m_ml = ml; op->func.m_self = (PyObject *) op; Py_XINCREF(closure); op->func_closure = closure; Py_XINCREF(module); op->func.m_module = module; op->func_dict = NULL; op->func_name = NULL; Py_INCREF(qualname); op->func_qualname = qualname; op->func_doc = NULL; op->func_classobj = NULL; Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_getter = NULL; PyObject_GC_Track(op); return (PyObject *) op; } static int __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) { Py_CLEAR(m->func_closure); Py_CLEAR(m->func.m_module); Py_CLEAR(m->func_dict); Py_CLEAR(m->func_name); Py_CLEAR(m->func_qualname); Py_CLEAR(m->func_doc); Py_CLEAR(m->func_code); Py_CLEAR(m->func_classobj); Py_CLEAR(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_XDECREF(pydefaults[i]); PyMem_Free(m->defaults); m->defaults = NULL; } return 0; } static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) { PyObject_GC_UnTrack(m); if (m->func_weakreflist != NULL) PyObject_ClearWeakRefs((PyObject *) m); __Pyx_CyFunction_clear(m); PyObject_GC_Del(m); } static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) { Py_VISIT(m->func_closure); Py_VISIT(m->func.m_module); Py_VISIT(m->func_dict); Py_VISIT(m->func_name); Py_VISIT(m->func_qualname); Py_VISIT(m->func_doc); Py_VISIT(m->func_code); Py_VISIT(m->func_classobj); Py_VISIT(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_VISIT(pydefaults[i]); } return 0; } static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { Py_INCREF(func); return func; } if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { if (type == NULL) type = (PyObject *)(Py_TYPE(obj)); return PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); } if (obj == Py_None) obj = NULL; return PyMethod_New(func, obj, type); } static PyObject* __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", op->func_qualname, (void *)op); #else return PyString_FromFormat("", PyString_AsString(op->func_qualname), (void *)op); #endif } #if CYTHON_COMPILING_IN_PYPY static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyCFunctionObject* f = (PyCFunctionObject*)func; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); Py_ssize_t size; switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { case METH_VARARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) return (*meth)(self, arg); break; case METH_VARARGS | METH_KEYWORDS: return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); case METH_NOARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 0) return (*meth)(self, NULL); PyErr_Format(PyExc_TypeError, "%.200s() takes no arguments (%zd given)", f->m_ml->ml_name, size); return NULL; } break; case METH_O: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 1) return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); PyErr_Format(PyExc_TypeError, "%.200s() takes exactly one argument (%zd given)", f->m_ml->ml_name, size); return NULL; } break; default: PyErr_SetString(PyExc_SystemError, "Bad call flags in " "__Pyx_CyFunction_Call. METH_OLDARGS is no " "longer supported!"); return NULL; } PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", f->m_ml->ml_name); return NULL; } #else static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { return PyCFunction_Call(func, arg, kw); } #endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_CyFunction_methods, /*tp_methods*/ __pyx_CyFunction_members, /*tp_members*/ __pyx_CyFunction_getsets, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ __Pyx_CyFunction_descr_get, /*tp_descr_get*/ 0, /*tp_descr_set*/ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static int __Pyx_CyFunction_init(void) { #if !CYTHON_COMPILING_IN_PYPY __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; #endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, sizeof(size)); m->defaults_pyobjects = pyobjects; return m->defaults; } static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; #else PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); PyErr_SetExcInfo(*type, *value, *tb); #endif *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } static PyObject *__Pyx_Generator_Next(PyObject *self); static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); static PyObject *__Pyx_Generator_Close(PyObject *self); static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); static PyTypeObject *__pyx_GeneratorType = 0; #define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) #define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { PyObject *et, *ev, *tb; PyObject *value = NULL; __Pyx_ErrFetch(&et, &ev, &tb); if (!et) { Py_XDECREF(tb); Py_XDECREF(ev); Py_INCREF(Py_None); *pvalue = Py_None; return 0; } if (unlikely(et != PyExc_StopIteration) && unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) { __Pyx_ErrRestore(et, ev, tb); return -1; } if (likely(et == PyExc_StopIteration)) { if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) { if (!ev) { Py_INCREF(Py_None); ev = Py_None; } Py_XDECREF(tb); Py_DECREF(et); *pvalue = ev; return 0; } } PyErr_NormalizeException(&et, &ev, &tb); if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) { __Pyx_ErrRestore(et, ev, tb); return -1; } Py_XDECREF(tb); Py_DECREF(et); #if PY_VERSION_HEX >= 0x030300A0 value = ((PyStopIterationObject *)ev)->value; Py_INCREF(value); Py_DECREF(ev); #else { PyObject* args = PyObject_GetAttrString(ev, "args"); Py_DECREF(ev); if (likely(args)) { value = PyObject_GetItem(args, 0); Py_DECREF(args); } if (unlikely(!value)) { __Pyx_ErrRestore(NULL, NULL, NULL); Py_INCREF(Py_None); value = Py_None; } } #endif *pvalue = value; return 0; } #endif static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) { PyObject *exc_type = self->exc_type; PyObject *exc_value = self->exc_value; PyObject *exc_traceback = self->exc_traceback; self->exc_type = NULL; self->exc_value = NULL; self->exc_traceback = NULL; Py_XDECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_traceback); } static CYTHON_INLINE int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) { if (unlikely(gen->is_running)) { PyErr_SetString(PyExc_ValueError, "generator already executing"); return 1; } return 0; } static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) { PyObject *retval; assert(!self->is_running); if (unlikely(self->resume_label == 0)) { if (unlikely(value && value != Py_None)) { PyErr_SetString(PyExc_TypeError, "can't send non-None value to a " "just-started generator"); return NULL; } } if (unlikely(self->resume_label == -1)) { PyErr_SetNone(PyExc_StopIteration); return NULL; } if (value) { #if CYTHON_COMPILING_IN_PYPY #else /* Generators always return to their most recent caller, not * necessarily their creator. */ if (self->exc_traceback) { PyThreadState *tstate = PyThreadState_GET(); PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; PyFrameObject *f = tb->tb_frame; Py_XINCREF(tstate->frame); assert(f->f_back == NULL); f->f_back = tstate->frame; } #endif __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); } else { __Pyx_Generator_ExceptionClear(self); } self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; if (retval) { __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); #if CYTHON_COMPILING_IN_PYPY #else /* Don't keep the reference to f_back any longer than necessary. It * may keep a chain of frames alive or it could create a reference * cycle. */ if (self->exc_traceback) { PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; PyFrameObject *f = tb->tb_frame; Py_CLEAR(f->f_back); } #endif } else { __Pyx_Generator_ExceptionClear(self); } return retval; } static CYTHON_INLINE PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) { PyObject *ret; PyObject *val = NULL; __Pyx_Generator_Undelegate(gen); __Pyx_PyGen_FetchStopIterationValue(&val); ret = __Pyx_Generator_SendEx(gen, val); Py_XDECREF(val); return ret; } static PyObject *__Pyx_Generator_Next(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; PyObject *yf = gen->yieldfrom; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; gen->is_running = 1; ret = Py_TYPE(yf)->tp_iternext(yf); gen->is_running = 0; if (likely(ret)) { return ret; } return __Pyx_Generator_FinishDelegation(gen); } return __Pyx_Generator_SendEx(gen, Py_None); } static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; PyObject *yf = gen->yieldfrom; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; gen->is_running = 1; if (__Pyx_Generator_CheckExact(yf)) { ret = __Pyx_Generator_Send(yf, value); } else { if (value == Py_None) ret = PyIter_Next(yf); else ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value); } gen->is_running = 0; if (likely(ret)) { return ret; } return __Pyx_Generator_FinishDelegation(gen); } return __Pyx_Generator_SendEx(gen, value); } static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) { PyObject *retval = NULL; int err = 0; if (__Pyx_Generator_CheckExact(yf)) { retval = __Pyx_Generator_Close(yf); if (!retval) return -1; } else { PyObject *meth; gen->is_running = 1; meth = PyObject_GetAttrString(yf, "close"); if (unlikely(!meth)) { if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_WriteUnraisable(yf); } PyErr_Clear(); } else { retval = PyObject_CallFunction(meth, NULL); Py_DECREF(meth); if (!retval) err = -1; } gen->is_running = 0; } Py_XDECREF(retval); return err; } static PyObject *__Pyx_Generator_Close(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *retval, *raised_exception; PyObject *yf = gen->yieldfrom; int err = 0; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { Py_INCREF(yf); err = __Pyx_Generator_CloseIter(gen, yf); __Pyx_Generator_Undelegate(gen); Py_DECREF(yf); } if (err == 0) #if PY_VERSION_HEX < 0x02050000 PyErr_SetNone(PyExc_StopIteration); #else PyErr_SetNone(PyExc_GeneratorExit); #endif retval = __Pyx_Generator_SendEx(gen, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, "generator ignored GeneratorExit"); return NULL; } raised_exception = PyErr_Occurred(); if (!raised_exception || raised_exception == PyExc_StopIteration #if PY_VERSION_HEX >= 0x02050000 || raised_exception == PyExc_GeneratorExit || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit) #endif || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration)) { if (raised_exception) PyErr_Clear(); /* ignore these errors */ Py_INCREF(Py_None); return Py_None; } return NULL; } static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; PyObject *yf = gen->yieldfrom; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; Py_INCREF(yf); #if PY_VERSION_HEX >= 0x02050000 if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) { int err = __Pyx_Generator_CloseIter(gen, yf); Py_DECREF(yf); __Pyx_Generator_Undelegate(gen); if (err < 0) return __Pyx_Generator_SendEx(gen, NULL); goto throw_here; } #endif gen->is_running = 1; if (__Pyx_Generator_CheckExact(yf)) { ret = __Pyx_Generator_Throw(yf, args); } else { PyObject *meth = PyObject_GetAttrString(yf, "throw"); if (unlikely(!meth)) { Py_DECREF(yf); if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { gen->is_running = 0; return NULL; } PyErr_Clear(); __Pyx_Generator_Undelegate(gen); gen->is_running = 0; goto throw_here; } ret = PyObject_CallObject(meth, args); Py_DECREF(meth); } gen->is_running = 0; Py_DECREF(yf); if (!ret) { ret = __Pyx_Generator_FinishDelegation(gen); } return ret; } throw_here: __Pyx_Raise(typ, val, tb, NULL); return __Pyx_Generator_SendEx(gen, NULL); } static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_VISIT(gen->closure); Py_VISIT(gen->classobj); Py_VISIT(gen->yieldfrom); Py_VISIT(gen->exc_type); Py_VISIT(gen->exc_value); Py_VISIT(gen->exc_traceback); return 0; } static int __Pyx_Generator_clear(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_CLEAR(gen->closure); Py_CLEAR(gen->classobj); Py_CLEAR(gen->yieldfrom); Py_CLEAR(gen->exc_type); Py_CLEAR(gen->exc_value); Py_CLEAR(gen->exc_traceback); return 0; } static void __Pyx_Generator_dealloc(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject_GC_UnTrack(gen); if (gen->gi_weakreflist != NULL) PyObject_ClearWeakRefs(self); PyObject_GC_Track(self); if (gen->resume_label > 0) { Py_TYPE(gen)->tp_del(self); if (self->ob_refcnt > 0) return; /* resurrected. :( */ } PyObject_GC_UnTrack(self); __Pyx_Generator_clear(self); PyObject_GC_Del(gen); } static void __Pyx_Generator_del(PyObject *self) { PyObject *res; PyObject *error_type, *error_value, *error_traceback; __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; if (gen->resume_label <= 0) return ; assert(self->ob_refcnt == 0); self->ob_refcnt = 1; __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); res = __Pyx_Generator_Close(self); if (res == NULL) PyErr_WriteUnraisable(self); else Py_DECREF(res); __Pyx_ErrRestore(error_type, error_value, error_traceback); /* Undo the temporary resurrection; can't use DECREF here, it would * cause a recursive call. */ assert(self->ob_refcnt > 0); if (--self->ob_refcnt == 0) return; /* this is the normal path out */ /* close() resurrected it! Make it look like the original Py_DECREF * never happened. */ { Py_ssize_t refcnt = self->ob_refcnt; _Py_NewReference(self); self->ob_refcnt = refcnt; } #if CYTHON_COMPILING_FOR_CPYTHON assert(PyType_IS_GC(self->ob_type) && _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so * we need to undo that. */ _Py_DEC_REFTOTAL; #endif /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object * chain, so no more to do there. * If COUNT_ALLOCS, the original decref bumped tp_frees, and * _Py_NewReference bumped tp_allocs: both of those need to be * undone. */ #ifdef COUNT_ALLOCS --Py_TYPE(self)->tp_frees; --Py_TYPE(self)->tp_allocs; #endif } static PyMemberDef __pyx_Generator_memberlist[] = { {(char *) "gi_running", #if PY_VERSION_HEX >= 0x02060000 T_BOOL, #else T_BYTE, #endif offsetof(__pyx_GeneratorObject, is_running), READONLY, NULL}, {0, 0, 0, 0, 0} }; static PyMethodDef __pyx_Generator_methods[] = { {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, {0, 0, 0, 0} }; static PyTypeObject __pyx_GeneratorType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("generator"), /*tp_name*/ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ __pyx_Generator_methods, /*tp_methods*/ __pyx_Generator_memberlist, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ __Pyx_Generator_del, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure) { __pyx_GeneratorObject *gen = PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type); if (gen == NULL) return NULL; gen->body = body; gen->closure = closure; Py_XINCREF(closure); gen->is_running = 0; gen->resume_label = 0; gen->classobj = NULL; gen->yieldfrom = NULL; gen->exc_type = NULL; gen->exc_value = NULL; gen->exc_traceback = NULL; gen->gi_weakreflist = NULL; PyObject_GC_Track(gen); return gen; } static int __pyx_Generator_init(void) { __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr; __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter; if (PyType_Ready(&__pyx_GeneratorType_type)) { return -1; } __pyx_GeneratorType = &__pyx_GeneratorType_type; return 0; } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static void* __Pyx_GetVtable(PyObject *dict) { void* ptr; PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__"); if (!ob) goto bad; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) ptr = PyCapsule_GetPointer(ob, 0); #else ptr = PyCObject_AsVoidPtr(ob); #endif if (!ptr && !PyErr_Occurred()) PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); Py_DECREF(ob); return ptr; bad: Py_XDECREF(ob); return NULL; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ pysam-0.7.7/pysam/TabProxies.c0000664000076400007650000200065412241546215016073 0ustar andreasandreas/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) #else #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) #endif #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include #define __PYX_HAVE__pysam__TabProxies #define __PYX_HAVE_API__pysam__TabProxies #include "stdlib.h" #include "string.h" #include "stdint.h" #include "stdio.h" #include "pythread.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif #endif typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "TabProxies.pyx", "type.pxd", "bool.pxd", "complex.pxd", }; /*--- Type declarations ---*/ struct __pyx_obj_5pysam_10TabProxies_TupleProxy; struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; struct __pyx_obj_5pysam_10TabProxies_GTFProxy; struct __pyx_obj_5pysam_10TabProxies_BedProxy; struct __pyx_obj_5pysam_10TabProxies_VCFProxy; /* "pysam/TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; int index; int nbytes; int offset; int is_modified; }; /* "pysam/TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; /* "pysam/TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_GTFProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; char *_attributes; int hasOwnAttributes; }; /* "pysam/TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_BedProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; int bedfields; }; /* "pysam/TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_VCFProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t pos; }; /* "pysam/TabProxies.pyx":84 * return not (buffer <= p < buffer + nbytes ) * * cdef class TupleProxy: # <<<<<<<<<<<<<< * '''Proxy class for access to parsed row as a tuple. * */ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy { int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t); PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t); }; static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy; /* "pysam/TabProxies.pyx":571 * self.fromDict( r ) * * cdef class NamedTupleProxy( TupleProxy ): # <<<<<<<<<<<<<< * * map_key2field = {} */ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "pysam/TabProxies.pyx":656 * TupleProxy._setindex(self, idx, str(value) ) * * cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<< * '''Proxy class for access to VCF fields. * */ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy; /* "pysam/TabProxies.pyx":326 * return str(v) * * cdef class GTFProxy( TupleProxy ): # <<<<<<<<<<<<<< * '''Proxy class for access to GTF fields. * */ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *); }; static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy; /* "pysam/TabProxies.pyx":590 * return f( self.fields[idx] ) * * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<< * '''Proxy class for access to Bed fields. * */ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy; #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif #if CYTHON_REFNANNY typedef struct { void (*INCREF)(void*, PyObject*, int); 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static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ #include static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ const char* function_name); /*proto*/ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (unlikely(PyList_Append(L, x) < 0)) return NULL; Py_INCREF(Py_None); return Py_None; /* this is just to have an accurate signature */ } else { PyObject *r, *m; m = __Pyx_GetAttrString(L, "append"); if (!m) return NULL; r = PyObject_CallFunctionObjArgs(m, x, NULL); Py_DECREF(m); return r; } } static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; r = PyObject_GetItem(o, j); Py_DECREF(j); return r; } #define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ __Pyx_GetItemInt_List_Fast(o, i) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i))) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { #if CYTHON_COMPILING_IN_CPYTHON if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, i); 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if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, n); Py_INCREF(r); return r; } } else if (PyTuple_CheckExact(o)) { Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { PyObject *r = PyTuple_GET_ITEM(o, n); Py_INCREF(r); return r; } } else { /* inlined PySequence_GetItem() */ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; if (likely(m && m->sq_item)) { if (unlikely(i < 0) && likely(m->sq_length)) { Py_ssize_t l = m->sq_length(o); if (unlikely(l < 0)) return NULL; i += l; } return m->sq_item(o, i); } } #else if (PySequence_Check(o)) { return PySequence_GetItem(o, i); } #endif return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyObject_AsDouble(obj) \ (likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \ likely(PyInt_CheckExact(obj)) ? \ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj)) #else #define __Pyx_PyObject_AsDouble(obj) \ ((likely(PyFloat_CheckExact(obj))) ? \ PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj)) #endif #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); Py_SIZE(list) = len+1; return 0; } return PyList_Append(list, x); } #else #define __Pyx_PyList_Append(L,x) PyList_Append(L,x) #endif static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename); /*proto*/ static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.version' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'cpython.exc' */ /* Module declarations from 'cpython.module' */ /* Module declarations from 'cpython.mem' */ /* Module declarations from 'cpython.tuple' */ /* Module declarations from 'cpython.list' */ /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from 'cpython.sequence' */ /* Module declarations from 'cpython.mapping' */ /* Module declarations from 'cpython.iterator' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'cpython.number' */ /* Module declarations from 'cpython.int' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.bool' */ static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; /* Module declarations from 'cpython.long' */ /* Module declarations from 'cpython.float' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.complex' */ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython.string' */ /* Module declarations from 'cpython.unicode' */ /* Module declarations from 'cpython.dict' */ /* Module declarations from 'cpython.instance' */ /* Module declarations from 'cpython.function' */ /* Module declarations from 'cpython.method' */ /* Module declarations from 'cpython.weakref' */ /* Module declarations from 'cpython.getargs' */ /* Module declarations from 'cpython.pythread' */ /* Module declarations from 'cpython.pystate' */ /* Module declarations from 'cpython.cobject' */ /* Module declarations from 'cpython.oldbuffer' */ /* Module declarations from 'cpython.set' */ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* Module declarations from 'pysam.TabProxies' */ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0; static PyObject *__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = 0; static PyObject *__pyx_f_5pysam_10TabProxies__force_bytes(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_10TabProxies__force_str(PyObject *); /*proto*/ static char *__pyx_f_5pysam_10TabProxies_StrOrEmpty(char *); /*proto*/ static int __pyx_f_5pysam_10TabProxies_isNew(char *, char *, size_t); /*proto*/ #define __Pyx_MODULE_NAME "pysam.TabProxies" int __pyx_module_is_main_pysam__TabProxies = 0; /* Implementation of 'pysam.TabProxies' */ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_xrange; static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_KeyError; static int __pyx_pf_5pysam_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, int __pyx_v_index); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5pysam_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ static Py_ssize_t __pyx_pf_5pysam_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6source___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_d); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, int __pyx_v_lcontig); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5pysam_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_15NamedTupleProxy_2__getattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8BedProxy___str__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */ static Py_ssize_t __pyx_pf_5pysam_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "malformatted entry at %s"; static char __pyx_k_6[] = ""; static char __pyx_k_7[] = "out of memory"; static char __pyx_k_9[] = "incomplete line at %s"; static char __pyx_k_11[] = "row too large - more than %i fields"; static char __pyx_k_12[] = "list index out of range"; static char __pyx_k_14[] = "list index out of range %i >= %i"; static char __pyx_k_18[] = "\t"; static char __pyx_k_21[] = "."; static char __pyx_k_22[] = "\"%s\""; static char __pyx_k_32[] = ";"; static char __pyx_k_34[] = " "; static char __pyx_k_36[] = "\""; static char __pyx_k_37[] = "%s \"%s\""; static char __pyx_k_38[] = "%s %s"; static char __pyx_k_39[] = "; "; static char __pyx_k_41[] = "-"; static char __pyx_k_44[] = "'GTFProxy' has no attribute '%s'"; static char __pyx_k_45[] = "field %s not set"; static char __pyx_k_46[] = "bed format requires at least three columns"; static char __pyx_k_48[] = "contig of feature."; static char __pyx_k_49[] = "feature source."; static char __pyx_k_50[] = "feature name."; static char __pyx_k_51[] = "feature start (in 0-based open/closed coordinates)."; static char __pyx_k_52[] = "feature end (in 0-based open/closed coordinates)."; static char __pyx_k_53[] = "feature score."; static char __pyx_k_54[] = "feature strand."; static char __pyx_k_55[] = "feature frame."; static char __pyx_k_56[] = "feature attributes (as a string)."; static char __pyx_k_57[] = "getfilesystemencoding"; static char __pyx_k_60[] = "/home/andreas/devel/pysam/pysam/TabProxies.pyx"; static char __pyx_k_61[] = "pysam.TabProxies"; static char __pyx_k__v[] = "v"; static char __pyx_k__id[] = "id"; static char __pyx_k__alt[] = "alt"; static char __pyx_k__end[] = "end"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__ref[] = "ref"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__info[] = "info"; static char __pyx_k__join[] = "join"; static char __pyx_k__name[] = "name"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__frame[] = "frame"; static char __pyx_k__index[] = "index"; static char __pyx_k__items[] = "items"; static char __pyx_k__quote[] = "quote"; static char __pyx_k__range[] = "range"; static char __pyx_k__score[] = "score"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__toDot[] = "toDot"; static char __pyx_k__types[] = "types"; static char __pyx_k__value[] = "value"; static char __pyx_k__asDict[] = "asDict"; static char __pyx_k__contig[] = "contig"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; static char __pyx_k__filter[] = "filter"; static char __pyx_k__format[] = "format"; static char __pyx_k__source[] = "source"; static char __pyx_k__strand[] = "strand"; static char __pyx_k__xrange[] = "xrange"; static char __pyx_k____str__[] = "__str__"; static char __pyx_k__feature[] = "feature"; 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static PyObject *__pyx_n_s__v; static PyObject *__pyx_n_s__value; static PyObject *__pyx_n_s__xrange; static PyObject *__pyx_int_0; static PyObject *__pyx_int_1; static PyObject *__pyx_int_2; static PyObject *__pyx_int_3; static PyObject *__pyx_int_4; static PyObject *__pyx_int_5; static PyObject *__pyx_int_6; static PyObject *__pyx_int_7; static PyObject *__pyx_int_8; static PyObject *__pyx_int_9; static PyObject *__pyx_int_10; static PyObject *__pyx_int_11; static PyObject *__pyx_k_tuple_2; static PyObject *__pyx_k_tuple_4; static PyObject *__pyx_k_tuple_8; static PyObject *__pyx_k_tuple_10; static PyObject *__pyx_k_tuple_13; static PyObject *__pyx_k_tuple_15; static PyObject *__pyx_k_tuple_16; static PyObject *__pyx_k_tuple_17; static PyObject *__pyx_k_tuple_19; static PyObject *__pyx_k_tuple_20; static PyObject *__pyx_k_tuple_23; static PyObject *__pyx_k_tuple_24; static PyObject *__pyx_k_tuple_25; static PyObject *__pyx_k_tuple_26; static PyObject *__pyx_k_tuple_27; static PyObject *__pyx_k_tuple_28; 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static PyTypeObject __pyx_type_5pysam_10TabProxies_TupleProxy = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.TabProxies.TupleProxy"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_TupleProxy, /*tp_as_number*/ &__pyx_tp_as_sequence_TupleProxy, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TupleProxy, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n\n Access to individual fields is via the [] operator.\n \n Only read-only access is implemented.\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/ __pyx_methods_5pysam_10TabProxies_TupleProxy, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_10TabProxies_TupleProxy, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy __pyx_vtable_5pysam_10TabProxies_GTFProxy; static PyObject *__pyx_tp_new_5pysam_10TabProxies_GTFProxy(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_10TabProxies_GTFProxy *p; PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_GTFProxy; if (__pyx_pw_5pysam_10TabProxies_8GTFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_10TabProxies_8GTFProxy_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy(o); } static PyObject *__pyx_sq_item_5pysam_10TabProxies_GTFProxy(PyObject *o, Py_ssize_t i) { PyObject *r; PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); Py_DECREF(x); return r; } static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_GTFProxy(PyObject *o, PyObject *n) { PyObject *v = PyObject_GenericGetAttr(o, n); if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_Clear(); v = __pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__(o, n); } return v; } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_strand(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_frame(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_1__get__(o); } static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyMethodDef __pyx_methods_5pysam_10TabProxies_GTFProxy[] = { {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_5asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_4asDict)}, {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_7fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_6fromDict)}, {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_11invert, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_10invert)}, {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_13keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_12keys)}, {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_16__getattr__)}, {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_19setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_18setAttribute)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_10TabProxies_GTFProxy[] = { {(char *)"contig", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_contig, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_48), 0}, {(char *)"source", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_source, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_49), 0}, {(char *)"feature", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_feature, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_50), 0}, {(char *)"start", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_start, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_51), 0}, {(char *)"end", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_end, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_52), 0}, {(char *)"score", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_score, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_53), 0}, {(char *)"strand", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_strand, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_54), 0}, {(char *)"frame", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_frame, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_55), 0}, {(char *)"attributes", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_56), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_GTFProxy = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = { #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/ #else 0, /*sq_length*/ #endif 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5pysam_10TabProxies_GTFProxy, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = { #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/ #else 0, /*mp_length*/ #endif __pyx_pw_5pysam_10TabProxies_8GTFProxy_15__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_GTFProxy = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_10TabProxies_GTFProxy = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.TabProxies.GTFProxy"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_GTFProxy, /*tp_as_number*/ &__pyx_tp_as_sequence_GTFProxy, /*tp_as_sequence*/ &__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_10TabProxies_8GTFProxy_9__str__, /*tp_str*/ __pyx_tp_getattro_5pysam_10TabProxies_GTFProxy, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/ #else 0, /*tp_iternext*/ #endif __pyx_methods_5pysam_10TabProxies_GTFProxy, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_10TabProxies_GTFProxy, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_10TabProxies_GTFProxy, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_vtable_5pysam_10TabProxies_NamedTupleProxy; static PyObject *__pyx_tp_new_5pysam_10TabProxies_NamedTupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *p; PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; return o; } static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n) { PyObject *v = PyObject_GenericGetAttr(o, n); if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_Clear(); v = __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__(o, n); } return v; } static int __pyx_tp_setattro_5pysam_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n, PyObject *v) { if (v) { return __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_1__setattr__(o, n, v); } else { if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_setattro) return __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_setattro(o, n, v); return PyObject_GenericSetAttr(o, n, 0); } } static PyMethodDef __pyx_methods_5pysam_10TabProxies_NamedTupleProxy[] = { {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_NamedTupleProxy = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_NamedTupleProxy = { #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/ #else 0, /*sq_length*/ #endif 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 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tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if 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(PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static CYTHON_INLINE int __Pyx_CheckKeywordStrings( PyObject *kwdict, const char* function_name, int kw_allowed) { PyObject* key = 0; Py_ssize_t pos = 0; #if CPYTHON_COMPILING_IN_PYPY if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0)) goto invalid_keyword; return 1; #else while (PyDict_Next(kwdict, &pos, &key, 0)) { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) #endif if (unlikely(!PyUnicode_Check(key))) goto invalid_keyword_type; } if ((!kw_allowed) && unlikely(key)) goto invalid_keyword; return 1; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); return 0; #endif invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif return 0; } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static double __Pyx__PyObject_AsDouble(PyObject* obj) { PyObject* float_value; #if CYTHON_COMPILING_IN_PYPY float_value = PyNumber_Float(obj); #else if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) { return PyFloat_AsDouble(obj); } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) { #if PY_MAJOR_VERSION >= 3 float_value = PyFloat_FromString(obj); #else float_value = PyFloat_FromString(obj, 0); #endif } else { PyObject* args = PyTuple_New(1); if (unlikely(!args)) goto bad; PyTuple_SET_ITEM(args, 0, obj); float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0); PyTuple_SET_ITEM(args, 0, 0); Py_DECREF(args); } #endif if (likely(float_value)) { double value = PyFloat_AS_DOUBLE(float_value); Py_DECREF(float_value); return value; } bad: return (double)-1; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint32_t) == sizeof(char)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint32_t) == sizeof(short)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint32_t) == sizeof(int)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint32_t) == sizeof(long)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else uint32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (uint32_t)-1; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); #if PY_MAJOR_VERSION < 3 ctx = PyString_FromString(name); #else ctx = PyUnicode_FromString(name); #endif __Pyx_ErrRestore(old_exc, old_val, old_tb); if (!ctx) { PyErr_WriteUnraisable(Py_None); } else { PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ pysam-0.7.7/pysam/pysam_util.c0000664000076400007650000003252012216701366016176 0ustar andreasandreas#include #include #include "bam.h" #include "khash.h" #include "ksort.h" #include "bam_endian.h" #include "knetfile.h" #include "pysam_util.h" #include "errmod.h" // for pysam_dump // for sequence parsing #include "kseq.h" #ifndef inline #define inline __inline #endif // Definition of pysamerr #include "stdio.h" FILE * pysamerr = NULL; FILE * pysam_set_stderr(int fd) { if (pysamerr != NULL) fclose(pysamerr); pysamerr = fdopen(fd, "w"); return pysamerr; } void pysam_unset_stderr() { if (pysamerr != NULL) fclose(pysamerr); pysamerr = fopen("/dev/null", "w"); } // ####################################################### // utility routines to avoid using callbacks in bam_fetch // taken from bam_index.c // The order of the following declarations is important. // ####################################################### #define BAM_MAX_BIN 37450 // =(8^6-1)/7+1 // initialize hashes typedef struct { uint64_t u, v; } pair64_t; #define pair64_lt(a,b) ((a).u < (b).u) KSORT_INIT(myoff, pair64_t, pair64_lt); typedef struct { uint32_t m, n; pair64_t *list; } bam_binlist_t; typedef struct { int32_t n, m; uint64_t *offset; } bam_lidx_t; // initialize hashes ('i' and 's' are idenditifiers) KHASH_MAP_INIT_INT(i, bam_binlist_t); KHASH_MAP_INIT_STR(s, int) struct __bam_index_t { int32_t n; uint64_t n_no_coor; // unmapped reads without coordinate khash_t(i) **index; bam_lidx_t *index2; }; typedef struct __linkbuf_t { bam1_t b; uint32_t beg, end; struct __linkbuf_t *next; } lbnode_t; typedef struct { int cnt, n, max; lbnode_t **buf; } mempool_t; struct __bam_plbuf_t { mempool_t *mp; lbnode_t *head, *tail, *dummy; bam_pileup_f func; void *func_data; int32_t tid, pos, max_tid, max_pos; int max_pu, is_eof; bam_pileup1_t *pu; int flag_mask; }; static mempool_t *mp_init() { mempool_t *mp; mp = (mempool_t*)calloc(1, sizeof(mempool_t)); return mp; } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) { free(mp->buf[k]->b.data); free(mp->buf[k]); } free(mp->buf); free(mp); } static inline lbnode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, lbnode_t *p) { --mp->cnt; p->next = 0; // clear lbnode_t::next here if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max); } mp->buf[mp->n++] = p; } static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos) { unsigned k; bam1_t *b = p->b; bam1_core_t *c = &b->core; uint32_t x = c->pos, y = 0; int ret = 1, is_restart = 1; if (c->flag&BAM_FUNMAP) return 0; // unmapped read assert(x <= pos); // otherwise a bug p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0; for (k = 0; k < c->n_cigar; ++k) { int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip if (x + l > pos) { // overlap with pos p->indel = p->is_del = 0; p->qpos = y + (pos - x); if (x == pos && is_restart) p->is_head = 1; if (x + l - 1 == pos) { // come to the end of a match if (k < c->n_cigar - 1) { // there are additional operation(s) uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP) p->is_tail = 1; // tail } else p->is_tail = 1; // this is the last operation; set tail } } x += l; y += l; } else if (op == BAM_CDEL) { // then set ->is_del if (x + l > pos) { p->indel = 0; p->is_del = 1; p->qpos = y + (pos - x); } x += l; } else if (op == BAM_CREF_SKIP) x += l; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP); if (x > pos) { if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all break; } } assert(x > pos); // otherwise a bug return ret; } // the following code has been taken from bam_plbuf_push // and modified such that instead of a function call // the function returns and will continue (if cont is true). // from where it left off. // returns // 1: if buf is full and can be emitted // 0: if b has been added // -1: if there was an error int pysam_pileup_next(const bam1_t *b, bam_plbuf_t *buf, bam_pileup1_t ** plp, int * tid, int * pos, int * n_plp ) { *plp = bam_plp_next(buf->iter, tid, pos, n_plp); if (plp == NULL) return 0; return 1; } typedef struct __bmc_aux_t { int max; uint32_t *info; uint16_t *info16; errmod_t *em; } bmc_aux_t; // Return number of mapped reads on tid. // If tid < 0, return mapped reads without a coordinate (0) uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid ) { // return no values if index data not present if (idx==NULL) return 0; if (tid >= 0) { khint_t k; khash_t(i) *h = idx->index[tid]; k = kh_get(i, h, BAM_MAX_BIN); if (k != kh_end(h)) return kh_val(h, k).list[1].u; else return 0; } return 0; } uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid ) { if (tid >= 0) { khint_t k; khash_t(i) *h = idx->index[tid]; k = kh_get(i, h, BAM_MAX_BIN); if (k != kh_end(h)) return kh_val(h, k).list[1].v; else return 0; } return idx->n_no_coor; } /* uint32_t pysam_glf_depth( glf1_t * g ) */ /* { */ /* return g->depth; */ /* } */ /* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ) */ /* { */ /* int x = 0; */ /* fprintf(stderr, */ /* "glf: ref_base=%i, max_mapQ=%i, min_lk=%i, depth=%i", */ /* g->ref_base, */ /* g->max_mapQ, */ /* g->min_lk, */ /* g->depth ); */ /* for (x = 0; x < 10; ++x) */ /* fprintf(stderr, ", lk%x=%i, ", x, g->lk[x]); */ /* fprintf(stderr, */ /* "maqcns: het_rate=%f, theta=%f, n_hap=%i, cap_mapQ=%i, errmod=%i, min_baseQ=%i, eta=%f, q_r=%f, aux_max=%i", */ /* c->het_rate, */ /* c->theta, */ /* c->n_hap, */ /* c->cap_mapQ, */ /* c->errmod, */ /* c->min_baseQ, */ /* c->eta, */ /* c->q_r, */ /* c->aux->max); */ /* for (x = 0; x < c->aux->max; ++x) */ /* { */ /* fprintf(stderr, ", info-%i=%i ", x, c->aux->info[x]); */ /* if (c->aux->info[x] == 0) break; */ /* } */ /* for (x = 0; x < c->aux->max; ++x) */ /* { */ /* fprintf(stderr, ", info16-%i=%i ", x, c->aux->info16[x]); */ /* if (c->aux->info16[x] == 0) break; */ /* } */ /* } */ // pysam dispatch function to emulate the samtools // command line within python. // taken from the main function in bamtk.c // added code to reset getopt int bam_taf2baf(int argc, char *argv[]); int bam_mpileup(int argc, char *argv[]); int bam_merge(int argc, char *argv[]); int bam_index(int argc, char *argv[]); int bam_sort(int argc, char *argv[]); int bam_tview_main(int argc, char *argv[]); int bam_mating(int argc, char *argv[]); int bam_rmdup(int argc, char *argv[]); int bam_flagstat(int argc, char *argv[]); int bam_fillmd(int argc, char *argv[]); int bam_idxstats(int argc, char *argv[]); int main_samview(int argc, char *argv[]); int main_import(int argc, char *argv[]); int main_reheader(int argc, char *argv[]); int main_cut_target(int argc, char *argv[]); int main_phase(int argc, char *argv[]); int main_cat(int argc, char *argv[]); int main_depth(int argc, char *argv[]); int main_bam2fq(int argc, char *argv[]); int main_pad2unpad(int argc, char *argv[]); int main_bedcov(int argc, char *argv[]); int main_bamshuf(int argc, char *argv[]); int faidx_main(int argc, char *argv[]); int pysam_dispatch(int argc, char *argv[] ) { extern int optind; #ifdef _WIN32 setmode(fileno(stdout), O_BINARY); setmode(fileno(stdin), O_BINARY); #ifdef _USE_KNETFILE knet_win32_init(); #endif #endif // reset getopt optind = 1; if (argc < 2) return 1; int retval = 0; if (strcmp(argv[1], "view") == 0) retval = main_samview(argc-1, argv+1); else if (strcmp(argv[1], "import") == 0) retval = main_import(argc-1, argv+1); else if (strcmp(argv[1], "mpileup") == 0) retval = bam_mpileup(argc-1, argv+1); else if (strcmp(argv[1], "merge") == 0) retval = bam_merge(argc-1, argv+1); else if (strcmp(argv[1], "sort") == 0) retval = bam_sort(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) retval = bam_index(argc-1, argv+1); else if (strcmp(argv[1], "faidx") == 0) retval = faidx_main(argc-1, argv+1); else if (strcmp(argv[1], "idxstats") == 0) retval = bam_idxstats(argc-1, argv+1); else if (strcmp(argv[1], "fixmate") == 0) retval = bam_mating(argc-1, argv+1); else if (strcmp(argv[1], "rmdup") == 0) retval = bam_rmdup(argc-1, argv+1); else if (strcmp(argv[1], "flagstat") == 0) retval = bam_flagstat(argc-1, argv+1); else if (strcmp(argv[1], "calmd") == 0) retval = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "fillmd") == 0) retval = bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "reheader") == 0) retval = main_reheader(argc-1, argv+1); else if (strcmp(argv[1], "cat") == 0) retval = main_cat(argc-1, argv+1); else if (strcmp(argv[1], "targetcut") == 0) retval = main_cut_target(argc-1, argv+1); else if (strcmp(argv[1], "phase") == 0) retval = main_phase(argc-1, argv+1); else if (strcmp(argv[1], "depth") == 0) retval = main_depth(argc-1, argv+1); else if (strcmp(argv[1], "bam2fq") == 0) retval = main_bam2fq(argc-1, argv+1); else if (strcmp(argv[1], "pad2unpad") == 0) retval = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "depad") == 0) retval = main_pad2unpad(argc-1, argv+1); else if (strcmp(argv[1], "bedcov") == 0) retval = main_bedcov(argc-1, argv+1); else if (strcmp(argv[1], "bamshuf") == 0) retval = main_bamshuf(argc-1, argv+1); #if _CURSES_LIB != 0 else if (strcmp(argv[1], "tview") == 0) retval = bam_tview_main(argc-1, argv+1); #endif else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } fflush( stdout ); return retval; } // taken from samtools/bam_import.c static inline uint8_t *alloc_data(bam1_t *b, size_t size) { if (b->m_data < size) { b->m_data = size; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } return b->data; } // update the variable length data within a bam1_t entry. // Adds *nbytes_new* - *nbytes_old* into the variable length data of *src* at *pos*. // Data within the bam1_t entry is moved so that it is // consistent with the data field lengths. bam1_t * pysam_bam_update( bam1_t * b, const size_t nbytes_old, const size_t nbytes_new, uint8_t * pos ) { int d = nbytes_new-nbytes_old; int new_size; size_t offset; // no change if (d == 0) return b; new_size = d + b->data_len; offset = pos - b->data; //printf("d=%i, old=%i, new=%i, old_size=%i, new_size=%i\n", // d, nbytes_old, nbytes_new, b->data_len, new_size); // increase memory if required if (d > 0) { alloc_data( b, new_size ); pos = b->data + offset; } if (b->data_len != 0) { if (offset < 0 || offset > b->data_len) fprintf(stderr, "[pysam_bam_insert] illegal offset: '%i'\n", (int)offset); } // printf("dest=%p, src=%p, n=%i\n", pos+nbytes_new, pos + nbytes_old, b->data_len - (offset+nbytes_old)); memmove( pos + nbytes_new, pos + nbytes_old, b->data_len - (offset + nbytes_old)); b->data_len = new_size; return b; } // translate a nucleotide character to binary code unsigned char pysam_translate_sequence( const unsigned char s ) { return bam_nt16_table[s]; } void bam_init_header_hash(bam_header_t *header); // translate a reference string *s* to a tid // code taken from bam_parse_region int pysam_reference2tid( bam_header_t *header, const char * s ) { khiter_t iter; khash_t(s) *h; bam_init_header_hash(header); h = (khash_t(s)*)header->hash; iter = kh_get(s, h, s); /* get the ref_id */ if (iter == kh_end(h)) { // name not found return -1; } return kh_value(h, iter); } // Auxiliary functions for B support void bam_aux_appendB(bam1_t *b, const char tag[2], char type, char subtype, int len, uint8_t *data) { int ori_len; int data_len; // check that type is 'B' if('B' != type) return; ori_len = b->data_len; data_len = len * bam_aux_type2size(subtype); // infer the data length from the sub-type b->data_len += 8 + data_len; b->l_aux += 8 + data_len; if (b->m_data < b->data_len) { b->m_data = b->data_len; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1]; // tag b->data[ori_len + 2] = type; // type b->data[ori_len + 3] = subtype; // subtype (*(int32_t*)(b->data + ori_len + 4)) = len; // size memcpy(b->data + ori_len + 8, data, data_len); // data } /* // return size of auxiliary type int bam_aux_type2size(int x) { if (x == 'C' || x == 'c' || x == 'A') return 1; else if (x == 'S' || x == 's') return 2; else if (x == 'I' || x == 'i' || x == 'f') return 4; else return 0; } */ pysam-0.7.7/pysam/version.py0000664000076400007650000000016412241574744015710 0ustar andreasandreas# pysam versioning information __version__ = "0.7.7" __samtools_version__ = "0.1.19" __tabix_version__ = "0.2.6" pysam-0.7.7/pysam/cvcf.pyx0000664000076400007650000014413012147525721015332 0ustar andreasandreas# # Code to read, write and edit VCF files # # VCF lines are encoded as a dictionary with these keys (note: all lowercase): # 'chrom': string # 'pos': integer # 'id': string # 'ref': string # 'alt': list of strings # 'qual': integer # 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"] # 'info': dictionary of values (see below) # 'format': list of keys (strings) # sample keys: dictionary of values (see below) # # The sample keys are accessible through vcf.getsamples() # # A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map # to a list, containign integers, floats, strings, or characters. Missing values are replaced # by a particular value, often -1 or . # # Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples), # the first (and last) the integer representing an allele, and the second the separation character. # Note that there is just one genotype per sample, but for consistency the single element is stored in a list. # # Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible # through getheader() # # The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding # 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions # parser is available under parse_regions. # # When instantiated, a reference can be passed to the VCF class. This may be any class that supports a # fetch(chrom, start, end) method. # # # # NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file. # # # # TODO: # only v4.0 writing is complete; alleles are not converted to v3.3 format # from collections import namedtuple, defaultdict from operator import itemgetter import sys, re, copy, bisect cimport ctabix cimport TabProxies import pysam gtsRegEx = re.compile("[|/\\\\]") alleleRegEx = re.compile('^[ACGTN]+$') # Utility function. Uses 0-based coordinates def get_sequence(chrom, start, end, fa): # obtain sequence from .fa file, without truncation if end<=start: return "" if not fa: return "N"*(end-start) if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() sequence = fa.fetch(chrom, start, end).upper() if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) return sequence # Utility function. Parses a region string def parse_regions( string ): result = [] for r in string.split(','): elts = r.split(':') chrom, start, end = elts[0], 0, 3000000000 if len(elts)==1: pass elif len(elts)==2: if len(elts[1])>0: ielts = elts[1].split('-') if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) try: start, end = int(ielts[0])-1, int(ielts[1]) except: raise ValueError("Don't understand region string '%s'" % r) else: raise ValueError("Don't understand region string '%s'" % r) result.append( (chrom,start,end) ) return result FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') ########################################################################################################### # # New class # ########################################################################################################### cdef class VCFRecord( TabProxies.TupleProxy): '''vcf record. initialized from data and vcf meta ''' cdef vcf cdef char * contig cdef uint32_t pos def __init__(self, vcf): self.vcf = vcf # if len(data) != len(self.vcf._samples): # self.vcf.error(str(data), # self.BAD_NUMBER_OF_COLUMNS, # "expected %s for %s samples (%s), got %s" % \ # (len(self.vcf._samples), # len(self.vcf._samples), # self.vcf._samples, # len(data))) def __cinit__(self, vcf ): # start indexed access at genotypes self.offset = 9 self.vcf = vcf def error(self,line,error,opt=None): '''raise error.''' # pass to vcf file for error handling return self.vcf.error( line, error, opt ) cdef update( self, char * buffer, size_t nbytes ): '''update internal data. nbytes does not include the terminal '\0'. ''' TabProxies.TupleProxy.update( self, buffer, nbytes ) self.contig = self.fields[0] # vcf counts from 1 - correct here self.pos = atoi( self.fields[1] ) - 1 def __len__(self): return max(0, self.nfields - 9) property contig: def __get__(self): return self.contig property pos: def __get__(self): return self.pos property id: def __get__(self): return self.fields[2] property ref: def __get__(self): return self.fields[3] property alt: def __get__(self): # convert v3.3 to v4.0 alleles below alt = self.fields[4] if alt == ".": alt = [] else: alt = alt.upper().split(',') return alt property qual: def __get__(self): qual = self.fields[5] if qual == b".": qual = -1 else: try: qual = float(qual) except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL) return qual property filter: def __get__(self): f = self.fields[6] # postpone checking that filters exist. Encode missing filter or no filtering as empty list if f == b"." or f == b"PASS" or f == b"0": return [] else: return f.split(';') property info: def __get__(self): col = self.fields[7] # dictionary of keys, and list of values info = {} if col != b".": for blurp in col.split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.vcf.error(str(self),self.ERROR_INFO_STRING) info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self)) return info property format: def __get__(self): return self.fields[8].split(':') property samples: def __get__(self): return self.vcf._samples def __getitem__(self, key): # parse sample columns values = self.fields[self.vcf._sample2column[key]].split(':') alt = self.alt format = self.format if len(values) > len(format): self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ (len(values),key,len(format))) result = {} for idx in range(len(format)): expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) if expected != -1 and len(result[format[idx]]) != expected: self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) result[format[idx]] = result[format[idx]][:expected] return result cdef class asVCFRecord( ctabix.Parser ): '''converts a :term:`tabix row` into a VCF record.''' cdef vcffile def __init__(self, vcffile ): self.vcffile = vcffile def __call__(self, char * buffer, int len ): cdef VCFRecord r r = VCFRecord( self.vcffile ) r.copy( buffer, len ) return r class VCF(object): # types NT_UNKNOWN = 0 NT_NUMBER = 1 NT_ALLELES = 2 NT_NR_ALLELES = 3 NT_GENOTYPES = 4 NT_PHASED_GENOTYPES = 5 _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string", 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s", 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)", 4:"POS_NOT_NUMERICAL:Position column is not numerical", 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field", 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF", 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF", 8:"POS_NOT_POSITIVE:Position field must be >0", 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'", 10:"ERROR_INFO_STRING:Error while parsing info field", 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)", 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s", 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string", 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header", 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header", 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)", 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)", 18:"BAD_GENOTYPE:Cannot parse genotype (%s)", 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)", 20:"MISSING_REF:Reference allele missing", 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)", 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets", 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes", 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields", 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs", 26:"WRONG_REF:Wrong reference %s", 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data", 28:"BAD_CHR_TAG:Error calculating chr tag for %s", 29:"ZERO_LENGTH_ALLELE:Found zero-length allele", 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base", 31:"ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'", 32:"ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s", 33:"ERROR_FLAG_HAS_VALUE:Flag fields should not have a value", } # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields _header = [] # version number; 33=v3.3; 40=v4.0 _version = 40 # info, filter and format data _info = {} _filter = {} _format = {} # header; and required columns _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] _samples = [] # control behaviour _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD _warn_errors = set([]) _leftalign = False # reference sequence _reference = None # regions to include; None includes everything _regions = None # statefull stuff _lineno = -1 _line = None _lines = None def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # make error identifiers accessible by name for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id if _copy != None: self._leftalign = _copy._leftalign self._header = _copy._header[:] self._version = _copy._version self._info = copy.deepcopy(_copy._info) self._filter = copy.deepcopy(_copy._filter) self._format = copy.deepcopy(_copy._format) self._samples = _copy._samples[:] self._sample2column = copy.deepcopy(_copy._sample2column) self._ignored_errors = copy.deepcopy(_copy._ignored_errors) self._warn_errors = copy.deepcopy(_copy._warn_errors) self._reference = _copy._reference self._regions = _copy._regions if reference: self._reference = reference if regions: self._regions = regions if leftalign: self._leftalign = leftalign self._lines = lines def error(self,line,error,opt=None): if error in self._ignored_errors: return errorlabel, errorstring = self._errors[error].split(':') if opt: errorstring = errorstring % opt errwarn = ["Error","Warning"][error in self._warn_errors] errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) if error in self._warn_errors: return raise ValueError(errorstring) def parse_format(self,line,format,filter=False): if self._version == 40: if not format.startswith('<'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format = "<"+format if not format.endswith('>'): self.error(line,self.V40_MISSING_ANGLE_BRACKETS) format += ">" format = format[1:-1] data = {'id':None,'number':None,'type':None,'descr':None} idx = 0 while len(format.strip())>0: elts = format.strip().split(',') first, rest = elts[0], ','.join(elts[1:]) if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) first = ["ID=","Number=","Type=","Description="][idx] + first if first.startswith('ID='): data['id'] = first.split('=')[1] elif first.startswith('Number='): data['number'] = first.split('=')[1] elif first.startswith('Type='): data['type'] = first.split('=')[1] elif first.startswith('Description='): elts = format.split('"') if len(elts)<3: self.error(line,self.FORMAT_MISSING_QUOTES) elts = first.split('=') + [rest] data['descr'] = elts[1] rest = '"'.join(elts[2:]) if rest.startswith(','): rest = rest[1:] else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) format = rest idx += 1 if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) if 'descr' not in data: # missing description self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) data['descr'] = "" if not data['type'] and not data['number']: # fine, ##filter format return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') if not data['type'] in ["Integer","Float","Character","String","Flag"]: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # I would like a missing-value field, but it isn't there if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value else: data['missing'] = '.' if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) try: n = int(data['number']) t = self.NT_NUMBER except ValueError: n = -1 if data['number'] == '.': t = self.NT_UNKNOWN elif data['number'] == '#alleles': t = self.NT_ALLELES elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES elif data['number'] == '#genotypes': t = self.NT_GENOTYPES elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # abbreviations added in VCF version v4.1 elif data['number'] == 'A': t = self.NT_ALLELES elif data['number'] == 'G': t = self.NT_GENOTYPES else: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # if number is 0 - type must be Flag if n == 0 and data['type'] != 'Flag': self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) # force type 'Flag' if no number data['type'] = 'Flag' return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) def format_format( self, fmt, filter=False ): values = [('ID',fmt.id)] if fmt.number != None and not filter: if fmt.numbertype == self.NT_UNKNOWN: nmb = "." elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" else: raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) values.append( ('Number',nmb) ) values.append( ('Type', fmt.type) ) values.append( ('Description', '"' + fmt.description + '"') ) if self._version == 33: format = ",".join([v for k,v in values]) else: format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" return format def get_expected(self, format, formatdict, alt): fmt = formatdict[format] if fmt.numbertype == self.NT_UNKNOWN: return -1 if fmt.numbertype == self.NT_NUMBER: return fmt.number if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) return 0 def _add_definition(self, formatdict, key, data, line ): if key in formatdict: return self.error(line,self.ERROR_UNKNOWN_KEY,key) if data == None: formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") return if data == []: data = [""] # unsure what type -- say string if type(data[0]) == type(0.0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) return if type(data[0]) == type(0): formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) return formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # todo: trim trailing missing values def format_formatdata( self, data, format, key=True, value=True, separator=":" ): output, sdata = [], [] if type(data) == type([]): # for FORMAT field, make data with dummy values d = {} for k in data: d[k] = [] data = d # convert missing values; and silently add definitions if required for k in data: self._add_definition( format, k, data[k], "(output)" ) for idx,v in enumerate(data[k]): if v == format[k].missingvalue: data[k][idx] = "." # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string for k in data: if k != 'GT': sdata.append( (k,data[k]) ) sdata.sort() if 'GT' in data: sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata for k,v in sdata: if v == []: v = None if key and value: if v != None: output.append( k+"="+','.join(map(str,v)) ) else: output.append( k ) elif key: output.append(k) elif value: if v != None: output.append( ','.join(map(str,v)) ) else: output.append( "." ) # should not happen # snip off trailing missing data while len(output) > 1: last = output[-1].replace(',','').replace('.','') if len(last)>0: break output = output[:-1] return separator.join(output) def enter_default_format(self): for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), ]: if f.id not in self._format: self._format[f.id] = f def parse_header( self, line ): assert line.startswith('##') elts = line[2:].split('=') key = elts[0].strip() value = '='.join(elts[1:]).strip() if key == "fileformat": if value == "VCFv3.3": self._version = 33 elif value == "VCFv4.0": self._version = 40 elif value == "VCFv4.1": # AH - for testing self._version = 40 else: self.error(line,self.UNKNOWN_FORMAT_STRING) elif key == "INFO": f = self.parse_format(line, value) self._info[ f.id ] = f elif key == "FILTER": f = self.parse_format(line, value, filter=True) self._filter[ f.id ] = f elif key == "FORMAT": f = self.parse_format(line, value) self._format[ f.id ] = f else: # keep other keys in the header field self._header.append( (key,value) ) def write_header( self, stream ): stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) def parse_heading( self, line ): assert line.startswith('#') assert not line.startswith('##') headings = line[1:].split('\t') # test for 8, as FORMAT field might be missing if len(headings)==1 and len(line[1:].split()) >= 8: self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) headings = line[1:].split() for i,s in enumerate(self._required): if len(headings)<=i or headings[i] != s: if len(headings) <= i: err = "(%sth entry not found)" % (i+1) else: err = "(found %s, expected %s)" % (headings[i],s) #self.error(line,self.BADLY_FORMATTED_HEADING,err) # allow FORMAT column to be absent if len(headings) == 8: headings.append("FORMAT") else: self.error(line,self.BADLY_FORMATTED_HEADING,err) self._samples = headings[9:] self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) def write_heading( self, stream ): stream.write("#" + "\t".join(self._required + self._samples) + "\n") def convertGT(self, GTstring): if GTstring == ".": return ["."] try: gts = gtsRegEx.split(GTstring) if len(gts) == 1: return [int(gts[0])] if len(gts) != 2: raise ValueError() if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] except ValueError: self.error(self._line,self.BAD_GENOTYPE,GTstring) return [".","|","."] def convertGTback(self, GTdata): return ''.join(map(str,GTdata)) def parse_formatdata( self, key, value, formatdict, line ): # To do: check that the right number of values is present f = formatdict.get(key,None) if f == None: self._add_definition(formatdict, key, value, line ) f = formatdict[key] if f.type == "Flag": if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) return [] values = value.split(',') # deal with trailing data in some early VCF files if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: self.error(line,self.ERROR_TRAILING_DATA,values[-1]) values[-1] = values[-1].split(';')[0] if f.type == "Integer": for idx,v in enumerate(values): try: if v == ".": values[idx] = f.missingvalue else: values[idx] = int(v) except: self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) return [0] * len(values) return values elif f.type == "String": self._line = line if f.id == "GT": values = list(map( self.convertGT, values )) return values elif f.type == "Character": for v in values: if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) return values elif f.type == "Float": for idx,v in enumerate(values): if v == ".": values[idx] = f.missingvalue try: return list(map(float,values)) except: self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) return [0.0] * len(values) else: # can't happen self.error(line,self.ERROR_INFO_STRING) def inregion(self, chrom, pos): if not self._regions: return True for r in self._regions: if r[0] == chrom and r[1] <= pos < r[2]: return True return False def parse_data( self, line, lineparse=False ): cols = line.split('\t') if len(cols) != len(self._samples)+9: # gracefully deal with absent FORMAT column # and those missing samples if len(cols) == 8: cols.append("") else: self.error(line, self.BAD_NUMBER_OF_COLUMNS, "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) chrom = cols[0] # get 0-based position try: pos = int(cols[1])-1 except: self.error(line,self.POS_NOT_NUMERICAL) if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # implement filtering if not self.inregion(chrom,pos): return None # end of first-pass parse for sortedVCF if lineparse: return chrom, pos, line id = cols[2] ref = cols[3].upper() if ref == ".": self.error(line,self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # make sure reference is sane if self._reference: left = max(0,pos-100) faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # convert v3.3 to v4.0 alleles below if cols[4] == ".": alt = [] else: alt = cols[4].upper().split(',') if cols[5] == ".": qual = -1 else: try: qual = float(cols[5]) except: self.error(line,self.QUAL_NOT_NUMERICAL) # postpone checking that filters exist. Encode missing filter or no filtering as empty list if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] else: filter = cols[6].split(';') # dictionary of keys, and list of values info = {} if cols[7] != ".": for blurp in cols[7].split(';'): elts = blurp.split('=') if len(elts) == 1: v = None elif len(elts) == 2: v = elts[1] else: self.error(line,self.ERROR_INFO_STRING) info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line) # Gracefully deal with absent FORMAT column if cols[8] == "": format = [] else: format = cols[8].split(':') # check: all filters are defined for f in filter: if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # check: format fields are defined if self._format: for f in format: if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(line,self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(line,self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(line,self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(line,self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles if alt: for i in range(1,min(len(ref),min(map(len,alt)))): if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): break ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 # parse sample columns samples = [] for sample in cols[9:]: dict = {} values = sample.split(':') if len(values) > len(format): self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) for idx in range(len(format)): expected = self.get_expected(format[idx], self._format, alt) if idx < len(values): value = values[idx] else: if expected == -1: value = "." else: value = ",".join(["."]*expected) dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line) if expected != -1 and len(dict[format[idx]]) != expected: self.error(line,self.BAD_NUMBER_OF_PARAMETERS, "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) dict[format[idx]] = dict[format[idx]][:expected] samples.append( dict ) # done d = {'chrom':chrom, 'pos':pos, # return 0-based position 'id':id, 'ref':ref, 'alt':alt, 'qual':qual, 'filter':filter, 'info':info, 'format':format} for key,value in zip(self._samples,samples): d[key] = value return d def write_data(self, stream, data): required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples for k in required: if k not in data: raise ValueError("Required key %s not found in data" % str(k)) if data['alt'] == []: alt = "." else: alt = ",".join(data['alt']) if data['filter'] == None: filter = "." elif data['filter'] == []: if self._version == 33: filter = "0" else: filter = "PASS" else: filter = ';'.join(data['filter']) if data['qual'] == -1: qual = "." else: qual = str(data['qual']) output = [data['chrom'], str(data['pos']+1), # change to 1-based position data['id'], data['ref'], alt, qual, filter, self.format_formatdata( data['info'], self._info, separator=";" ), self.format_formatdata( data['format'], self._format, value=False ) ] for s in self._samples: output.append( self.format_formatdata( data[s], self._format, key=False ) ) stream.write( "\t".join(output) + "\n" ) def _parse_header(self, stream): self._lineno = 0 for line in stream: self._lineno += 1 if line.startswith('##'): self.parse_header( line.strip() ) elif line.startswith('#'): self.parse_heading( line.strip() ) self.enter_default_format() else: break return line def _parse(self, line, stream): # deal with files with header only if line.startswith("##"): return if len(line.strip()) > 0: d = self.parse_data( line.strip() ) if d: yield d for line in stream: self._lineno += 1 if self._lines and self._lineno > self._lines: raise StopIteration d = self.parse_data( line.strip() ) if d: yield d ###################################################################################################### # # API follows # ###################################################################################################### def getsamples(self): """ List of samples in VCF file """ return self._samples def setsamples(self,samples): """ List of samples in VCF file """ self._samples = samples def getheader(self): """ List of header key-value pairs (strings) """ return self._header def setheader(self,header): """ List of header key-value pairs (strings) """ self._header = header def getinfo(self): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ return self._info def setinfo(self,info): """ Dictionary of ##INFO tags, as VCF.FORMAT values """ self._info = info def getformat(self): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ return self._format def setformat(self,format): """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """ self._format = format def getfilter(self): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ return self._filter def setfilter(self,filter): """ Dictionary of ##FILTER tags, as VCF.FORMAT values """ self._filter = filter def setversion(self, version): if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") self._version = version def setregions(self, regions): self._regions = regions def setreference(self, ref): """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """ self._reference = ref def ignoreerror(self, errorstring): try: self._ignored_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def warnerror(self, errorstring): try: self._warn_errors.add(self.__dict__[errorstring]) except KeyError: raise ValueError("Invalid error string: %s" % errorstring) def parse(self, stream): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ last_line = self._parse_header(stream) # now return a generator that does the actual work. In this way the pre-processing is done # before the first piece of data is yielded return self._parse(last_line, stream) def write(self, stream, datagenerator): """ Writes a VCF file to a stream, using a data generator (or list) """ self.write_header(stream) self.write_heading(stream) for data in datagenerator: self.write_data(stream,data) def writeheader(self, stream): """ Writes a VCF header """ self.write_header(stream) self.write_heading(stream) def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): """ Utility function: compares two calls for equality """ # a variant should always be assigned to a unique position, one base before # the leftmost position of the alignment gap. If this rule is implemented # correctly, the two positions must be equal for the calls to be identical. if pos1 != pos2: return False # from both calls, trim rightmost bases when identical. Do this safely, i.e. # only when the reference bases are not Ns while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: ref1 = ref1[:-1] alt1 = alt1[:-1] while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: ref2 = ref2[:-1] alt2 = alt2[:-1] # now, the alternative alleles must be identical return alt1 == alt2 ########################################################################################################### ########################################################################################################### ## API functions added by Andreas ########################################################################################################### def connect( self, filename ): '''connect to tabix file.''' self.tabixfile = pysam.Tabixfile( filename ) self._parse_header(self.tabixfile.header) def fetch(self, reference = None, start = None, end = None, region = None ): """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """ return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) def validate( self, record ): '''validate vcf record. returns a validated record. ''' raise NotImplementedError( "needs to be checked" ) chrom, pos = record.chrom, record.pos # check reference ref = record.ref if ref == ".": self.error(str(record),self.MISSING_REF) if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) else: ref = "" else: for c in ref: if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF) if "N" in ref: ref = get_sequence(chrom, pos, pos+len(ref), self._reference) # make sure reference is sane if self._reference: left = max(0,self.pos-100) faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference) faref = faref_leftflank[pos-left:] if faref != ref: self.error(str(record),self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) ref = faref # check: format fields are defined for f in record.format: if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f) # check: all filters are defined for f in record.filter: if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f) # convert v3.3 alleles if self._version == 33: if len(ref) != 1: self.error(str(record),self.V33_BAD_REF) newalts = [] have_deletions = False for a in alt: if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference elif a.startswith('D'): # allow D and D have_deletions = True try: l = int(a[1:]) # throws ValueError if sequence if len(ref) < l: # add to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[l:] # new deletion, deleting pos...pos+l except ValueError: s = a[1:] if len(ref) < len(s): # add Ns to reference if necessary addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) if not s.endswith(addns) and addns != 'N'*len(addns): self.error(str(record),self.V33_UNMATCHED_DELETION, "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) ref += addns for i,na in enumerate(newalts): newalts[i] = na+addns a = ref[len(s):] # new deletion, deleting from pos else: self.error(str(record),self.V33_BAD_ALLELE) newalts.append(a) alt = newalts # deletion alleles exist, add dummy 1st reference allele, and account for leading base if have_deletions: if pos == 0: # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) ref += addn alt = [allele+addn for allele in alt] else: addn = get_sequence(chrom,pos-1,pos,self._reference) ref = addn + ref alt = [addn + allele for allele in alt] pos -= 1 else: # format v4.0 -- just check for nucleotides for allele in alt: if not alleleRegEx.match(allele): self.error(str(record),self.V40_BAD_ALLELE,allele) # check for leading nucleotide in indel calls for allele in alt: if len(allele) != len(ref): if len(allele) == 0: self.error(str(record),self.ZERO_LENGTH_ALLELE) if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): self.error(str(record),self.MISSING_INDEL_ALLELE_REF_BASE) # trim trailing bases in alleles for i in range(1,min(len(ref),min(map(len,alt)))): if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): break ref, alt = ref[:-1], [allele[:-1] for allele in alt] # left-align alleles, if a reference is available if self._leftalign and self._reference: while left < pos: movable = True for allele in alt: if len(allele) > len(ref): longest, shortest = allele, ref else: longest, shortest = ref, allele if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): movable = False if longest[-1].upper() != longest[len(shortest)-1].upper(): movable = False if not movable: break ref = ref[:-1] alt = [allele[:-1] for allele in alt] if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: ref = faref_leftflank[pos-left-1] + ref alt = [faref_leftflank[pos-left-1] + allele for allele in alt] pos -= 1 __all__ = [ "VCF", "VCFRecord", ] pysam-0.7.7/pysam/include/0000775000076400007650000000000012241575073015267 5ustar andreasandreaspysam-0.7.7/pysam/include/__init__.py0000664000076400007650000000000012075240750017362 0ustar andreasandreaspysam-0.7.7/pysam/ctabix.c0000664000076400007650000210607412241546207015271 0ustar andreasandreas/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? 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PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "ctabix.pyx", "TabProxies.pxd", "type.pxd", "bool.pxd", "complex.pxd", }; /*--- Type declarations ---*/ struct __pyx_obj_5pysam_6ctabix_TabixIterator; struct __pyx_obj_5pysam_6ctabix_Parser; struct __pyx_obj_5pysam_6ctabix_asGTF; struct __pyx_obj_5pysam_10TabProxies_TupleProxy; struct __pyx_obj_5pysam_10TabProxies_GTFProxy; struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator; struct __pyx_obj_5pysam_6ctabix_asVCF; struct __pyx_obj_5pysam_6ctabix_Tabixfile; struct __pyx_obj_5pysam_6ctabix_asTuple; struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed; struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy; struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator; struct __pyx_obj_5pysam_10TabProxies_BedProxy; struct __pyx_obj_5pysam_6ctabix_asBed; struct __pyx_obj_5pysam_10TabProxies_VCFProxy; /* "pysam/ctabix.pxd":224 * cdef Parser parser * * cdef class TabixIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "pysam/ctabix.pxd":232 * cdef tabix_t * tabixfile * * cdef class Parser: # <<<<<<<<<<<<<< * cdef parse( self, char * buffer, int len ) * */ struct __pyx_obj_5pysam_6ctabix_Parser { PyObject_HEAD struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtab; }; /* "pysam/ctabix.pxd":239 * * * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asGTF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":41 * ctypedef int uint64_t * * cdef class TupleProxy: # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_TupleProxy { PyObject_HEAD struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab; char *data; char **fields; int nfields; int index; int nbytes; int offset; int is_modified; }; /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_GTFProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; char *_attributes; int hasOwnAttributes; }; /* "pysam/ctabix.pxd":201 * int ks_getuntil( kstream_t *, int, kstring_t *, int * ) * * cdef class tabix_file_iterator: # <<<<<<<<<<<<<< * cdef gzFile fh * cdef kstream_t * ks */ struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator { PyObject_HEAD struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab; gzFile fh; kstream_t *ks; kstring_t buffer; size_t size; struct __pyx_obj_5pysam_6ctabix_Parser *parser; int fd; PyObject *infile; }; /* "pysam/ctabix.pxd":245 * pass * * cdef class asVCF(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asVCF { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "pysam/ctabix.pxd":212 * cdef __cnext__(self) * * cdef class Tabixfile: # <<<<<<<<<<<<<< * * # pointer to tabixfile */ struct __pyx_obj_5pysam_6ctabix_Tabixfile { PyObject_HEAD tabix_t *tabixfile; int isremote; char *_filename; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "pysam/ctabix.pxd":235 * cdef parse( self, char * buffer, int len ) * * cdef class asTuple(Parser): # <<<<<<<<<<<<<< * cdef parse( self, char * buffer, int len ) * */ struct __pyx_obj_5pysam_6ctabix_asTuple { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "pysam/ctabix.pxd":248 * pass * * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; struct __pyx_obj_5pysam_6ctabix_Parser *parser; }; /* "TabProxies.pxd":69 * cdef char * getAttributes( self ) * * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy { struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base; }; /* "pysam/ctabix.pxd":228 * cdef tabix_t * tabixfile * * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<< * cdef ti_iter_t iterator * cdef tabix_t * tabixfile */ struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator { PyObject_HEAD ti_iter_t iterator; tabix_t *tabixfile; }; /* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_BedProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t start; uint32_t end; int bedfields; }; /* "pysam/ctabix.pxd":242 * pass * * cdef class asBed(Parser): # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_6ctabix_asBed { struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base; }; /* "TabProxies.pxd":83 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_obj_5pysam_10TabProxies_VCFProxy { struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base; char *contig; uint32_t pos; }; /* "pysam/ctabix.pyx":392 * ######################################################### * ######################################################### * cdef class Parser: # <<<<<<<<<<<<<< * * cdef parse(self, char * buffer, int length): */ struct __pyx_vtabstruct_5pysam_6ctabix_Parser { PyObject *(*parse)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int); }; static struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtabptr_5pysam_6ctabix_Parser; /* "pysam/ctabix.pyx":400 * return self.parse( buffer, length ) * * cdef class asTuple(Parser): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a python tuple. * */ struct __pyx_vtabstruct_5pysam_6ctabix_asTuple { struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base; }; static struct __pyx_vtabstruct_5pysam_6ctabix_asTuple *__pyx_vtabptr_5pysam_6ctabix_asTuple; /* "pysam/ctabix.pyx":450 * return r * * cdef class asBed( Parser ): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a bed record * with the following fields: */ struct __pyx_vtabstruct_5pysam_6ctabix_asBed { struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base; }; static struct __pyx_vtabstruct_5pysam_6ctabix_asBed *__pyx_vtabptr_5pysam_6ctabix_asBed; /* "pysam/ctabix.pyx":802 * * * cdef class tabix_file_iterator: # <<<<<<<<<<<<<< * '''iterate over a compressed or uncompressed ``infile``. * ''' */ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator { PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *); }; static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_file_iterator; /* "pysam/ctabix.pyx":490 * return r * * cdef class asVCF( Parser ): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a VCF record with * the following fields: */ struct __pyx_vtabstruct_5pysam_6ctabix_asVCF { struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base; 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}; static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy; /* "TabProxies.pxd":72 * pass * * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base; }; static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy; /* "pysam/ctabix.pyx":413 * return r * * cdef class asGTF(Parser): # <<<<<<<<<<<<<< * '''converts a :term:`tabix row` into a GTF record with the following * fields: */ struct __pyx_vtabstruct_5pysam_6ctabix_asGTF { struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base; }; static struct __pyx_vtabstruct_5pysam_6ctabix_asGTF *__pyx_vtabptr_5pysam_6ctabix_asGTF; /* "TabProxies.pxd":60 * cdef update( self, char * buffer, size_t nbytes ) * * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<< * * cdef: */ struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy { struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base; 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/* Module declarations from 'cpython.long' */ /* Module declarations from 'cpython.float' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.complex' */ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython.string' */ /* Module declarations from 'cpython.unicode' */ /* Module declarations from 'cpython.dict' */ /* Module declarations from 'cpython.instance' */ /* Module declarations from 'cpython.function' */ /* Module declarations from 'cpython.method' */ /* Module declarations from 'cpython.weakref' */ /* Module declarations from 'cpython.getargs' */ /* Module declarations from 'cpython.pythread' */ /* Module declarations from 'cpython.pystate' */ /* Module declarations from 'cpython.cobject' */ /* Module declarations from 'cpython.oldbuffer' */ /* Module declarations from 'cpython.set' */ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* Module declarations from 'libc.errno' */ /* Module declarations from 'libc.stdint' */ /* Module declarations from 'pysam.ctabix' */ static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0; static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0; static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0; static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *); /*proto*/ #define __Pyx_MODULE_NAME "pysam.ctabix" int __pyx_module_is_main_pysam__ctabix = 0; /* Implementation of 'pysam.ctabix' */ static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_OSError; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_MemoryError; static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_parser, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_10close(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_6Parser___call__(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length); /* proto */ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */ static int __pyx_pf_5pysam_6ctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_6ctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_8next(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "invalid file opening mode `%s`"; static char __pyx_k_6[] = ".tbi"; static char __pyx_k_7[] = "http:"; static char __pyx_k_9[] = "ftp:"; static char __pyx_k_12[] = "writing to tabix files not implemented"; static char __pyx_k_14[] = "file `%s` not found"; static char __pyx_k_15[] = "index `%s` not found"; static char __pyx_k_16[] = "could not open file `%s`"; static char __pyx_k_17[] = "%s:%i-%i"; static char __pyx_k_18[] = "invalid region: start (%i) > end (%i)"; static char __pyx_k_19[] = "start out of range (%i)"; static char __pyx_k_20[] = "end out of range (%i)"; static char __pyx_k_21[] = "I/O operation on closed file"; static char __pyx_k_24[] = "malformatted query or wrong sequence name.\n"; static char __pyx_k_26[] = "can't open header.\n"; static char __pyx_k_30[] = "Filename '%s' already exists, use *force* to overwrite"; static char __pyx_k_31[] = "could not open '%s' for writing"; static char __pyx_k_33[] = "could not open '%s' for reading"; static char __pyx_k_35[] = "writing failed"; static char __pyx_k_39[] = "#"; static char __pyx_k_41[] = "No such file '%s'"; static char __pyx_k_42[] = "neither preset nor seq_col,start_col and end_col given"; static char __pyx_k_44[] = ".gz"; static char __pyx_k_46[] = "Filename '%s.tbi' already exists, use *force* to overwrite"; static char __pyx_k_48[] = "unknown preset '%s', valid presets are '%s'"; static char __pyx_k_49[] = ","; static char __pyx_k_50[] = "error (%d): %s (%d: %s)"; static char __pyx_k_51[] = "I/O operation on closed file."; static char __pyx_k_54[] = "%s"; static char __pyx_k_57[] = "incomplete line at %s"; static char __pyx_k_58[] = "tabix_generic_iterator"; static char __pyx_k_59[] = "filename associated with this object."; static char __pyx_k_60[] = "the file header.\n \n .. note::\n The header is returned as an iterator over lines without the\n newline character.\n "; static char __pyx_k_61[] = "chromosome names"; static char __pyx_k_62[] = "getfilesystemencoding"; static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx"; static char __pyx_k_66[] = "pysam.ctabix"; static char __pyx_k_71[] = "tabix_generic_iterator.__init__"; static char __pyx_k_74[] = "tabix_generic_iterator.__iter__"; static char __pyx_k_77[] = "tabix_generic_iterator.__next__"; static char __pyx_k_80[] = "tabix_generic_iterator.next"; static char __pyx_k_81[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n "; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__w[] = "w"; static char __pyx_k__fn[] = "fn"; static char __pyx_k__fp[] = "fp"; static char __pyx_k__io[] = "io"; static char __pyx_k__os[] = "os"; static char __pyx_k__bed[] = "bed"; static char __pyx_k__cpy[] = "cpy"; static char __pyx_k__end[] = "end"; static char __pyx_k__gff[] = "gff"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__sam[] = "sam"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__tid[] = "tid"; static char __pyx_k__vcf[] = "vcf"; static char __pyx_k__conf[] = "conf"; static char __pyx_k__gzip[] = "gzip"; static char __pyx_k__join[] = "join"; static char __pyx_k__line[] = "line"; static char __pyx_k__mode[] = "mode"; static char __pyx_k__next[] = "next"; static char __pyx_k__path[] = "path"; static char __pyx_k__self[] = "self"; static char __pyx_k___open[] = "_open"; static char __pyx_k__asBed[] = "asBed"; static char __pyx_k__asGTF[] = "asGTF"; static char __pyx_k__asVCF[] = "asVCF"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__close[] = "close"; static char __pyx_k__force[] = "force"; static char __pyx_k__start[] = "start"; static char __pyx_k__types[] = "types"; static char __pyx_k__buffer[] = "buffer"; static char __pyx_k__closed[] = "closed"; static char __pyx_k__ctypes[] = "ctypes"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; static char __pyx_k__exists[] = "exists"; static char __pyx_k__fd_src[] = "fd_src"; static char __pyx_k__infile[] = "infile"; static char __pyx_k__length[] = "length"; static char __pyx_k__nbytes[] = "nbytes"; static char __pyx_k__parser[] = "parser"; static char __pyx_k__pileup[] = "pileup"; static char __pyx_k__preset[] = "preset"; static char __pyx_k__psltbl[] = "psltbl"; static char __pyx_k__region[] = "region"; static char __pyx_k__struct[] = "struct"; static char __pyx_k__unlink[] = "unlink"; static char __pyx_k__IOError[] = "IOError"; static char __pyx_k__OSError[] = "OSError"; static char __pyx_k__PYTHON3[] = "PYTHON3"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k___isOpen[] = "_isOpen"; static char __pyx_k__asTuple[] = "asTuple"; static char __pyx_k__end_col[] = "end_col"; static char __pyx_k__seq_col[] = "seq_col"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k__O_RDONLY[] = "O_RDONLY"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____iter__[] = "__iter__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____next__[] = "__next__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__endswith[] = "endswith"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__readline[] = "readline"; static char __pyx_k__tempfile[] = "tempfile"; static char __pyx_k__Tabixfile[] = "Tabixfile"; static char __pyx_k__TypeError[] = "TypeError"; static char __pyx_k__conf_data[] = "conf_data"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__meta_char[] = "meta_char"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__start_col[] = "start_col"; static char __pyx_k__tabixfile[] = "tabixfile"; static char __pyx_k__zerobased[] = "zerobased"; static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__MemoryError[] = "MemoryError"; static char __pyx_k__WINDOW_SIZE[] = "WINDOW_SIZE"; static char __pyx_k__buffer_size[] = "buffer_size"; static char __pyx_k__filename_in[] = "filename_in"; static char __pyx_k__preset2conf[] = "preset2conf"; static char __pyx_k__tabix_index[] = "tabix_index"; static char __pyx_k___parseRegion[] = "_parseRegion"; static char __pyx_k__filename_out[] = "filename_out"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k__tabix_compress[] = "tabix_compress"; static char __pyx_k__tabix_iterator[] = "tabix_iterator"; static char __pyx_k__getdefaultencoding[] = "getdefaultencoding"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__tabix_file_iterator[] = "tabix_file_iterator"; static PyObject *__pyx_kp_u_1; static PyObject *__pyx_kp_s_12; static PyObject *__pyx_kp_s_14; static PyObject *__pyx_kp_s_15; static PyObject *__pyx_kp_s_16; static PyObject *__pyx_kp_s_17; static PyObject *__pyx_kp_s_18; static PyObject *__pyx_kp_s_19; static PyObject *__pyx_kp_s_20; static PyObject *__pyx_kp_s_21; static PyObject *__pyx_kp_s_24; static PyObject *__pyx_kp_s_26; static PyObject *__pyx_kp_u_3; static PyObject *__pyx_kp_s_30; static PyObject *__pyx_kp_s_31; static PyObject *__pyx_kp_s_33; static PyObject *__pyx_kp_s_35; static PyObject *__pyx_kp_s_39; static PyObject *__pyx_kp_s_41; static PyObject *__pyx_kp_s_42; static PyObject *__pyx_kp_s_44; static PyObject *__pyx_kp_s_46; static PyObject *__pyx_kp_s_48; static PyObject *__pyx_kp_s_49; static PyObject *__pyx_kp_s_5; static PyObject *__pyx_kp_s_50; static PyObject *__pyx_kp_s_51; static PyObject *__pyx_kp_s_54; static PyObject *__pyx_kp_s_57; static PyObject *__pyx_n_s_58; static PyObject *__pyx_kp_s_6; static PyObject *__pyx_n_s_62; static PyObject *__pyx_kp_s_65; static PyObject *__pyx_n_s_66; static PyObject *__pyx_kp_s_7; static PyObject *__pyx_n_s_71; static PyObject *__pyx_n_s_74; static PyObject *__pyx_n_s_77; static PyObject *__pyx_n_s_80; static PyObject *__pyx_kp_s_81; static PyObject *__pyx_kp_s_9; static PyObject *__pyx_n_s__IOError; static PyObject *__pyx_n_s__IndexError; static PyObject *__pyx_n_s__KeyError; static PyObject *__pyx_n_s__MemoryError; static PyObject *__pyx_n_s__NotImplementedError; static PyObject *__pyx_n_s__OSError; static PyObject *__pyx_n_s__O_RDONLY; static PyObject *__pyx_n_s__PYTHON3; static PyObject *__pyx_n_s__StopIteration; static PyObject *__pyx_n_s__Tabixfile; static PyObject *__pyx_n_s__TypeError; static PyObject *__pyx_n_s__ValueError; static PyObject *__pyx_n_s__WINDOW_SIZE; static PyObject *__pyx_n_s____all__; static PyObject *__pyx_n_s____init__; static PyObject *__pyx_n_s____iter__; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____next__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___isOpen; static PyObject *__pyx_n_s___open; static PyObject *__pyx_n_s___parseRegion; static PyObject *__pyx_n_s__asBed; static PyObject *__pyx_n_s__asGTF; static PyObject *__pyx_n_s__asTuple; static PyObject *__pyx_n_s__asVCF; static PyObject *__pyx_n_s__ascii; 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{ PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_19tabix_file_iterator_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->parser); Py_CLEAR(p->infile); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_6ctabix_tabix_file_iterator(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } if (p->infile) { e = (*v)(p->infile, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_6ctabix_tabix_file_iterator(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->infile); p->infile = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_file_iterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_file_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)}, {__Pyx_NAMESTR("next"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_file_iterator_9next, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19tabix_file_iterator_8next)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_tabix_file_iterator = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_tabix_file_iterator = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_tabix_file_iterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_tabix_file_iterator = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_file_iterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.tabix_file_iterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_tabix_file_iterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_tabix_file_iterator, /*tp_as_number*/ &__pyx_tp_as_sequence_tabix_file_iterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_tabix_file_iterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_tabix_file_iterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterate over a compressed or uncompressed ``infile``.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_6ctabix_tabix_file_iterator, /*tp_traverse*/ __pyx_tp_clear_5pysam_6ctabix_tabix_file_iterator, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_19tabix_file_iterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_19tabix_file_iterator_7__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_tabix_file_iterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_tabix_file_iterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_Tabixfile *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_9Tabixfile_13__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->parser); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_6ctabix_Tabixfile(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o; if (p->parser) { e = (*v)(((PyObject*)p->parser), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_6ctabix_Tabixfile(PyObject *o) { struct __pyx_obj_5pysam_6ctabix_Tabixfile *p = (struct __pyx_obj_5pysam_6ctabix_Tabixfile *)o; PyObject* tmp; tmp = ((PyObject*)p->parser); p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_filename(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(o); } static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(o); } static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_Tabixfile[] = { {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_2_isOpen)}, {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_4_open)}, {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_6_parseRegion)}, {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_8fetch)}, {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_11close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_10close)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_6ctabix_Tabixfile[] = { {(char *)"filename", __pyx_getprop_5pysam_6ctabix_9Tabixfile_filename, 0, __Pyx_DOCSTR(__pyx_k_59), 0}, {(char *)"header", __pyx_getprop_5pysam_6ctabix_9Tabixfile_header, 0, __Pyx_DOCSTR(__pyx_k_60), 0}, {(char *)"contigs", __pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs, 0, __Pyx_DOCSTR(__pyx_k_61), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Tabixfile = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_Tabixfile = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_Tabixfile = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Tabixfile = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_Tabixfile = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.Tabixfile"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_Tabixfile, /*tp_as_number*/ &__pyx_tp_as_sequence_Tabixfile, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Tabixfile, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Tabixfile, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("*(filename, mode='r', parser = None)*\n\n opens a :term:`tabix file` for reading. A missing\n index (*filename* + \".tbi\") will raise an exception.\n\n *parser* sets the default parser for this tabix file. If *parser*\n is None, the results are returned as an unparsed string.\n Otherwise, *parser* is assumed to be a functor that will return\n parsed data (see for example :meth:`asTuple` and :meth:`asGTF`).\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_6ctabix_Tabixfile, /*tp_traverse*/ __pyx_tp_clear_5pysam_6ctabix_Tabixfile, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_Tabixfile, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_6ctabix_Tabixfile, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_Tabixfile, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; if (__pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_13TabixIterator_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_TabixIterator = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_TabixIterator = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_TabixIterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_TabixIterator = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_TabixIterator, /*tp_as_number*/ &__pyx_tp_as_sequence_TabixIterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TabixIterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TabixIterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("iterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_TabixHeaderIterator = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_TabixHeaderIterator = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_TabixHeaderIterator = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_TabixHeaderIterator, /*tp_as_number*/ &__pyx_tp_as_sequence_TabixHeaderIterator, /*tp_as_sequence*/ &__pyx_tp_as_mapping_TabixHeaderIterator, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_TabixHeaderIterator, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("return header lines.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_vtable_5pysam_6ctabix_Parser; static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_6ctabix_Parser *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_Parser *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_Parser; return o; } static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Parser = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_Parser = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_Parser = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Parser = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_Parser, /*tp_as_number*/ &__pyx_tp_as_sequence_Parser, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Parser, /*tp_as_mapping*/ 0, /*tp_hash*/ __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Parser, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ 0, /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_Parser, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_asTuple __pyx_vtable_5pysam_6ctabix_asTuple; static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_asTuple *p; PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_asTuple *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asTuple; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asTuple = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asTuple = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asTuple = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asTuple = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_asTuple, /*tp_as_number*/ &__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/ 0, /*tp_hash*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/ #else 0, /*tp_call*/ #endif 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asTuple, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a python tuple.\n\n Access is by numeric index.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asTuple, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_asGTF __pyx_vtable_5pysam_6ctabix_asGTF; static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_asGTF *p; PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_asGTF *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asGTF; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asGTF = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asGTF = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asGTF = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asGTF = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_asGTF, /*tp_as_number*/ &__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/ 0, /*tp_hash*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/ #else 0, /*tp_call*/ #endif 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asGTF, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a GTF record with the following \n fields:\n\n contig\n contig\n feature\n feature\n source\n source\n start\n genomic start coordinate (0-based)\n end\n genomic end coordinate plus one (0-based)\n score\n feature score\n strand\n strand\n frame\n frame\n attributes\n attribute string.\n\n GTF formatted entries also defined the attributes:\n\n gene_id\n the gene identifier\n transcript_ind\n the transcript identifier\n \n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asGTF, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_asBed __pyx_vtable_5pysam_6ctabix_asBed; static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_asBed *p; PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_asBed *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asBed; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asBed = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asBed = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asBed = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asBed = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_asBed, /*tp_as_number*/ &__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/ 0, /*tp_hash*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/ #else 0, /*tp_call*/ #endif 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asBed, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts a :term:`tabix row` into a bed record\n with the following fields:\n\n contig\n contig\n start\n genomic start coordinate (zero-based)\n end\n genomic end coordinate plus one (zero-based)\n name\n name of feature.\n score\n score of feature\n strand\n strand of feature\n thickStart\n thickStart\n thickEnd\n thickEnd\n itemRGB\n itemRGB\n blockCount\n number of bocks\n blockSizes\n ',' separated string of block sizes\n blockStarts\n ',' separated string of block genomic start positions\n\n Only the first three fields are required. Additional\n fields are optional, but if one is defined, all the preceeding\n need to be defined as well.\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_6ctabix_asBed, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_6ctabix_asVCF __pyx_vtable_5pysam_6ctabix_asVCF; static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_6ctabix_asVCF *p; PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_6ctabix_asVCF *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_Parser*)__pyx_vtabptr_5pysam_6ctabix_asVCF; return o; } static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_asVCF = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_asVCF = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_asVCF = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_asVCF = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_asVCF, /*tp_as_number*/ &__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/ &__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/ 0, /*tp_hash*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_6ctabix_6Parser_1__call__, /*tp_call*/ #else 0, /*tp_call*/ #endif 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_asVCF, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("converts 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value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = PyObject_GetAttrString(base, (char *)"__class__"); if (!metaclass) { PyErr_Clear(); metaclass = (PyObject*) Py_TYPE(base); } } else { metaclass = (PyObject *) &PyClass_Type; } #else if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = (PyObject*) Py_TYPE(base); } else { metaclass = (PyObject *) &PyType_Type; } #endif Py_INCREF(metaclass); return metaclass; } static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *qualname, PyObject *modname) { PyObject *result; PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0) return NULL; metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); } else { metaclass = __Pyx_FindPy2Metaclass(bases); } result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); Py_DECREF(metaclass); return result; } static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { if (op->func.m_ml->ml_doc) { #if PY_MAJOR_VERSION >= 3 op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); #else op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); #endif if (unlikely(op->func_doc == NULL)) return NULL; } else { Py_INCREF(Py_None); return Py_None; } } Py_INCREF(op->func_doc); return op->func_doc; } static int __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp = op->func_doc; if (value == NULL) value = Py_None; /* Mark as deleted */ Py_INCREF(value); op->func_doc = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) { if (unlikely(op->func_name == NULL)) { #if PY_MAJOR_VERSION >= 3 op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); #else op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); #endif if (unlikely(op->func_name == NULL)) return NULL; } Py_INCREF(op->func_name); return op->func_name; } static int __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__name__ must be set to a string object"); return -1; } tmp = op->func_name; Py_INCREF(value); op->func_name = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op) { Py_INCREF(op->func_qualname); return op->func_qualname; } static int __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__qualname__ must be set to a string object"); return -1; } tmp = op->func_qualname; Py_INCREF(value); op->func_qualname = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) { PyObject *self; self = m->func_closure; if (self == NULL) self = Py_None; Py_INCREF(self); return self; } static PyObject * __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) { if (unlikely(op->func_dict == NULL)) { op->func_dict = PyDict_New(); if (unlikely(op->func_dict == NULL)) return NULL; } Py_INCREF(op->func_dict); return op->func_dict; } static int __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; if (unlikely(value == NULL)) { PyErr_SetString(PyExc_TypeError, "function's dictionary may not be deleted"); return -1; } if (unlikely(!PyDict_Check(value))) { PyErr_SetString(PyExc_TypeError, "setting function's dictionary to a non-dict"); return -1; } tmp = op->func_dict; Py_INCREF(value); op->func_dict = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) { PyObject* dict = PyModule_GetDict(__pyx_m); Py_XINCREF(dict); return dict; } static PyObject * __Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) { Py_INCREF(Py_None); return Py_None; } static PyObject * __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) { PyObject* result = (op->func_code) ? op->func_code : Py_None; Py_INCREF(result); return result; } static PyObject * __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { if (op->defaults_tuple) { Py_INCREF(op->defaults_tuple); return op->defaults_tuple; } if (op->defaults_getter) { PyObject *res = op->defaults_getter((PyObject *) op); if (likely(res)) { Py_INCREF(res); op->defaults_tuple = res; } return res; } Py_INCREF(Py_None); return Py_None; } static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {0, 0, 0, 0, 0} }; #ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ #define PY_WRITE_RESTRICTED WRITE_RESTRICTED #endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} }; static PyObject * __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromString(m->func.m_ml->ml_name); #else return PyString_FromString(m->func.m_ml->ml_name); #endif } static PyMethodDef __pyx_CyFunction_methods[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, {0, 0, 0, 0} }; static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *closure, PyObject *module, PyObject* code) { __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; op->flags = flags; op->func_weakreflist = NULL; op->func.m_ml = ml; op->func.m_self = (PyObject *) op; Py_XINCREF(closure); op->func_closure = closure; Py_XINCREF(module); op->func.m_module = module; op->func_dict = NULL; op->func_name = NULL; Py_INCREF(qualname); op->func_qualname = qualname; op->func_doc = NULL; op->func_classobj = NULL; Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_getter = NULL; PyObject_GC_Track(op); return (PyObject *) op; } static int __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) { Py_CLEAR(m->func_closure); Py_CLEAR(m->func.m_module); Py_CLEAR(m->func_dict); Py_CLEAR(m->func_name); Py_CLEAR(m->func_qualname); Py_CLEAR(m->func_doc); Py_CLEAR(m->func_code); Py_CLEAR(m->func_classobj); Py_CLEAR(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_XDECREF(pydefaults[i]); PyMem_Free(m->defaults); m->defaults = NULL; } return 0; } static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) { PyObject_GC_UnTrack(m); if (m->func_weakreflist != NULL) PyObject_ClearWeakRefs((PyObject *) m); __Pyx_CyFunction_clear(m); PyObject_GC_Del(m); } static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) { Py_VISIT(m->func_closure); Py_VISIT(m->func.m_module); Py_VISIT(m->func_dict); Py_VISIT(m->func_name); Py_VISIT(m->func_qualname); Py_VISIT(m->func_doc); Py_VISIT(m->func_code); Py_VISIT(m->func_classobj); Py_VISIT(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_VISIT(pydefaults[i]); } return 0; } static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { Py_INCREF(func); return func; } if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { if (type == NULL) type = (PyObject *)(Py_TYPE(obj)); return PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); } if (obj == Py_None) obj = NULL; return PyMethod_New(func, obj, type); } static PyObject* __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", op->func_qualname, (void *)op); #else return PyString_FromFormat("", PyString_AsString(op->func_qualname), (void *)op); #endif } #if CYTHON_COMPILING_IN_PYPY static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyCFunctionObject* f = (PyCFunctionObject*)func; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); Py_ssize_t size; switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { case METH_VARARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) return (*meth)(self, arg); break; case METH_VARARGS | METH_KEYWORDS: return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); case METH_NOARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 0) return (*meth)(self, NULL); PyErr_Format(PyExc_TypeError, "%.200s() takes no arguments (%zd given)", f->m_ml->ml_name, size); return NULL; } break; case METH_O: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 1) return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); PyErr_Format(PyExc_TypeError, "%.200s() takes exactly one argument (%zd given)", f->m_ml->ml_name, size); return NULL; } break; default: PyErr_SetString(PyExc_SystemError, "Bad call flags in " "__Pyx_CyFunction_Call. METH_OLDARGS is no " "longer supported!"); return NULL; } PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", f->m_ml->ml_name); return NULL; } #else static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { return PyCFunction_Call(func, arg, kw); } #endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_CyFunction_methods, /*tp_methods*/ __pyx_CyFunction_members, /*tp_members*/ __pyx_CyFunction_getsets, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ __Pyx_CyFunction_descr_get, /*tp_descr_get*/ 0, /*tp_descr_set*/ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static int __Pyx_CyFunction_init(void) { #if !CYTHON_COMPILING_IN_PYPY __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; #endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, sizeof(size)); m->defaults_pyobjects = pyobjects; return m->defaults; } static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); } static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(int32_t) == sizeof(char)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (int32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(int32_t) == sizeof(short)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (int32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(int32_t) == sizeof(int)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (int32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(int32_t) == sizeof(long)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (int32_t)-1; } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static void* __Pyx_GetVtable(PyObject *dict) { void* ptr; PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__"); if (!ob) goto bad; #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) ptr = PyCapsule_GetPointer(ob, 0); #else ptr = PyCObject_AsVoidPtr(ob); #endif if (!ptr && !PyErr_Occurred()) PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type"); Py_DECREF(ob); return ptr; bad: Py_XDECREF(ob); return NULL; } static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ pysam-0.7.7/pysam/tabix_util.c0000664000076400007650000000111712241244604016145 0ustar andreasandreas// Definition of pysamerr #include "stdio.h" #include "unistd.h" FILE * pysamerr = NULL; #if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700) /* * A rudimentary emulation of getline() for systems that dont support it * natively. Since this is used for PPD file reading, it assumes (possibly * falsely) that BUFSIZ is big enough. */ ssize_t getline(char **line, size_t *linelen, FILE *fp) { if (*linelen == 0) { *linelen = BUFSIZ; *line = malloc(*linelen); } memset(*line, 0, *linelen); fgets(*line, *linelen, fp); return (strlen(*line)); } #endif pysam-0.7.7/pysam/TabProxies.pxd0000664000076400007650000000436612052716017016445 0ustar andreasandreascdef extern from "stdlib.h": void free(void *) void *malloc(size_t) void *calloc(size_t,size_t) void *realloc(void *,size_t) int c_abs "abs" (int) int c_abs "abs" (int) int atoi( char *nptr) long atol( char *nptr) double atof( char *nptr) cdef extern from "Python.h": ctypedef struct FILE char *fgets(char *str, int size, FILE *ifile) int feof(FILE *stream) size_t strlen(char *s) size_t getline(char **lineptr, size_t *n, FILE *stream) char *strstr(char *, char *) char *strchr(char *string, int c) int fileno(FILE *stream) cdef extern from "string.h": int strcmp(char *s1, char *s2) int strncmp(char *s1,char *s2,size_t len) char *strcpy(char *dest,char *src) char *strncpy(char *dest,char *src, size_t len) char *strdup(char *) char *strcat(char *,char *) size_t strlen(char *s) int memcmp( void * s1, void *s2, size_t len ) void *memcpy(void *dest, void *src, size_t n) void *memchr(void *s, int c, size_t n) cdef extern from "stdint.h": ctypedef int int64_t ctypedef int int32_t ctypedef int uint32_t ctypedef int uint8_t ctypedef int uint64_t cdef class TupleProxy: cdef: char * data char ** fields int nfields int index int nbytes int offset cdef bint is_modified cdef int getMaxFields( self, size_t nbytes ) # cdef char * _getindex( self, int idx ) cdef take( self, char * buffer, size_t nbytes ) cdef present( self, char * buffer, size_t nbytes ) cdef copy( self, char * buffer, size_t nbytes ) cdef update( self, char * buffer, size_t nbytes ) cdef class GTFProxy( TupleProxy) : cdef: char * _attributes cdef bint hasOwnAttributes cdef int getMaxFields( self, size_t nbytes ) cdef char * getAttributes( self ) cdef class NamedTupleProxy( TupleProxy) : pass cdef class BedProxy( NamedTupleProxy) : cdef: char * contig uint32_t start uint32_t end int bedfields cdef int getMaxFields( self, size_t nbytes ) cdef update( self, char * buffer, size_t nbytes ) cdef class VCFProxy( NamedTupleProxy) : cdef: char * contig uint32_t pos cdef update( self, char * buffer, size_t nbytes ) pysam-0.7.7/pysam/cvcf.pxd0000664000076400007650000000225012075244202015271 0ustar andreasandreascdef extern from "stdlib.h": void free(void *) void *malloc(size_t) void *calloc(size_t,size_t) void *realloc(void *,size_t) int c_abs "abs" (int) int c_abs "abs" (int) int atoi( char *nptr) long atol( char *nptr) double atof( char *nptr) cdef extern from "Python.h": ctypedef struct FILE FILE* PyFile_AsFile(object) char *fgets(char *str, int size, FILE *ifile) int feof(FILE *stream) size_t strlen(char *s) size_t getline(char **lineptr, size_t *n, FILE *stream) char *strstr(char *, char *) char *strchr(char *string, int c) int fileno(FILE *stream) cdef extern from "string.h": int strcmp(char *s1, char *s2) int strncmp(char *s1,char *s2,size_t len) char *strcpy(char *dest,char *src) char *strncpy(char *dest,char *src, size_t len) char *strdup(char *) char *strcat(char *,char *) size_t strlen(char *s) int memcmp( void * s1, void *s2, size_t len ) void *memcpy(void *dest, void *src, size_t n) void *memchr(void *s, int c, size_t n) cdef extern from "stdint.h": ctypedef int int64_t ctypedef int int32_t ctypedef int uint32_t ctypedef int uint8_t ctypedef int uint64_t pysam-0.7.7/pysam/csamtools.pxd0000664000076400007650000003364712241515323016372 0ustar andreasandreascdef extern from "string.h": ctypedef int size_t void *memcpy(void *dst,void *src,size_t len) void *memmove(void *dst,void *src,size_t len) void *memset(void *b,int c,size_t len) cdef extern from "stdlib.h": void free(void *) void *malloc(size_t) void *calloc(size_t,size_t) void *realloc(void *,size_t) int c_abs "abs" (int) void qsort(void *base, size_t nmemb, size_t size, int (*compar)(void *,void *)) cdef extern from "math.h": double sqrt(double x) cdef extern from "stdio.h": ctypedef struct FILE: pass FILE *fopen(char *,char *) FILE *freopen(char *path, char *mode, FILE *stream) int fileno(FILE *stream) int dup2(int oldfd, int newfd) int fflush(FILE *stream) FILE * stderr FILE * stdout int fclose(FILE *) int sscanf(char *str,char *fmt,...) int printf(char *fmt,...) int sprintf(char *str,char *fmt,...) int fprintf(FILE *ifile,char *fmt,...) char *fgets(char *str,int size,FILE *ifile) cdef extern from "ctype.h": int toupper(int c) int tolower(int c) cdef extern from "unistd.h": char *ttyname(int fd) int isatty(int fd) cdef extern from "string.h": int strcmp(char *s1, char *s2) int strncmp(char *s1,char *s2,size_t len) char *strcpy(char *dest,char *src) char *strncpy(char *dest,char *src, size_t len) char *strdup(char *) char *strcat(char *,char *) size_t strlen(char *s) int memcmp( void * s1, void *s2, size_t len ) cdef extern from "Python.h": long _Py_HashPointer(void*) FILE* PyFile_AsFile(object) cdef extern from "razf.h": pass cdef extern from "stdint.h": ctypedef int int8_t ctypedef int int16_t ctypedef int int32_t ctypedef int int64_t ctypedef int uint8_t ctypedef int uint16_t ctypedef int uint32_t ctypedef int uint64_t cdef extern from "bam.h": # constants int BAM_DEF_MASK # IF _IOLIB=2, bamFile = BGZF, see bgzf.h # samtools uses KNETFILE, check how this works ctypedef struct tamFile: pass ctypedef struct bamFile: pass ctypedef struct bam1_core_t: int32_t tid int32_t pos uint32_t bin uint32_t qual uint32_t l_qname uint32_t flag uint32_t n_cigar int32_t l_qseq int32_t mtid int32_t mpos int32_t isize ctypedef struct bam1_t: bam1_core_t core int l_aux int data_len int m_data uint8_t *data ctypedef struct bam_pileup1_t: bam1_t *b int32_t qpos int indel int level uint32_t is_del uint32_t is_head uint32_t is_tail ctypedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *data) ctypedef int (*bam_fetch_f)(bam1_t *b, void *data) ctypedef struct bam_header_t: int32_t n_targets char **target_name uint32_t *target_len void *hash void *rg2lib int l_text char *text ctypedef struct bam_index_t: int32_t n uint64_t n_no_coor ctypedef struct bam_plbuf_t: pass ctypedef struct pair64_t: uint64_t u, v ctypedef struct bam_iter_t: int from_first int tid, beg, end, n_off, i, finished uint64_t curr_off pair64_t *off # ctypedef __bam_iter_t * bam_iter_t bam1_t * bam_init1() void bam_destroy1(bam1_t *) bamFile razf_dopen(int data_fd, char *mode) int64_t bam_seek( bamFile fp, uint64_t voffset, int where) int64_t bam_tell( bamFile fp ) # void bam_init_header_hash(bam_header_t *header) ############################################### # stand-ins for samtools macros uint32_t * bam1_cigar( bam1_t * b) char * bam1_qname( bam1_t * b) uint8_t * bam1_seq( bam1_t * b) uint8_t * bam1_qual( bam1_t * b) uint8_t * bam1_aux( bam1_t * b) ############################################### # bam iterator interface bam_iter_t bam_iter_query( bam_index_t *idx, int tid, int beg, int end) int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b) void bam_iter_destroy(bam_iter_t iter) ############################################### bam1_t * bam_dup1( bam1_t *src ) bam1_t * bam_copy1(bam1_t *bdst, bam1_t *bsrc) bam_index_t *bam_index_load(char *f ) void bam_index_destroy(bam_index_t *idx) int bam_parse_region(bam_header_t *header, char *str, int *ref_id, int *begin, int *end) ############################################### bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) int bam_fetch(bamFile fp, bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) int bam_plbuf_push(bam1_t *b, bam_plbuf_t *buf) void bam_plbuf_destroy(bam_plbuf_t *buf) ######################################## # pileup iterator interface ctypedef struct bam_plp_t: pass ctypedef bam_pileup1_t * const_bam_pileup1_t_ptr "const bam_pileup1_t *" ctypedef int (*bam_plp_auto_f)(void *data, bam1_t *b) bam_plp_t bam_plp_init( bam_plp_auto_f func, void *data) int bam_plp_push( bam_plp_t iter, bam1_t *b) bam_pileup1_t * bam_plp_next( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) bam_pileup1_t * bam_plp_auto( bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) void bam_plp_set_mask(bam_plp_t iter, int mask) void bam_plp_reset(bam_plp_t iter) void bam_plp_destroy(bam_plp_t iter) void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt) ################################################## int bam_read1( bamFile fp, bam1_t *b) int bam_validate1( bam_header_t *header, bam1_t *b) int bam_write1( bamFile fp, bam1_t *b) bam_header_t *bam_header_init() int bam_header_write( bamFile fp, bam_header_t *header) bam_header_t *bam_header_read( bamFile fp ) void bam_header_destroy(bam_header_t *header) bam1_t * bam_dup1( bam1_t *src ) bam1_t * bam_copy1(bam1_t *bdst, bam1_t *bsrc) uint8_t *bam_aux_get(bam1_t *b, char tag[2]) int32_t bam_aux2i(uint8_t *s) float bam_aux2f(uint8_t *s) double bam_aux2d(uint8_t *s) char bam_aux2A( uint8_t *s) char *bam_aux2Z( uint8_t *s) int bam_reg2bin(uint32_t beg, uint32_t end) uint32_t bam_calend(bam1_core_t *c, uint32_t *cigar) int bam_aux_type2size( int ) cdef extern from *: ctypedef char* const_char_ptr "const char*" cdef extern from "sam.h": ctypedef struct samfile_t_un: tamFile tamr bamFile bam FILE *tamw ctypedef struct samfile_t: int type samfile_t_un x bam_header_t *header samfile_t *samopen( const_char_ptr fn, char * mode, void *aux) int sampileup( samfile_t *fp, int mask, bam_pileup_f func, void *data) void samclose(samfile_t *fp) int samread(samfile_t *fp, bam1_t *b) int samwrite(samfile_t *fp, bam1_t *b) int bam_prob_realn(bam1_t *b, char *ref) int bam_cap_mapQ(bam1_t *b, char *ref, int thres) #cdef extern from "glf.h": # ctypedef struct glf1_t: # pass #cdef extern from "bam_maqcns.h": # # ctypedef struct bam_maqcns_t: # float het_rate, theta # int n_hap, cap_mapQ, errmod, min_baseQ # float eta, q_r # double *fk, *coef # double *lhet # void *aux # glf1_t *bam_maqcns_glfgen(int n, # bam_pileup1_t *pl, # uint8_t ref_base, # bam_maqcns_t *bm) # ctypedef struct bam_maqindel_opt_t: # int q_indel # float r_indel # float r_snp # int mm_penalty, indel_err, ambi_thres # uint32_t bam_maqcns_call(int n, bam_pileup1_t *pl, bam_maqcns_t *bm) # bam_maqcns_t * bam_maqcns_init() # void bam_maqcns_destroy(bam_maqcns_t *bm) # void bam_maqcns_prepare(bam_maqcns_t *bm) # uint32_t glf2cns(glf1_t *g, int q_r) # int BAM_ERRMOD_MAQ2 # int BAM_ERRMOD_MAQ # int BAM_ERRMOD_SOAP # ctypedef struct bam_maqindel_ret_t: # int indel1 # int indel2 # int cnt1 # int cnt2 # int cnt_anti # int cnt_ref # int cnt_ambi # char *s[2] # int gt # int gl[2] # int q_cns # int q_ref # void bam_maqindel_ret_destroy( bam_maqindel_ret_t * ) # bam_maqindel_opt_t *bam_maqindel_opt_init() # bam_maqindel_ret_t * bam_maqindel(int n, # int pos, # bam_maqindel_opt_t * mi, # bam_pileup1_t * pl, # char *ref, # int _n_types, # int * _types ) cdef extern from "faidx.h": ctypedef struct faidx_t: pass int fai_build(char *fn) void fai_destroy(faidx_t *fai) faidx_t *fai_load(char *fn) char *fai_fetch(faidx_t *fai, char *reg, int *len) int faidx_fetch_nseq(faidx_t *fai) char *faidx_fetch_seq(faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) cdef extern from "pysam_util.h": int pysam_pileup_next(bam1_t *b, bam_plbuf_t *buf, bam_pileup1_t ** plp, int * tid, int * pos, int * n_plp ) int pysam_dispatch(int argc, char *argv[] ) # stand-in functions for samtools macros void pysam_bam_destroy1( bam1_t * b) # add *nbytes* into the variable length data of *src* at *pos* bam1_t * pysam_bam_update( bam1_t * b, size_t nbytes_old, size_t nbytes_new, uint8_t * pos ) # translate char to unsigned char unsigned char pysam_translate_sequence( char s ) unsigned char * bam_nt16_table int pysam_reference2tid( bam_header_t *header, char * s ) void pysam_set_stderr( int fd ) void pysam_unset_stderr() # return mapped/unmapped reads on tid uint32_t pysam_get_mapped( bam_index_t *idx, int tid ) uint32_t pysam_get_unmapped( bam_index_t *idx, int tid ) # uint32_t pysam_glf_depth( glf1_t * g ) # void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ) ctypedef struct gzFile: pass ctypedef struct kstring_t: size_t l size_t m char *s ctypedef struct kseq_t: kstring_t name kstring_t comment kstring_t seq kstring_t qual gzFile gzopen( char *, char * ) kseq_t * kseq_init( gzFile ) int kseq_read( kseq_t * ) void kseq_destroy( kseq_t * ) void gzclose( gzFile ) #################################################################### # Utility types ctypedef struct __iterdata: samfile_t * samfile bam_iter_t iter faidx_t * fastafile int tid char * seq int seq_len #################################################################### # # Exposing pysam extension classes # # Note: need to declare all C fields and methods here # cdef class Fastafile: cdef object _filename, _references, _lengths, reference2length cdef faidx_t* fastafile cdef char* _fetch(self, char* reference, int start, int end, int* length) cdef class FastqProxy: cdef kseq_t * _delegate cdef class Fastqfile: cdef object _filename cdef gzFile fastqfile cdef kseq_t * entry cdef kseq_t * getCurrent( self ) cdef int cnext(self) cdef class AlignedRead: # object that this AlignedRead represents cdef bam1_t * _delegate cdef class Samfile: cdef object _filename # pointer to samfile cdef samfile_t * samfile # pointer to index cdef bam_index_t *index # true if file is a bam file cdef int isbam # true if not a file but a stream cdef int isstream # true if file is not on the local filesystem cdef int isremote # current read within iteration cdef bam1_t * b # file opening mode cdef char * mode # beginning of read section cdef int64_t start_offset cdef bam_header_t * _buildHeader( self, new_header ) cdef bam1_t * getCurrent( self ) cdef int cnext(self) # write an aligned read cpdef int write( self, AlignedRead read ) cdef char * _getrname( self, int tid ) cdef class PileupProxy: cdef bam_pileup1_t ** plp cdef int tid cdef int pos cdef int n_pu cdef class PileupRead: cdef AlignedRead _alignment cdef int32_t _qpos cdef int _indel cdef int _level cdef uint32_t _is_del cdef uint32_t _is_head cdef uint32_t _is_tail cdef class IteratorRow: pass cdef class IteratorRowRegion(IteratorRow): cdef bam_iter_t iter # iterator state object cdef bam1_t * b cdef int retval cdef Samfile samfile cdef samfile_t * fp # true if samfile belongs to this object cdef int owns_samfile cdef bam1_t * getCurrent( self ) cdef int cnext(self) cdef class IteratorRowAll(IteratorRow): cdef bam1_t * b cdef samfile_t * fp cdef int owns_samfile cdef bam1_t * getCurrent( self ) cdef int cnext(self) cdef class IteratorRowAllRefs(IteratorRow): cdef Samfile samfile cdef int tid cdef IteratorRowRegion rowiter cdef class IteratorRowSelection(IteratorRow): cdef bam1_t * b cdef int current_pos cdef samfile_t * fp cdef positions # true if samfile belongs to this object cdef int owns_samfile cdef bam1_t * getCurrent( self ) cdef int cnext(self) cdef class IteratorColumn: # result of the last plbuf_push cdef IteratorRowRegion iter cdef int tid cdef int pos cdef int n_plp cdef int mask cdef const_bam_pileup1_t_ptr plp cdef bam_plp_t pileup_iter cdef __iterdata iterdata cdef Samfile samfile cdef Fastafile fastafile cdef stepper cdef int max_depth cdef int cnext(self) cdef char * getSequence( self ) cdef setMask( self, mask ) cdef setupIteratorData( self, int tid, int start, int end, int reopen = ? ) cdef reset( self, tid, start, end ) cdef class IteratorColumnRegion(IteratorColumn): cdef int start cdef int end cdef int truncate cdef class IteratorColumnAllRefs(IteratorColumn): pass cdef class IndexedReads: cdef Samfile samfile cdef samfile_t * fp cdef index # true if samfile belongs to this object cdef int owns_samfile pysam-0.7.7/pysam/ctabix.pxd0000664000076400007650000001466512241337202015635 0ustar andreasandreas cdef extern from "string.h": ctypedef int size_t void *memcpy(void *dst,void *src,size_t len) void *memmove(void *dst,void *src,size_t len) void *memset(void *b,int c,size_t len) char *strtok_r(char *str, char *delim, char **saveptr) char *strncpy(char *dest, char *src, size_t n) void *memchr(void *s, int c, size_t n) cdef extern from "stdlib.h": void free(void *) void *malloc(size_t) void *calloc(size_t,size_t) void *realloc(void *,size_t) void qsort(void *base, size_t nmemb, size_t size, int (*compar)(void *,void *)) int c_abs "abs" (int) int atoi( char *nptr) long atol( char *nptr) double atof( char *nptr) cdef extern from "stdio.h": ctypedef struct FILE: pass FILE *fopen(char *,char *) FILE *freopen(char *path, char *mode, FILE *stream) int fileno(FILE *stream) int dup2(int oldfd, int newfd) int fflush(FILE *stream) FILE * stderr FILE * stdout int fclose(FILE *) int sscanf(char *str,char *fmt,...) int printf(char *str,char *fmt,...) int sprintf(char *str,char *fmt,...) int fprintf(FILE *ifile,char *fmt,...) char *fgets(char *str,int size,FILE *ifile) cdef extern from "ctype.h": int toupper(int c) int tolower(int c) cdef extern from "sys/types.h": pass cdef extern from "sys/stat.h": pass cdef extern from "fcntl.h": int open(char *pathname, int flags) cdef extern from "unistd.h": ctypedef int ssize_t char *ttyname(int fd) int isatty(int fd) ssize_t read(int fd, void *buf, size_t count) cdef extern from "string.h": int strcmp(char *s1, char *s2) int strncmp(char *s1,char *s2,size_t len) char *strcpy(char *dest,char *src) char *strncpy(char *dest,char *src, size_t len) char *strdup(char *) char *strcat(char *,char *) size_t strlen(char *s) int memcmp( void * s1, void *s2, size_t len ) cdef extern from "stdint.h": ctypedef int int64_t ctypedef int int32_t ctypedef int uint32_t ctypedef int uint8_t ctypedef int uint64_t cdef extern from "zlib.h": ctypedef void * gzFile ctypedef int64_t z_off_t int gzclose(gzFile fp) int gzread(gzFile fp, void *buf, unsigned int n) char *gzerror(gzFile fp, int *errnum) gzFile gzopen( char *path, char *mode) gzFile gzdopen (int fd, char *mode) char * gzgets(gzFile file, char *buf, int len) int gzeof( gzFile file ) cdef extern from "Python.h": ctypedef struct FILE char *fgets(char *str, int size, FILE *ifile) int feof(FILE *stream) size_t strlen(char *s) size_t getline(char **lineptr, size_t *n, FILE *stream) char *strstr(char *, char *) char *strchr(char *string, int c) int fileno(FILE *stream) FILE *fdopen(int fd, char *mode) cdef extern from "bgzf.h": ctypedef struct BGZF: pass int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) BGZF * bgzf_open(char * path, char * mode) int bgzf_write(BGZF * fp, void* data, int length) int bgzf_close(BGZF* fp) # tabix support cdef extern from "tabix.h": ctypedef struct ti_conf_t: int32_t preset int32_t sc, bc, ec int32_t meta_char, line_skip ctypedef struct ti_index_t: pass ctypedef struct tabix_t: BGZF *fp ti_index_t *idx char *fn char *fnidx ctypedef struct ti_iter_t: pass tabix_t *ti_open(char *fn, char *fnidx) int ti_lazy_index_load(tabix_t *t) void ti_close(tabix_t *t) ti_iter_t ti_query(tabix_t *t, char *name, int beg, int end) ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end) ti_iter_t ti_querys(tabix_t *t, char *reg) char * ti_read(tabix_t *t, ti_iter_t iter, int *len) # Get the list of sequence names. Each "char*" pointer points to a # internal member of the index, so DO NOT modify the returned # pointer; otherwise the index will be corrupted. The returned # pointer should be freed by a single free() call by the routine # calling this function. The number of sequences is returned at *n char **ti_seqname(ti_index_t *idx, int *n) # Destroy the iterator void ti_iter_destroy(ti_iter_t iter) # Build the index for file . File .tbi will be generated # and overwrite the file of the same name. Return -1 on failure. */ int ti_index_build(char *fn, ti_conf_t *conf) #/* Load the index from file .tbi. If is a URL and the index # * file is not in the working directory, .tbi will be # * downloaded. Return NULL on failure. */ ti_index_t *ti_index_load( char *fn) ti_index_t *ti_index_load_local(char *fnidx) #/* Destroy the index */ void ti_index_destroy(ti_index_t *idx) #/* Parse a region like: chr2, chr2:100, chr2:100-200. Return -1 on failure. */ int ti_parse_region( ti_index_t *idx, char *str, int *tid, int *begin, int *end) int ti_get_tid( ti_index_t *idx, char *name) # /* Get the iterator pointing to the first record at the current file # * position. If the file is just openned, the iterator points to the # * first record in the file. */ ti_iter_t ti_iter_first() # /* Get the iterator pointing to the first record in region tid:beg-end */ ti_iter_t ti_iter_query( ti_index_t *idx, int tid, int beg, int end) # /* Get the data line pointed by the iterator and iterate to the next record. */ # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len) cdef extern from "tabix_util.h": ctypedef struct kstring_t: size_t l size_t m char * s ctypedef struct kstream_t: pass kstream_t * ks_init( gzFile ) int ks_read( kstream_t * ) void ks_destroy( kstream_t * ) int ks_getuntil( kstream_t *, int, kstring_t *, int * ) cdef class tabix_file_iterator: cdef gzFile fh cdef kstream_t * ks cdef kstring_t buffer cdef size_t size cdef Parser parser cdef int fd cdef infile cdef __cnext__(self) cdef class Tabixfile: # pointer to tabixfile cdef tabix_t * tabixfile # flag indicating whether file is remote cdef int isremote cdef char * _filename cdef Parser parser cdef class TabixIterator: cdef ti_iter_t iterator cdef tabix_t * tabixfile cdef class TabixHeaderIterator: cdef ti_iter_t iterator cdef tabix_t * tabixfile cdef class Parser: cdef parse( self, char * buffer, int len ) cdef class asTuple(Parser): cdef parse( self, char * buffer, int len ) cdef class asGTF(Parser): pass cdef class asBed(Parser): pass cdef class asVCF(Parser): pass cdef class TabixIteratorParsed: cdef ti_iter_t iterator cdef tabix_t * tabixfile cdef Parser parser pysam-0.7.7/pysam/pysam_util.h0000664000076400007650000000440412216701366016203 0ustar andreasandreas#ifndef PYSAM_UTIL_H #define PYSAM_UTIL_H #include "kseq.h" // ####################################################### // fastq parsing KSEQ_INIT(gzFile, gzread) ////////////////////////////////////////////////////////////////// /*! set pysam standard error to point to file descriptor Setting the stderr will close the previous stderr. */ FILE * pysam_set_stderr( int fd ); ////////////////////////////////////////////////////////////////// /*! set pysam standard error to /dev/null. Unsetting the stderr will close the previous stderr. */ void pysam_unset_stderr(); ////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////// // various helper functions // // fill pileup buffer for next position. int pysam_pileup_next(const bam1_t *b, bam_plbuf_t *buf, bam_pileup1_t ** plp, int * tid, int * pos, int * n_plp); int pysam_dispatch(int argc, char *argv[] ); /*! @abstract Update the variable length data within a bam1_t entry Old data is deleted and the data within b are re-arranged to make place for new data. @discussion Returns b @param b bam1_t data @param nbytes_old size of old data @param nbytes_new size of new data @param pos position of data */ bam1_t * pysam_bam_update( bam1_t * b, const size_t nbytes_old, const size_t nbytes_new, uint8_t * pos ); // translate a nucleotide character to binary code unsigned char pysam_translate_sequence( const unsigned char s ); // defined in bam_import.c extern unsigned char bam_nt16_table[256]; // translate a reference string *s* to a tid int pysam_reference2tid( bam_header_t *header, const char * s ); // return number of mapped reads for tid uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid ); // return number of unmapped reads for tid uint32_t pysam_get_unmapped( const bam_index_t *idx, const int tid ); // debugging functions /* #include "glf.h" */ /* uint32_t pysam_glf_depth( glf1_t * g); */ /* #include "bam_maqcns.h" */ /* void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c ); */ // return size of auxilliary type // int bam_aux_type2size(int x); #endif pysam-0.7.7/pysam/ctabix.pyx0000664000076400007650000007122512241534720015661 0ustar andreasandreas# cython: embedsignature=True # adds doc-strings for sphinx # Helper functions for python 3 compatibility - taken # from csamtools.pyx import tempfile, os, sys, types, itertools, struct, ctypes, gzip import io cimport TabProxies from cpython cimport PyErr_SetString, PyBytes_Check, \ PyUnicode_Check, PyBytes_FromStringAndSize, \ PyObject_AsFileDescriptor from libc.stdio cimport printf, fprintf, stderr from libc.string cimport strerror from libc.errno cimport errno from libc.stdint cimport int64_t PYTHON3 = PY_MAJOR_VERSION >= 3 # from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING from cpython.version cimport PY_MAJOR_VERSION cdef from_string_and_size(char* s, size_t length): if PY_MAJOR_VERSION < 3: return s[:length] else: return s[:length].decode("ascii") # filename encoding (copied from lxml.etree.pyx) cdef str _FILENAME_ENCODING _FILENAME_ENCODING = sys.getfilesystemencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = sys.getdefaultencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = 'ascii' #cdef char* _C_FILENAME_ENCODING #_C_FILENAME_ENCODING = _FILENAME_ENCODING cdef bytes _my_encodeFilename(object filename): u"""Make sure a filename is 8-bit encoded (or None). """ if filename is None: return None elif PyBytes_Check(filename): return filename elif PyUnicode_Check(filename): return filename.encode(_FILENAME_ENCODING) else: raise TypeError, u"Argument must be string or unicode." cdef bytes _force_bytes(object s): u"""convert string or unicode object to bytes, assuming ascii encoding. """ if PY_MAJOR_VERSION < 3: return s elif s is None: return None elif PyBytes_Check(s): return s elif PyUnicode_Check(s): return s.encode('ascii') else: raise TypeError, u"Argument must be string, bytes or unicode." cdef inline bytes _force_cmdline_bytes(object s): return _force_bytes(s) cdef _charptr_to_str(char* s): if PY_MAJOR_VERSION < 3: return s else: return s.decode("ascii") cdef _force_str(object s): """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" if s is None: return None if PY_MAJOR_VERSION < 3: return s elif PyBytes_Check(s): return s.decode('ascii') else: # assume unicode return s cdef class Tabixfile: '''*(filename, mode='r', parser = None)* opens a :term:`tabix file` for reading. A missing index (*filename* + ".tbi") will raise an exception. *parser* sets the default parser for this tabix file. If *parser* is None, the results are returned as an unparsed string. Otherwise, *parser* is assumed to be a functor that will return parsed data (see for example :meth:`asTuple` and :meth:`asGTF`). ''' def __cinit__(self, filename, mode = 'r', parser = None, *args, **kwargs ): self.tabixfile = NULL self.parser = parser self._open( filename, mode, *args, **kwargs ) def _isOpen( self ): '''return true if samfile has been opened.''' return self.tabixfile != NULL def _open( self, filename, mode ='r', ): '''open a :term:`tabix file` for reading. ''' assert mode in ( "r",), "invalid file opening mode `%s`" % mode # close a previously opened file if self.tabixfile != NULL: self.close() self.tabixfile = NULL filename_index = filename + ".tbi" self.isremote = filename.startswith( "http:") or filename.startswith( "ftp:" ) # encode all the strings filename = _my_encodeFilename(filename) filename_index = _my_encodeFilename(filename_index) cdef bytes bmode = mode.encode('ascii') if self._filename != NULL: free(self._filename ) self._filename = strdup(filename) if mode[0] == 'w': # open file for writing raise NotImplementedError("writing to tabix files not implemented" ) elif mode[0] == "r": # open file for reading if not self.isremote: if not os.path.exists( filename ): raise IOError( "file `%s` not found" % filename) if not os.path.exists( filename_index ): raise IOError( "index `%s` not found" % filename_index) # open file and load index self.tabixfile = ti_open( filename, filename_index ) if self.tabixfile == NULL: raise IOError("could not open file `%s`" % filename ) def _parseRegion( self, reference = None, start = None, end = None, region = None ): '''parse region information. raise ValueError for for invalid regions. returns a tuple of region, tid, start and end. Region is a valid samtools :term:`region` or None if the region extends over the whole file. Note that regions are 1-based, while start,end are python coordinates. ''' ti_lazy_index_load( self.tabixfile ) cdef int rtid cdef int rstart cdef int rend cdef int max_pos max_pos = 2 << 29 rtid = rstart = rend = 0 # translate to a region if reference: if start != None and end != None: region = "%s:%i-%i" % (reference, start+1, end) elif start == None and end != None: region = "%s:%i-%i" % (reference, 1, end) elif end == None and start != None: region = "%s:%i-%i" % (reference, start+1, max_pos-1) else: region = reference if region: region = _force_bytes(region) ti_parse_region( self.tabixfile.idx, region, &rtid, &rstart, &rend) if rtid < 0: raise KeyError( reference ) if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) ) if not 0 <= rstart < max_pos: raise IndexError( 'start out of range (%i)' % rstart ) if not 0 <= rend < max_pos: raise IndexError( 'end out of range (%i)' % rend ) return region, rtid, rstart, rend def fetch( self, reference = None, start = None, end = None, region = None, parser = None ): ''' fetch one or more rows in a :term:`region` using 0-based indexing. The region is specified by :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied. Without *reference* or *region* all entries will be fetched. If only *reference* is set, all reads matching on *reference* will be fetched. If *parser* is None, the default parser will be used for parsing. ''' ti_lazy_index_load( self.tabixfile ) if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # the following will raise errors for invalid regions region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # use default parser if no parser is specified if parser == None: parser = self.parser if parser == None: if region: return TabixIterator( self, rtid, rstart, rend ) else: return TabixIterator( self, -1, 0, 0 ) else: if region: return TabixIteratorParsed( self, rtid, rstart, rend, parser ) else: return TabixIteratorParsed( self, -1, 0, 0, parser ) ############################################################### ############################################################### ############################################################### ## properties ############################################################### property filename: '''filename associated with this object.''' def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) return self._filename property header: '''the file header. .. note:: The header is returned as an iterator over lines without the newline character. ''' def __get__( self ): return TabixHeaderIterator( self ) property contigs: '''chromosome names''' def __get__(self): cdef char ** sequences cdef int nsequences ti_lazy_index_load( self.tabixfile ) sequences = ti_seqname( self.tabixfile.idx, &nsequences ) cdef int x result = [] for x from 0 <= x < nsequences: result.append( sequences[x] ) return result def close( self ): ''' closes the :class:`pysam.Tabixfile`.''' if self.tabixfile != NULL: ti_close( self.tabixfile ) self.tabixfile = NULL def __dealloc__( self ): # remember: dealloc cannot call other python methods # note: no doc string # note: __del__ is not called. if self.tabixfile != NULL: ti_close( self.tabixfile ) self.tabixfile = NULL if self._filename != NULL: free( self._filename ) cdef class TabixIterator: """iterates over rows in *tabixfile* in region given by *tid*, *start* and *end*. """ def __cinit__(self, Tabixfile tabixfile, int tid, int start, int end ): assert tabixfile._isOpen() # makes sure that samfile stays alive as long as the # iterator is alive. self.tabixfile = tabixfile.tabixfile if tid < 0: # seek to start of file to ensure iteration is over # all entries. bgzf_seek( self.tabixfile.fp, 0, 0) self.iterator = ti_iter_first() else: self.iterator = ti_queryi(self.tabixfile, tid, start, end) if self.iterator == NULL: raise ValueError("malformatted query or wrong sequence name.\n") def __iter__(self): return self def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef char * s cdef int len # metachar filtering does not work within tabix # though it should. Getting the metachar is a pain # as ti_index_t is incomplete type. # simply use '#' for now. while 1: s = ti_read(self.tabixfile, self.iterator, &len) if s == NULL: raise StopIteration if s[0] != '#': break retval = _charptr_to_str( s ) return retval def __dealloc__(self): if self.iterator != NULL: ti_iter_destroy(self.iterator) cdef class TabixHeaderIterator: """return header lines. """ def __cinit__(self, Tabixfile tabixfile ): assert tabixfile._isOpen() # makes sure that samfile stays alive as long as the # iterator is alive. self.tabixfile = tabixfile.tabixfile self.iterator = ti_query(self.tabixfile, NULL, 0, 0) if self.iterator == NULL: raise ValueError("can't open header.\n") def __iter__(self): return self def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef char * s cdef int len # Getting the metachar is a pain as ti_index_t is incomplete type. # simply use '#' for now. s = ti_read(self.tabixfile, self.iterator, &len) if s == NULL: raise StopIteration # stop at first non-header line if s[0] != '#': raise StopIteration return s def __dealloc__(self): if self.iterator != NULL: ti_iter_destroy(self.iterator) ######################################################### ######################################################### ######################################################### cdef class Parser: cdef parse(self, char * buffer, int length): raise NotImplementedError def __call__(self, char * buffer, int length): return self.parse( buffer, length ) cdef class asTuple(Parser): '''converts a :term:`tabix row` into a python tuple. Access is by numeric index. ''' cdef parse(self, char * buffer, int len): cdef TabProxies.TupleProxy r r = TabProxies.TupleProxy() # need to copy - there were some # persistence issues with "present" r.copy( buffer, len ) return r cdef class asGTF(Parser): '''converts a :term:`tabix row` into a GTF record with the following fields: contig contig feature feature source source start genomic start coordinate (0-based) end genomic end coordinate plus one (0-based) score feature score strand strand frame frame attributes attribute string. GTF formatted entries also defined the attributes: gene_id the gene identifier transcript_ind the transcript identifier ''' cdef parse(self, char * buffer, int len): cdef TabProxies.GTFProxy r r = TabProxies.GTFProxy() r.copy( buffer, len ) return r cdef class asBed( Parser ): '''converts a :term:`tabix row` into a bed record with the following fields: contig contig start genomic start coordinate (zero-based) end genomic end coordinate plus one (zero-based) name name of feature. score score of feature strand strand of feature thickStart thickStart thickEnd thickEnd itemRGB itemRGB blockCount number of bocks blockSizes ',' separated string of block sizes blockStarts ',' separated string of block genomic start positions Only the first three fields are required. Additional fields are optional, but if one is defined, all the preceeding need to be defined as well. ''' cdef parse(self, char * buffer, int len): cdef TabProxies.BedProxy r r = TabProxies.BedProxy() r.copy( buffer, len ) return r cdef class asVCF( Parser ): '''converts a :term:`tabix row` into a VCF record with the following fields: contig contig pos chromosomal position, zero-based id id ref reference alt alt qual qual filter filter info info format format specifier. Access to genotypes is via index:: contig = vcf.contig first_sample_genotype = vcf[0] second_sample_genotype = vcf[1] ''' cdef parse(self, char * buffer, int len ): cdef TabProxies.VCFProxy r r = TabProxies.VCFProxy() r.copy( buffer, len ) return r ######################################################### ######################################################### ######################################################### cdef class TabixIteratorParsed: """iterates over mapped reads in a region. Returns parsed data. """ def __cinit__(self, Tabixfile tabixfile, int tid, int start, int end, Parser parser ): assert tabixfile._isOpen() self.parser = parser # makes sure that samfile stays alive as long as the # iterator is alive. self.tabixfile = tabixfile.tabixfile if tid < 0: # seek to start of file to ensure iteration is over # all entries. bgzf_seek( self.tabixfile.fp, 0, 0) self.iterator = ti_iter_first() else: self.iterator = ti_queryi(self.tabixfile, tid, start, end) if self.iterator == NULL: raise ValueError("malformatted query or wrong sequence name.\n") def __iter__(self): return self def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef char * s cdef int len while 1: s = ti_read(self.tabixfile, self.iterator, &len) if s == NULL: raise StopIteration if s[0] != '#': break return self.parser.parse(s, len) def __dealloc__(self): if self.iterator != NULL: ti_iter_destroy(self.iterator) def tabix_compress( filename_in, filename_out, force = False ): ''' compress *filename_in* writing the output to *filename_out*. Raise an IOError if *filename_out* already exists, unless *force* is set. ''' if not force and os.path.exists(filename_out ): raise IOError( "Filename '%s' already exists, use *force* to overwrite" % filename_out) cdef int WINDOW_SIZE cdef int c, r cdef void * buffer cdef BGZF * fp cdef int fd_src cdef int O_RDONLY O_RDONLY = os.O_RDONLY WINDOW_SIZE = 64 * 1024 fn = _force_bytes(filename_out) fp = bgzf_open( fn, "w") if fp == NULL: raise IOError( "could not open '%s' for writing" ) fn = _force_bytes(filename_in) fd_src = open(fn, O_RDONLY) if fd_src == 0: raise IOError( "could not open '%s' for reading" ) buffer = malloc(WINDOW_SIZE) c = 1 while c > 0: c = read(fd_src, buffer, WINDOW_SIZE) r = bgzf_write(fp, buffer, c) if r < 0: free( buffer ) raise OSError("writing failed") free( buffer ) r = bgzf_close(fp) if r < 0: raise OSError("writing failed") def tabix_index( filename, force = False, seq_col = None, start_col = None, end_col = None, preset = None, meta_char = "#", zerobased = False, ): ''' index tab-separated *filename* using tabix. An existing index will not be overwritten unless *force* is set. The index will be built from coordinates in columns *seq_col*, *start_col* and *end_col*. The contents of *filename* have to be sorted by contig and position - the method does not check if the file is sorted. Column indices are 0-based. Coordinates in the file are assumed to be 1-based. If *preset* is provided, the column coordinates are taken from a preset. Valid values for preset are "gff", "bed", "sam", "vcf", psltbl", "pileup". Lines beginning with *meta_char* and the first *line_skip* lines will be skipped. If *filename* does not end in ".gz", it will be automatically compressed. The original file will be removed and only the compressed file will be retained. If *filename* ends in *gz*, the file is assumed to be already compressed with bgzf. returns the filename of the compressed data ''' if not os.path.exists(filename): raise IOError("No such file '%s'" % filename) if preset == None and (seq_col == None or start_col == None or end_col == None): raise ValueError("neither preset nor seq_col,start_col and end_col given" ) if not filename.endswith(".gz"): tabix_compress( filename, filename + ".gz", force = force ) os.unlink( filename ) filename += ".gz" if not force and os.path.exists(filename + ".tbi" ): raise IOError( "Filename '%s.tbi' already exists, use *force* to overwrite" ) # columns (1-based) # preset-code, contig, start, end, metachar for commends, lines to ignore at beginning # 0 is a missing column preset2conf = { 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ), 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ), 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ), 'sam' : ( 1, 3, 4, 0, ord('@'), 0 ), 'vcf' : ( 2, 1, 2, 0, ord('#'), 0 ), 'pileup': (3, 1, 2, 0, ord('#'), 0 ), } if preset: try: conf_data = preset2conf[preset] except KeyError: raise KeyError( "unknown preset '%s', valid presets are '%s'" % (preset, ",".join(preset2conf.keys() ))) else: if end_col == None: end_col = -1 preset = 0 # note that tabix internally works with 0-based coordinates and open/closed intervals. # When using a preset, conversion is automatically taken care of. # Otherwise, the coordinates are assumed to be 1-based closed intervals and # -1 is subtracted from the start coordinate. To avoid doing this, set # the TI_FLAG_UCSC=0x10000 flag: if zerobased: preset = preset | 0x10000 conf_data = (preset, seq_col+1, start_col+1, end_col+1, ord(meta_char), 0) cdef ti_conf_t conf conf.preset, conf.sc, conf.bc, conf.ec, conf.meta_char, conf.line_skip = conf_data fn = _my_encodeFilename( filename ) ti_index_build( fn, &conf) return filename # ######################################################### # ######################################################### # ######################################################### # ## Iterators for parsing through unindexed files. # ######################################################### # cdef class tabix_file_iterator_old: # '''iterate over ``infile``. # This iterator is not safe. If the :meth:`__next__()` method is called # after ``infile`` is closed, the result is undefined (see ``fclose()``). # The iterator might either raise a StopIteration or segfault. # ''' # def __cinit__(self, # infile, # Parser parser, # int buffer_size = 65536 ): # cdef int fd = PyObject_AsFileDescriptor( infile ) # if fd == -1: raise ValueError( "I/O operation on closed file." ) # self.infile = fdopen( fd, 'r') # if self.infile == NULL: raise ValueError( "I/O operation on closed file." ) # self.buffer = malloc( buffer_size ) # self.size = buffer_size # self.parser = parser # def __iter__(self): # return self # cdef __cnext__(self): # cdef char * b # cdef size_t nbytes # b = self.buffer # while not feof( self.infile ): # nbytes = getline( &b, &self.size, self.infile) # # stop at first error or eof # if (nbytes == -1): break # # skip comments # if (b[0] == '#'): continue # # skip empty lines # if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # # make sure that entry is complete # if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': # result = b # raise ValueError( "incomplete line at %s" % result ) # # make sure that this goes fully through C # # otherwise buffer is copied to/from a # # Python object causing segfaults as # # the wrong memory is freed # return self.parser.parse( b, nbytes ) # raise StopIteration # def __dealloc__(self): # free(self.buffer) # def __next__(self): # return self.__cnext__() ######################################################### ######################################################### ######################################################### ## Iterators for parsing through unindexed files. ######################################################### cdef buildGzipError(void *gzfp): cdef int errnum = 0 cdef const char *s = gzerror(gzfp, &errnum) return "error (%d): %s (%d: %s)" % (errno, strerror(errno), errnum, s) cdef class tabix_file_iterator: '''iterate over a compressed or uncompressed ``infile``. ''' def __cinit__(self, infile, Parser parser, int buffer_size = 65536 ): if infile.closed: raise ValueError( "I/O operation on closed file." ) self.infile = infile cdef int fd = PyObject_AsFileDescriptor( infile ) if fd == -1: raise ValueError( "I/O operation on closed file." ) # From the manual: # gzopen can be used to read a file which is not in gzip format; # in this case gzread will directly read from the file without decompression. # When reading, this will be detected automatically by looking # for the magic two-byte gzip header. self.fh = gzdopen( fd, 'r') if self.fh == NULL: raise IOError('%s' % strerror(errno)) self.ks = ks_init( self.fh) self.buffer.s = malloc( buffer_size ) #if self.buffer == NULL: # raise MemoryError( "tabix_file_iterator: could not allocate %i bytes" % buffer_size) #self.size = buffer_size self.parser = parser def __iter__(self): return self cdef __cnext__(self): cdef char * b cdef int dret = 0 cdef int retval = 0 while 1: retval = ks_getuntil(self.ks, '\n', &self.buffer, &dret) if retval < 0: break #raise IOError('gzip error: %s' % buildGzipError( self.fh )) b = self.buffer.s # skip comments if (b[0] == '#'): continue # skip empty lines if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # gzgets terminates at \n, no need to test # parser creates a copy return self.parser.parse( b, self.buffer.l ) raise StopIteration def __dealloc__(self): free(self.buffer.s) def __next__(self): return self.__cnext__() def next(self): return self.__cnext__() class tabix_generic_iterator: '''iterate over ``infile``. Permits the use of file-like objects for example from the gzip module. ''' def __init__(self, infile, parser ): self.infile = infile if self.infile.closed: raise ValueError( "I/O operation on closed file." ) self.parser = parser def __iter__(self): return self # cython version - required for python 3 def __next__(self): cdef char * b, * cpy cdef size_t nbytes # note that GzipFile.close() does not close the file # reading is still possible. if self.infile.closed: raise ValueError( "I/O operation on closed file." ) while 1: line = self.infile.readline() if not line: break s = _force_bytes( line ) b = s nbytes = len( line ) assert b[nbytes] == '\0' # skip comments if (b[0] == '#'): continue # skip empty lines if b[0] == '\0' or b[0] == '\n' or b[0] == '\r': continue # make sure that entry is complete if b[nbytes-1] != '\n' and b[nbytes-1] != '\r': raise ValueError( "incomplete line at %s" % line ) # create a copy cpy = malloc(nbytes+1) if cpy == NULL: raise MemoryError() memcpy( cpy, b, nbytes+1) return self.parser(cpy, nbytes) raise StopIteration # python version - required for python 2.7 def next(self): return self.__next__() def tabix_iterator( infile, parser ): """return an iterator over all entries in a file.""" if PYTHON3: return tabix_generic_iterator( infile, parser ) else: return tabix_file_iterator( infile, parser ) # file objects can use C stdio # used to be: isinstance( infile, file): # if PYTHON3: # if isinstance( infile, io.IOBase ): # return tabix_copy_iterator( infile, parser ) # else: # return tabix_generic_iterator( infile, parser ) # else: # if isinstance( infile, file ): # return tabix_copy_iterator( infile, parser ) # else: # return tabix_generic_iterator( infile, parser ) __all__ = ["tabix_index", "tabix_compress", "Tabixfile", "asTuple", "asGTF", "asVCF", "asBed", "tabix_iterator", "tabix_generic_iterator", "tabix_file_iterator", ] pysam-0.7.7/pysam/csamtools.c0000664000076400007650001017247512241546137016034 0ustar andreasandreas/* Generated by Cython 0.18 on Sat Nov 16 01:37:33 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall #define __stdcall #endif #ifndef __cdecl #define __cdecl #endif #ifndef __fastcall #define __fastcall #endif #endif #ifndef DL_IMPORT #define DL_IMPORT(t) t #endif #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif #ifndef Py_HUGE_VAL #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION #define CYTHON_COMPILING_IN_PYPY 1 #define CYTHON_COMPILING_IN_CPYTHON 0 #else #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif #if PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type #define PyInt_Check(op) PyLong_Check(op) #define PyInt_CheckExact(op) PyLong_CheckExact(op) #define PyInt_FromString PyLong_FromString #define PyInt_FromUnicode PyLong_FromUnicode #define PyInt_FromLong PyLong_FromLong #define PyInt_FromSize_t PyLong_FromSize_t #define PyInt_FromSsize_t PyLong_FromSsize_t #define PyInt_AsLong PyLong_AsLong #define PyInt_AS_LONG PyLong_AS_LONG #define PyInt_AsSsize_t PyLong_AsSsize_t #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? 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PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) #else #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) #endif #ifndef __PYX_EXTERN_C #ifdef __cplusplus #define __PYX_EXTERN_C extern "C" #else #define __PYX_EXTERN_C extern #endif #endif #if defined(WIN32) || defined(MS_WINDOWS) #define _USE_MATH_DEFINES #endif #include #define __PYX_HAVE__pysam__csamtools #define __PYX_HAVE_API__pysam__csamtools #include "string.h" #include "stdlib.h" #include "math.h" #include "stdio.h" #include "ctype.h" #include "unistd.h" #include "razf.h" #include "stdint.h" #include "bam.h" #include "sam.h" #include "faidx.h" #include "pysam_util.h" #include "pythread.h" #ifdef _OPENMP #include #endif /* _OPENMP */ #ifdef PYREX_WITHOUT_ASSERTIONS #define CYTHON_WITHOUT_ASSERTIONS #endif #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ #elif defined(_MSC_VER) #define CYTHON_INLINE __inline #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_INLINE inline #else #define CYTHON_INLINE #endif #endif #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif # elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) # define CYTHON_UNUSED __attribute__ ((__unused__)) # else # define CYTHON_UNUSED # endif #endif typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) #define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? 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PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; static const char *__pyx_f[] = { "csamtools.pyx", "type.pxd", "bool.pxd", "complex.pxd", }; /*--- Type declarations ---*/ struct __pyx_obj_5pysam_9csamtools_PileupRead; struct __pyx_obj_5pysam_9csamtools_SNPCall; struct __pyx_obj_5pysam_9csamtools_IteratorColumn; struct __pyx_obj_5pysam_9csamtools_IteratorRow; struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion; struct __pyx_obj_5pysam_9csamtools_IndexedReads; struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr; struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr; struct __pyx_obj_5pysam_9csamtools_Fastqfile; struct __pyx_obj_5pysam_9csamtools_FastqProxy; struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr; struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open; struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs; struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs; struct __pyx_obj_5pysam_9csamtools_Fastafile; struct __pyx_obj_5pysam_9csamtools_AlignedRead; struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection; struct __pyx_obj_5pysam_9csamtools_Samfile; struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion; struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr; struct __pyx_obj_5pysam_9csamtools_PileupProxy; struct __pyx_obj_5pysam_9csamtools_IteratorRowAll; struct __pyx_t_5pysam_9csamtools___iterdata; typedef struct __pyx_t_5pysam_9csamtools___iterdata __pyx_t_5pysam_9csamtools___iterdata; struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData; struct __pyx_t_5pysam_9csamtools_MateData; typedef struct __pyx_t_5pysam_9csamtools_MateData __pyx_t_5pysam_9csamtools_MateData; /* "pysam/csamtools.pxd":414 * # Utility types * * ctypedef struct __iterdata: # <<<<<<<<<<<<<< * samfile_t * samfile * bam_iter_t iter */ struct __pyx_t_5pysam_9csamtools___iterdata { samfile_t *samfile; bam_iter_t iter; faidx_t *fastafile; int tid; char *seq; int seq_len; }; /* "pysam/csamtools.pxd":552 * cdef char * getSequence( self ) * cdef setMask( self, mask ) * cdef setupIteratorData( self, # <<<<<<<<<<<<<< * int tid, * int start, */ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData { int __pyx_n; int reopen; }; /* "pysam/csamtools.pyx":657 * counter[0] += 1; * * ctypedef struct MateData: # <<<<<<<<<<<<<< * char * name * bam1_t * mate */ struct __pyx_t_5pysam_9csamtools_MateData { char *name; bam1_t *mate; uint32_t flag; }; /* "pysam/csamtools.pxd":484 * cdef int n_pu * * cdef class PileupRead: # <<<<<<<<<<<<<< * cdef AlignedRead _alignment * cdef int32_t _qpos */ struct __pyx_obj_5pysam_9csamtools_PileupRead { PyObject_HEAD struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment; int32_t _qpos; int _indel; int _level; uint32_t _is_del; uint32_t _is_head; uint32_t _is_tail; }; /* "pysam/csamtools.pyx":3474 * return retval, out_stderr, out_stdout * * cdef class SNPCall: # <<<<<<<<<<<<<< * '''the results of a SNP call.''' * cdef int _tid */ struct __pyx_obj_5pysam_9csamtools_SNPCall { PyObject_HEAD int _tid; int _pos; char _reference_base; char _genotype; int _consensus_quality; int _snp_quality; int _rms_mapping_quality; int _coverage; }; /* "pysam/csamtools.pxd":533 * cdef int cnext(self) * * cdef class IteratorColumn: # <<<<<<<<<<<<<< * * # result of the last plbuf_push */ struct __pyx_obj_5pysam_9csamtools_IteratorColumn { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab; struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter; int tid; int pos; int n_plp; int mask; const bam_pileup1_t * plp; bam_plp_t pileup_iter; __pyx_t_5pysam_9csamtools___iterdata iterdata; struct __pyx_obj_5pysam_9csamtools_Samfile *samfile; struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile; PyObject *stepper; int max_depth; }; /* "pysam/csamtools.pxd":493 * cdef uint32_t _is_tail * * cdef class IteratorRow: # <<<<<<<<<<<<<< * pass * */ struct __pyx_obj_5pysam_9csamtools_IteratorRow { PyObject_HEAD }; /* "pysam/csamtools.pxd":496 * pass * * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<< * cdef bam_iter_t iter # iterator state object * cdef bam1_t * b */ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion { struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base; struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab; bam_iter_t iter; bam1_t *b; int retval; struct __pyx_obj_5pysam_9csamtools_Samfile *samfile; samfile_t *fp; int owns_samfile; }; /* "pysam/csamtools.pxd":568 * pass * * cdef class IndexedReads: # <<<<<<<<<<<<<< * cdef Samfile samfile * cdef samfile_t * fp */ struct __pyx_obj_5pysam_9csamtools_IndexedReads { PyObject_HEAD struct __pyx_obj_5pysam_9csamtools_Samfile *samfile; samfile_t *fp; PyObject *index; int owns_samfile; }; /* "pysam/csamtools.pyx":432 * data = [ x.split("\t") for x in inf ] * self._references = tuple(x[0] for x in data) * self._lengths = tuple(int(x[1]) for x in data) # <<<<<<<<<<<<<< * self.reference2length = dict(zip(self._references, self._lengths)) * */ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_4_genexpr { PyObject_HEAD struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *__pyx_outer_scope; PyObject *__pyx_v_x; PyObject *__pyx_t_0; Py_ssize_t __pyx_t_1; }; /* "pysam/csamtools.pyx":141 * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) * else: * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<< * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" ) * */ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr { PyObject_HEAD PyObject *__pyx_v_x; PyObject *__pyx_v_y; PyObject *__pyx_t_0; PyObject *__pyx_t_1; PyObject *(*__pyx_t_2)(PyObject *); }; /* "pysam/csamtools.pxd":436 * cdef kseq_t * _delegate * * cdef class Fastqfile: # <<<<<<<<<<<<<< * cdef object _filename * cdef gzFile fastqfile */ struct __pyx_obj_5pysam_9csamtools_Fastqfile { PyObject_HEAD struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtab; PyObject *_filename; gzFile fastqfile; kseq_t *entry; }; /* "pysam/csamtools.pxd":433 * cdef char* _fetch(self, char* reference, int start, int end, int* length) * * cdef class FastqProxy: # <<<<<<<<<<<<<< * cdef kseq_t * _delegate * */ struct __pyx_obj_5pysam_9csamtools_FastqProxy { PyObject_HEAD kseq_t *_delegate; }; /* "pysam/csamtools.pyx":431 * with open( self._filename + b".fai" ) as inf: * data = [ x.split("\t") for x in inf ] * self._references = tuple(x[0] for x in data) # <<<<<<<<<<<<<< * self._lengths = tuple(int(x[1]) for x in data) * self.reference2length = dict(zip(self._references, self._lengths)) */ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_3_genexpr { PyObject_HEAD struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_2__open *__pyx_outer_scope; 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Py_INCREF(Py_None); return Py_None; /* this is just to have an accurate signature */ } else { PyObject *r, *m; m = __Pyx_GetAttrString(L, "append"); if (!m) return NULL; r = PyObject_CallFunctionObjArgs(m, x, NULL); Py_DECREF(m); return r; } } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { int result = PyDict_Contains(dict, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) PyErr_SetObject(PyExc_KeyError, key); return NULL; } Py_INCREF(value); return value; } #else #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObject* default_value) { PyObject* value; #if PY_MAJOR_VERSION >= 3 value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (unlikely(PyErr_Occurred())) return NULL; value = default_value; } Py_INCREF(value); #else if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) { value = PyDict_GetItem(d, key); if (unlikely(!value)) { value = default_value; } Py_INCREF(value); } else { PyObject *m; m = __Pyx_GetAttrString(d, "get"); if (!m) return NULL; value = PyObject_CallFunctionObjArgs(m, key, (default_value == Py_None) ? 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} #endif return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i)); } static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *qualname, PyObject *modname); /*proto*/ #define __Pyx_CyFunction_USED 1 #include #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 #define __Pyx_CYFUNCTION_CCLASS 0x04 #define __Pyx_CyFunction_GetClosure(f) \ (((__pyx_CyFunctionObject *) (f))->func_closure) #define __Pyx_CyFunction_GetClassObj(f) \ (((__pyx_CyFunctionObject *) (f))->func_classobj) #define __Pyx_CyFunction_Defaults(type, f) \ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) #define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; int flags; PyObject *func_dict; PyObject *func_weakreflist; PyObject *func_name; PyObject *func_qualname; PyObject *func_doc; PyObject *func_code; PyObject *func_closure; PyObject *func_classobj; /* No-args super() class cell */ void *defaults; int defaults_pyobjects; PyObject *defaults_tuple; /* Const defaults tuple */ PyObject *(*defaults_getter)(PyObject *); } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; #define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, code) \ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *self, PyObject *module, PyObject* code); static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m, size_t size, int pyobjects); static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m, PyObject *tuple); static int __Pyx_CyFunction_init(void); static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *); static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int16_t(int16_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t); static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject *); static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t); static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ #define __Pyx_Generator_USED #include #include typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD __pyx_generator_body_t body; PyObject *closure; PyObject *exc_type; PyObject *exc_value; PyObject *exc_traceback; PyObject *gi_weakreflist; PyObject *classobj; PyObject *yieldfrom; int resume_label; char is_running; // using T_BOOL for property below requires char value } __pyx_GeneratorObject; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure); static int __pyx_Generator_init(void); static int __Pyx_Generator_clear(PyObject* self); #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue); #else #define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue) #endif static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename); /*proto*/ static int __Pyx_check_binary_version(void); static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ typedef struct { int code_line; PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; int max_count; __Pyx_CodeObjectCacheEntry* entries; }; static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.version' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'cpython.exc' */ /* Module declarations from 'cpython.module' */ /* Module declarations from 'cpython.mem' */ /* Module declarations from 'cpython.tuple' */ /* Module declarations from 'cpython.list' */ /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from 'cpython.sequence' */ /* Module declarations from 'cpython.mapping' */ /* Module declarations from 'cpython.iterator' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'cpython.number' */ /* Module declarations from 'cpython.int' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.bool' */ static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; /* Module declarations from 'cpython.long' */ /* Module declarations from 'cpython.float' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.complex' */ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython.string' */ /* Module declarations from 'cpython.unicode' */ /* Module declarations from 'cpython.dict' */ /* Module declarations from 'cpython.instance' */ /* Module declarations from 'cpython.function' */ /* Module declarations from 'cpython.method' */ /* Module declarations from 'cpython.weakref' */ /* Module declarations from 'cpython.getargs' */ /* Module declarations from 'cpython.pythread' */ /* Module declarations from 'cpython.pystate' */ /* Module declarations from 'cpython.cobject' */ /* Module declarations from 'cpython.oldbuffer' */ /* Module declarations from 'cpython.set' */ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* Module declarations from 'pysam.csamtools' */ static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_FastqProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastqfile = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_AlignedRead = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Samfile = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupProxy = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupRead = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRow = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowRegion = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAll = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowSelection = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumn = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IndexedReads = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools_SNPCall = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_2__open = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_3_genexpr = 0; static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_4_genexpr = 0; static PyObject *__pyx_v_5pysam_9csamtools__FILENAME_ENCODING = 0; static char *__pyx_v_5pysam_9csamtools_CODE2CIGAR; static char *__pyx_v_5pysam_9csamtools_bam_nt16_rev_table; static int __pyx_v_5pysam_9csamtools_max_pos; static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *, size_t); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools__encodeFilename(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools_makeFastqProxy(kseq_t *); /*proto*/ static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/ static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/ static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_5pysam_9csamtools_count_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *, void *); /*proto*/ static int __pyx_f_5pysam_9csamtools___advance_all(void *, bam1_t *); /*proto*/ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/ #define __Pyx_MODULE_NAME "pysam.csamtools" int __pyx_module_is_main_pysam__csamtools = 0; /* Implementation of 'pysam.csamtools' */ static PyObject *__pyx_builtin_object; static PyObject *__pyx_builtin_TypeError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_ord; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_IndexError; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_OverflowError; static PyObject *__pyx_builtin_NotImplementedError; static PyObject *__pyx_builtin_OSError; static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_sorted; static PyObject *__pyx_builtin_KeyError; static PyObject *__pyx_builtin_min; static PyObject *__pyx_builtin_max; static PyObject *__pyx_builtin_chr; static PyObject *__pyx_builtin_UnicodeDecodeError; static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_5_open_genexpr(PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_5_open_3genexpr(PyObject *__pyx_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_14getReferenceLength(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_16__getitem__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static int __pyx_pf_5pysam_9csamtools_9Fastafile_18__contains__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static int __pyx_pf_5pysam_9csamtools_10FastqProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_4name___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_8sequence___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7comment___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7quality___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_9Fastqfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_4_open(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_6close(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_9Fastqfile_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_10__iter__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_12__next__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other); /* proto */ static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15inferred_length___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */ static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */ static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */ static char __pyx_k_1[] = "Argument must be string or unicode."; static char __pyx_k_3[] = "Argument must be string, bytes or unicode."; static char __pyx_k_5[] = "\t"; static char __pyx_k_6[] = "\n"; static char __pyx_k_7[] = "calling len() on closed file"; static char __pyx_k_9[] = "could not open file `%s`"; static char __pyx_k_10[] = ".fai"; static char __pyx_k_11[] = "could not locate index file"; static char __pyx_k_15[] = "I/O operation on closed file"; static char __pyx_k_17[] = "no sequence/region supplied."; static char __pyx_k_19[] = "invalid region: start (%i) > end (%i)"; static char __pyx_k_20[] = ""; static char __pyx_k_21[] = "start out of range (%i)"; static char __pyx_k_22[] = "end out of range (%i)"; static char __pyx_k_23[] = "%s:%i-%i"; static char __pyx_k_25[] = "No such file or directory: %s"; static char __pyx_k_30[] = "invalid file opening mode `%s`"; static char __pyx_k_32[] = "-"; static char __pyx_k_33[] = "http:"; static char __pyx_k_35[] = "ftp:"; static char __pyx_k_37[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"; static char __pyx_k_38[] = "unequal names and lengths of reference sequences"; static char __pyx_k_39[] = "@SQ\tSN:%s\tLN:%s\n"; static char __pyx_k_40[] = "file `%s` not found"; static char __pyx_k_41[] = "could not open file (mode='%s') - is it SAM/BAM format?"; static char __pyx_k_42[] = "file does not have valid header (mode='%s') - is it BAM format?"; static char __pyx_k_43[] = "file does not have valid header (mode='%s') - is it SAM format?"; static char __pyx_k_44[] = "file header is empty (mode='%s') - is it SAM/BAM format?"; static char __pyx_k_45[] = ".bai"; static char __pyx_k_46[] = "error while opening index `%s` "; static char __pyx_k_49[] = "tid %i out of range 0<=tid<%i"; static char __pyx_k_51[] = "[:-]"; static char __pyx_k_53[] = "invalid reference `%s`"; static char __pyx_k_54[] = "invalid coordinates: start (%i) > end (%i)"; static char __pyx_k_56[] = "seek only available in bam files"; static char __pyx_k_58[] = "seek no available in streams"; static char __pyx_k_64[] = "fetch called on bamfile without index"; static char __pyx_k_66[] = "callback functionality requires a region/reference"; static char __pyx_k_68[] = "no index available for fetch"; static char __pyx_k_70[] = "fetching by region is not available for sam files"; static char __pyx_k_72[] = "callback not implemented yet"; static char __pyx_k_74[] = "fetch called for samfile without header"; static char __pyx_k_77[] = "read %s: is unpaired"; static char __pyx_k_78[] = "mate %s: is unmapped"; static char __pyx_k_79[] = "mate not found"; static char __pyx_k_84[] = "counting functionality requires a region/reference"; static char __pyx_k_87[] = "count for a region is not available for sam files"; static char __pyx_k_90[] = "no index available for pileup"; static char __pyx_k_93[] = "pileup of samfiles not implemented yet"; static char __pyx_k_99[] = "Samfile.mapped only available in bam files"; static char __pyx_k__A[] = "A"; static char __pyx_k__B[] = "B"; static char __pyx_k__C[] = "C"; static char __pyx_k__D[] = "D"; static char __pyx_k__F[] = "F"; static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__S[] = "S"; static char __pyx_k__Z[] = "Z"; static char __pyx_k__a[] = "a"; static char __pyx_k__b[] = "b"; static char __pyx_k__c[] = "c"; static char __pyx_k__d[] = "d"; static char __pyx_k__f[] = "f"; static char __pyx_k__h[] = "h"; static char __pyx_k__i[] = "i"; static char __pyx_k__n[] = "n"; static char __pyx_k__r[] = "r"; static char __pyx_k__s[] = "s"; static char __pyx_k__w[] = "w"; static char __pyx_k_101[] = "mapping information not recorded in index or index not available"; static char __pyx_k_104[] = "Samfile.unmapped only available in bam files"; static char __pyx_k_109[] = "@"; static char __pyx_k_111[] = "header line without '@': '%s'"; static char __pyx_k_113[] = "header line with invalid type '%s': '%s'"; static char __pyx_k_114[] = ":"; static char __pyx_k_115[] = "malformatted header: no ':' in field"; static char __pyx_k_118[] = "unknown field code '%s' in record '%s'"; static char __pyx_k_119[] = "multiple '%s' lines are not permitted"; static char __pyx_k_120[] = "@%s"; static char __pyx_k_121[] = "%s:%s"; static char __pyx_k_122[] = "invalid type for record %s: %s, expected %s"; static char __pyx_k_124[] = "incomplete sequence information in '%s'"; static char __pyx_k_127[] = "can not iterate over samfile without header"; static char __pyx_k_130[] = "no index available for iteration"; static char __pyx_k_136[] = "can only use this iterator on bam files"; static char __pyx_k_137[] = "reference sequence for '%s' (tid=%i) not found"; static char __pyx_k_138[] = "unknown stepper option `%s` in IteratorColumn"; static char __pyx_k_140[] = "error during iteration"; static char __pyx_k_143[] = "Invalid clipping in CIGAR string"; static char __pyx_k_146[] = "%i%c"; static char __pyx_k_147[] = "quality and sequence mismatch: %i != %i"; static char __pyx_k_148[] = "%c"; static char __pyx_k_149[] = "<"; static char __pyx_k_151[] = "integer %i out of range of BAM/SAM specification"; static char __pyx_k_152[] = "2sccI%i%s"; static char __pyx_k_156[] = "2sc%is"; static char __pyx_k_158[] = "create_string_buffer"; static char __pyx_k_159[] = "tag '%s' not present"; static char __pyx_k_160[] = "unknown auxilliary type '%s'"; static char __pyx_k_161[] = "Contig index"; static char __pyx_k_162[] = "Mapped position on contig"; static char __pyx_k_163[] = "Contig index for mate pair"; static char __pyx_k_164[] = "Position of mate pair"; static char __pyx_k_165[] = "Insert size"; static char __pyx_k_166[] = "Binary flag"; static char __pyx_k_167[] = "Count of cigar entries"; static char __pyx_k_168[] = "Cigar entries"; static char __pyx_k_169[] = "Mapping quality"; static char __pyx_k_170[] = "Bam index bin number"; static char __pyx_k_171[] = "Length of query name"; static char __pyx_k_172[] = "Query name"; static char __pyx_k_173[] = "Length of query sequence"; static char __pyx_k_174[] = "Query sequence"; static char __pyx_k_175[] = "Quality scores"; static char __pyx_k_176[] = "Length of auxilary data"; static char __pyx_k_177[] = "Maximum data length"; static char __pyx_k_178[] = "Current data length"; static char __pyx_k_179[] = "%-30s %-10s= %s"; static char __pyx_k_180[] = "("; static char __pyx_k_181[] = ")"; static char __pyx_k_182[] = "This class cannot be instantiated from Python"; static char __pyx_k_184[] = "PileupProxy accessed after iterator finished"; static char __pyx_k_188[] = "No such file or directory: '%s'"; static char __pyx_k_189[] = "-o"; static char __pyx_k_190[] = "option -o is forbidden in samtools view"; static char __pyx_k_196[] = "can only IndexReads on bam files"; static char __pyx_k_197[] = "read %s not found"; static char __pyx_k_198[] = "number of :term:`filename` associated with this object."; static char __pyx_k_199[] = "tuple with the names of :term:`reference` sequences."; static char __pyx_k_200[] = "number of :term:`reference` sequences in the file."; static char __pyx_k_201[] = "tuple with the lengths of :term:`reference` sequences."; static char __pyx_k_202[] = "the query name (None if not present)"; static char __pyx_k_203[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of tuples of (operation, length). \n The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+--------------+-----+\n |S |BAM_CSOFT_CLIP|4 |\n +-----+--------------+-----+\n |H |BAM_CHARD_CLIP|5 |\n +-----+--------------+-----+\n |P |BAM_CPAD |6 |\n +-----+--------------+-----+\n |= |BAM_CEQUAL |7 |\n +-----+--------------+-----+\n |X |BAM_CDIFF |8 |\n +-----+--------------+-----+\n\n .. note::\n The output is a list of (operation, length) tuples, such as\n ``[ (0, 30) ]``.\n This is different from the SAM specification and the\n the :meth:`cigarstring` property, which uses a\n (length,operation order, for example: ``30M``.\n\n "; static char __pyx_k_204[] = "the :term:`cigar` alignment as a string.\n \n The cigar string is a string of alternating integers\n and characters denoting the length and the type of\n an operation.\n\n .. note::\n The order length,operation is specified in the\n SAM format. It is different from the order of\n the :meth:`cigar` property.\n\n Returns the empty string if not present.\n "; static char __pyx_k_205[] = "read sequence bases, including :term:`soft clipped` bases \n (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that assigning to seq will invalidate any quality scores.\n Thus, to in-place edit the sequence and quality scores, copies of\n the quality scores need to be taken. Consider trimming for example::\n\n q = read.qual\n read.seq = read.seq[5:10]\n read.qual = q[5:10]\n\n "; static char __pyx_k_206[] = "read sequence base qualities, including :term:`soft\n clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that to set quality scores the sequence has to be set\n previously as this will determine the permitted length of\n the quality score array.\n\n This method raises a ValueError if the length of the \n quality scores and the sequence are not the same.\n "; static char __pyx_k_207[] = "aligned portion of the read and excludes any flanking bases\n that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorithms, which may not require alignments\n that begin at the first residue or end at the last. In addition,\n extra sequencing adapters, multiplex identifiers, and low-quality bases that\n were not considered for alignment may have been retained."; static char __pyx_k_208[] = "aligned query sequence quality values (None if not\n present). This property is read-only.\n\n In Python 3, this property is of type bytes."; static char __pyx_k_209[] = "start index of the aligned query portion of the sequence (0-based, inclusive)"; static char __pyx_k_210[] = "end index of the aligned query portion of the sequence (0-based, exclusive)"; static char __pyx_k_211[] = "Length of the aligned query sequence"; static char __pyx_k_212[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n "; static char __pyx_k_213[] = "properties flag"; static char __pyx_k_214[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n "; static char __pyx_k_215[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n "; static char __pyx_k_216[] = "0-based leftmost coordinate"; static char __pyx_k_217[] = "properties bin"; static char __pyx_k_218[] = "length of the read (read only). Returns 0 if not given."; static char __pyx_k_219[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available."; static char __pyx_k_220[] = "aligned length of the read on the reference genome. Returns None if\n not available."; static char __pyx_k_221[] = "mapping quality"; static char __pyx_k_222[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n "; static char __pyx_k_223[] = "the :term:`reference` id of the mate "; static char __pyx_k_224[] = "the position of the mate\n deprecated, use PNEXT instead."; static char __pyx_k_225[] = "the position of the mate"; static char __pyx_k_226[] = "the insert size\n deprecated: use tlen instead"; static char __pyx_k_227[] = "the insert size"; static char __pyx_k_228[] = "true if read is paired in sequencing"; static char __pyx_k_229[] = "true if read is mapped in a proper pair"; static char __pyx_k_230[] = "true if read itself is unmapped"; static char __pyx_k_231[] = "true if the mate is unmapped"; static char __pyx_k_232[] = "true if read is mapped to reverse strand"; static char __pyx_k_233[] = "true is read is mapped to reverse strand"; static char __pyx_k_234[] = "true if this is read1"; static char __pyx_k_235[] = "true if this is read2"; static char __pyx_k_236[] = "true if not primary alignment"; static char __pyx_k_237[] = "true if QC failure"; static char __pyx_k_238[] = "true if optical or PCR duplicate"; static char __pyx_k_239[] = "a list of reference positions that this read aligns to."; static char __pyx_k_240[] = "inferred read length from CIGAR string.\n\n Returns 0 if CIGAR string is not present.\n "; static char __pyx_k_241[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n "; static char __pyx_k_242[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n "; static char __pyx_k_243[] = "total number of mapped reads in file.\n "; static char __pyx_k_244[] = "total number of unmapped reads in file.\n "; static char __pyx_k_245[] = "full contents of the :term:`sam file` header as a string."; static char __pyx_k_246[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n "; static char __pyx_k_247[] = "the chromosome ID as is defined in the header"; static char __pyx_k_248[] = "number of reads mapping to this column."; static char __pyx_k_249[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column"; static char __pyx_k_250[] = "a :class:`pysam.AlignedRead` object of the aligned read"; static char __pyx_k_251[] = "position of the read base at the pileup site, 0-based"; static char __pyx_k_252[] = "indel length; 0 for no indel, positive for ins and negative for del"; static char __pyx_k_253[] = "1 iff the base on the padded read is a deletion"; static char __pyx_k_254[] = "current sequence length."; static char __pyx_k_255[] = "nucleotide position of SNP."; static char __pyx_k_256[] = "reference base at pos. ``N`` if no reference sequence supplied."; static char __pyx_k_257[] = "the genotype called."; static char __pyx_k_258[] = "the genotype quality (Phred-scaled)."; static char __pyx_k_259[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence."; static char __pyx_k_260[] = "the root mean square (rms) of the mapping quality of all reads involved in the call."; static char __pyx_k_261[] = "coverage or read depth - the number of reads involved in the call."; static char __pyx_k_262[] = "getfilesystemencoding"; static char __pyx_k_263[] = "MIDNSHP=X"; static char __pyx_k_264[] = "(\\d+)([MIDNSHP=X])"; static char __pyx_k_266[] = "=ACMGRSVTWYHKDBN"; static char __pyx_k_269[] = "/home/andreas/devel/pysam/pysam/csamtools.pyx"; static char __pyx_k_270[] = "PileupColumn.__str__"; static char __pyx_k_271[] = "pysam.csamtools"; static char __pyx_k_272[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n "; static char __pyx_k_275[] = "StderrStore.__init__"; static char __pyx_k_278[] = "StderrStore.readAndRelease"; static char __pyx_k_281[] = "StderrStore.release"; static char __pyx_k_284[] = "StderrStore.__del__"; static char __pyx_k_285[] = "\n stderr is captured.\n "; static char __pyx_k_288[] = "StderrStoreWindows.__init__"; static char __pyx_k_291[] = "StderrStoreWindows.readAndRelease"; static char __pyx_k_294[] = "StderrStoreWindows.release"; static char __pyx_k_295[] = "does nothing. stderr can't be redirected on windows"; static char __pyx_k_304[] = "Outs.__init__"; static char __pyx_k_307[] = "Outs.setdevice"; static char __pyx_k_310[] = "Outs.setfile"; static char __pyx_k_313[] = "Outs.setfd"; static char __pyx_k_316[] = "Outs.restore"; static char __pyx_k_317[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html"; static char __pyx_k__AS[] = "AS"; static char __pyx_k__CL[] = "CL"; static char __pyx_k__CN[] = "CN"; static char __pyx_k__CO[] = "CO"; static char __pyx_k__DS[] = "DS"; static char __pyx_k__DT[] = "DT"; static char __pyx_k__FO[] = "FO"; static char __pyx_k__GO[] = "GO"; static char __pyx_k__HD[] = "HD"; static char __pyx_k__ID[] = "ID"; static char __pyx_k__KS[] = "KS"; static char __pyx_k__LB[] = "LB"; static char __pyx_k__LN[] = "LN"; static char __pyx_k__M5[] = "M5"; static char __pyx_k__PG[] = "PG"; static char __pyx_k__PI[] = "PI"; static char __pyx_k__PL[] = "PL"; static char __pyx_k__PN[] = "PN"; static char __pyx_k__PP[] = "PP"; static char __pyx_k__PU[] = "PU"; static char __pyx_k__RG[] = "RG"; static char __pyx_k__SM[] = "SM"; static char __pyx_k__SN[] = "SN"; static char __pyx_k__SO[] = "SO"; static char __pyx_k__SP[] = "SP"; static char __pyx_k__SQ[] = "SQ"; static char __pyx_k__UR[] = "UR"; static char __pyx_k__VN[] = "VN"; static char __pyx_k__fd[] = "fd"; static char __pyx_k__id[] = "id"; static char __pyx_k__os[] = "os"; static char __pyx_k__rU[] = "rU"; static char __pyx_k__rb[] = "rb"; static char __pyx_k__re[] = "re"; static char __pyx_k__wb[] = "wb"; static char __pyx_k__wh[] = "wh"; static char __pyx_k__all[] = "all"; static char __pyx_k__beg[] = "beg"; static char __pyx_k__bin[] = "bin"; static char __pyx_k__chr[] = "chr"; static char __pyx_k__dup[] = "dup"; static char __pyx_k__end[] = "end"; static char __pyx_k__inf[] = "inf"; static char __pyx_k__map[] = "map"; static char __pyx_k__max[] = "max"; static char __pyx_k__min[] = "min"; static char __pyx_k__ofd[] = "ofd"; static char __pyx_k__ord[] = "ord"; static char __pyx_k__pos[] = "pos"; static char __pyx_k__raw[] = "raw"; static char __pyx_k__seq[] = "seq"; static char __pyx_k__sys[] = "sys"; static char __pyx_k__tid[] = "tid"; static char __pyx_k__wbu[] = "wbu"; static char __pyx_k__zip[] = "zip"; static char __pyx_k__2scB[] = "2scB"; static char __pyx_k__2scH[] = "2scH"; static char __pyx_k__2scI[] = "2scI"; static char __pyx_k__2scb[] = "2scb"; static char __pyx_k__2scc[] = "2scc"; static char __pyx_k__2scf[] = "2scf"; static char __pyx_k__2sch[] = "2sch"; static char __pyx_k__2sci[] = "2sci"; static char __pyx_k__Outs[] = "Outs"; static char __pyx_k__args[] = "args"; static char __pyx_k__dup2[] = "dup2"; static char __pyx_k__flag[] = "flag"; static char __pyx_k__join[] = "join"; static char __pyx_k__mapq[] = "mapq"; static char __pyx_k__mask[] = "mask"; static char __pyx_k__mode[] = "mode"; static char __pyx_k__mpos[] = "mpos"; static char __pyx_k__mrnm[] = "mrnm"; static char __pyx_k__mtid[] = "mtid"; static char __pyx_k__open[] = "open"; static char __pyx_k__path[] = "path"; static char __pyx_k__port[] = "port"; static char __pyx_k__qpos[] = "qpos"; static char __pyx_k__qseq[] = "qseq"; static char __pyx_k__qual[] = "qual"; static char __pyx_k__read[] = "read"; static char __pyx_k__rlen[] = "rlen"; static char __pyx_k__seek[] = "seek"; static char __pyx_k__self[] = "self"; static char __pyx_k__tags[] = "tags"; static char __pyx_k__text[] = "text"; static char __pyx_k__view[] = "view"; static char __pyx_k__warn[] = "warn"; static char __pyx_k___open[] = "_open"; static char __pyx_k__ascii[] = "ascii"; static char __pyx_k__bqual[] = "bqual"; static char __pyx_k__cargs[] = "cargs"; static char __pyx_k__cigar[] = "cigar"; static char __pyx_k__close[] = "close"; static char __pyx_k__fetch[] = "fetch"; static char __pyx_k__flush[] = "flush"; static char __pyx_k__indel[] = "indel"; static char __pyx_k__index[] = "index"; static char __pyx_k__isize[] = "isize"; static char __pyx_k__items[] = "items"; static char __pyx_k__l_aux[] = "l_aux"; static char __pyx_k__level[] = "level"; static char __pyx_k__qname[] = "qname"; static char __pyx_k__rname[] = "rname"; static char __pyx_k__setfd[] = "setfd"; static char __pyx_k__split[] = "split"; static char __pyx_k__start[] = "start"; static char __pyx_k__strip[] = "strip"; static char __pyx_k__types[] = "types"; static char __pyx_k__where[] = "where"; static char __pyx_k__write[] = "write"; static char __pyx_k__ctypes[] = "ctypes"; static char __pyx_k__decode[] = "decode"; static char __pyx_k__encode[] = "encode"; static char __pyx_k__exists[] = "exists"; static char __pyx_k__extend[] = "extend"; static char __pyx_k__fields[] = "fields"; static char __pyx_k__fileno[] = "fileno"; static char __pyx_k__gettid[] = "gettid"; static char __pyx_k__header[] = "header"; static char __pyx_k__is_del[] = "is_del"; static char __pyx_k__l_qseq[] = "l_qseq"; static char __pyx_k__m_data[] = "m_data"; static char __pyx_k__method[] = "method"; static char __pyx_k__object[] = "object"; static char __pyx_k__offset[] = "offset"; static char __pyx_k__record[] = "record"; static char __pyx_k__region[] = "region"; static char __pyx_k__remove[] = "remove"; static char __pyx_k__reopen[] = "reopen"; static char __pyx_k__retval[] = "retval"; static char __pyx_k__sorted[] = "sorted"; static char __pyx_k__stderr[] = "stderr"; static char __pyx_k__stdout[] = "stdout"; static char __pyx_k__struct[] = "struct"; static char __pyx_k__system[] = "system"; static char __pyx_k__IOError[] = "IOError"; static char __pyx_k__OSError[] = "OSError"; static char __pyx_k__O_CREAT[] = "O_CREAT"; static char __pyx_k__Samfile[] = "Samfile"; static char __pyx_k__Windows[] = "Windows"; static char __pyx_k____all__[] = "__all__"; static char __pyx_k____del__[] = "__del__"; static char __pyx_k____str__[] = "__str__"; static char __pyx_k___isOpen[] = "_isOpen"; static char __pyx_k__compile[] = "compile"; static char __pyx_k__findall[] = "findall"; static char __pyx_k__is_head[] = "is_head"; static char __pyx_k__is_tail[] = "is_tail"; static char __pyx_k__islower[] = "islower"; static char __pyx_k__isupper[] = "isupper"; static char __pyx_k__l_qname[] = "l_qname"; static char __pyx_k__lengths[] = "lengths"; static char __pyx_k__mkstemp[] = "mkstemp"; static char __pyx_k__n_cigar[] = "n_cigar"; static char __pyx_k__pileups[] = "pileups"; static char __pyx_k__release[] = "release"; static char __pyx_k__restore[] = "restore"; static char __pyx_k__samfile[] = "samfile"; static char __pyx_k__setfile[] = "setfile"; static char __pyx_k__stepper[] = "stepper"; static char __pyx_k__streams[] = "streams"; static char __pyx_k__KeyError[] = "KeyError"; static char __pyx_k__O_WRONLY[] = "O_WRONLY"; static char __pyx_k____dict__[] = "__dict__"; static char __pyx_k____exit__[] = "__exit__"; static char __pyx_k____init__[] = "__init__"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__calcsize[] = "calcsize"; static char __pyx_k__callback[] = "callback"; static char __pyx_k__check_sq[] = "check_sq"; static char __pyx_k__coverage[] = "coverage"; static char __pyx_k__data_len[] = "data_len"; static char __pyx_k__exc_type[] = "exc_type"; static char __pyx_k__filename[] = "filename"; static char __pyx_k__genotype[] = "genotype"; static char __pyx_k__nextiter[] = "nextiter"; static char __pyx_k__platform[] = "platform"; static char __pyx_k__samtools[] = "samtools"; static char __pyx_k__stderr_f[] = "stderr_f"; static char __pyx_k__stderr_h[] = "stderr_h"; static char __pyx_k__stdout_f[] = "stdout_f"; static char __pyx_k__stdout_h[] = "stdout_h"; static char __pyx_k__tempfile[] = "tempfile"; static char __pyx_k__template[] = "template"; static char __pyx_k__truncate[] = "truncate"; static char __pyx_k__warnings[] = "warnings"; static char __pyx_k__Fastafile[] = "Fastafile"; static char __pyx_k__Fastqfile[] = "Fastqfile"; static char __pyx_k__TypeError[] = "TypeError"; static char __pyx_k____enter__[] = "__enter__"; static char __pyx_k___hasIndex[] = "_hasIndex"; static char __pyx_k__alignment[] = "alignment"; static char __pyx_k__enumerate[] = "enumerate"; static char __pyx_k__exc_value[] = "exc_value"; static char __pyx_k__fastafile[] = "fastafile"; static char __pyx_k__itertools[] = "itertools"; static char __pyx_k__max_depth[] = "max_depth"; static char __pyx_k__pack_into[] = "pack_into"; static char __pyx_k__positions[] = "positions"; static char __pyx_k__readlines[] = "readlines"; static char __pyx_k__reference[] = "reference"; static char __pyx_k__setdevice[] = "setdevice"; static char __pyx_k__traceback[] = "traceback"; static char __pyx_k__until_eof[] = "until_eof"; static char __pyx_k__CIGAR2CODE[] = "CIGAR2CODE"; static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3"; static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k__PileupRead[] = "PileupRead"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k___buildLine[] = "_buildLine"; static char __pyx_k__out_stderr[] = "out_stderr"; static char __pyx_k__out_stdout[] = "out_stdout"; static char __pyx_k__references[] = "references"; static char __pyx_k__startswith[] = "startswith"; static char __pyx_k__AlignedRead[] = "AlignedRead"; static char __pyx_k__CIGAR_REGEX[] = "CIGAR_REGEX"; static char __pyx_k__IteratorRow[] = "IteratorRow"; static char __pyx_k__PileupProxy[] = "PileupProxy"; static char __pyx_k__StderrStore[] = "StderrStore"; static char __pyx_k__add_sq_text[] = "add_sq_text"; static char __pyx_k__collections[] = "collections"; static char __pyx_k__defaultdict[] = "defaultdict"; static char __pyx_k__nreferences[] = "nreferences"; static char __pyx_k__snp_quality[] = "snp_quality"; static char __pyx_k__stdout_save[] = "stdout_save"; static char __pyx_k__IndexedReads[] = "IndexedReads"; static char __pyx_k__PileupColumn[] = "PileupColumn"; static char __pyx_k___parseRegion[] = "_parseRegion"; static char __pyx_k__catch_stdout[] = "catch_stdout"; static char __pyx_k__check_header[] = "check_header"; static char __pyx_k__version_info[] = "version_info"; static char __pyx_k__OverflowError[] = "OverflowError"; static char __pyx_k__StopIteration[] = "StopIteration"; static char __pyx_k__VALID_HEADERS[] = "VALID_HEADERS"; static char __pyx_k__AttributeError[] = "AttributeError"; static char __pyx_k__IteratorColumn[] = "IteratorColumn"; static char __pyx_k__readAndRelease[] = "readAndRelease"; static char __pyx_k__reference_base[] = "reference_base"; static char __pyx_k__referencenames[] = "referencenames"; static char __pyx_k__mapping_quality[] = "mapping_quality"; static char __pyx_k____getattribute__[] = "__getattribute__"; static char __pyx_k__referencelengths[] = "referencelengths"; static char __pyx_k__consensus_quality[] = "consensus_quality"; static char __pyx_k__StderrStoreWindows[] = "StderrStoreWindows"; static char __pyx_k__UnicodeDecodeError[] = "UnicodeDecodeError"; static char __pyx_k__VALID_HEADER_ORDER[] = "VALID_HEADER_ORDER"; static char __pyx_k__VALID_HEADER_TYPES[] = "VALID_HEADER_TYPES"; static char __pyx_k___samtools_dispatch[] = "_samtools_dispatch"; static char __pyx_k__getdefaultencoding[] = "getdefaultencoding"; static char __pyx_k__NotImplementedError[] = "NotImplementedError"; static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS"; static PyObject *__pyx_kp_u_1; static PyObject *__pyx_kp_b_10; static PyObject *__pyx_kp_s_101; static PyObject *__pyx_kp_s_104; static PyObject *__pyx_kp_s_109; 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static PyObject *__pyx_kp_s__2scI; static PyObject *__pyx_kp_s__2scb; static PyObject *__pyx_kp_s__2scc; static PyObject *__pyx_kp_s__2scf; static PyObject *__pyx_kp_s__2sch; static PyObject *__pyx_kp_s__2sci; static PyObject *__pyx_n_s__A; static PyObject *__pyx_n_s__AS; static PyObject *__pyx_n_s__AlignedRead; static PyObject *__pyx_n_s__AttributeError; static PyObject *__pyx_n_s__B; static PyObject *__pyx_n_s__C; static PyObject *__pyx_n_s__CIGAR2CODE; static PyObject *__pyx_n_s__CIGAR_REGEX; static PyObject *__pyx_n_s__CL; static PyObject *__pyx_n_s__CN; static PyObject *__pyx_n_s__CO; static PyObject *__pyx_n_s__D; static PyObject *__pyx_n_s__DS; static PyObject *__pyx_n_s__DT; static PyObject *__pyx_n_s__F; static PyObject *__pyx_n_s__FO; static PyObject *__pyx_n_s__Fastafile; static PyObject *__pyx_n_s__Fastqfile; static PyObject *__pyx_n_s__GO; static PyObject *__pyx_n_s__H; static PyObject *__pyx_n_s__HD; static PyObject *__pyx_n_s__I; static PyObject *__pyx_n_s__ID; static PyObject *__pyx_n_s__IOError; static PyObject *__pyx_n_s__IS_PYTHON3; static PyObject *__pyx_n_s__IndexError; static PyObject *__pyx_n_s__IndexedReads; static PyObject *__pyx_n_s__IteratorColumn; static PyObject *__pyx_n_s__IteratorRow; static PyObject *__pyx_n_s__KS; static PyObject *__pyx_n_s__KeyError; static PyObject *__pyx_n_s__LB; static PyObject *__pyx_n_s__LN; static PyObject *__pyx_n_s__M5; static PyObject *__pyx_n_s__NotImplementedError; static PyObject *__pyx_n_s__OSError; static PyObject *__pyx_n_s__O_CREAT; static PyObject *__pyx_n_s__O_WRONLY; static PyObject *__pyx_n_s__Outs; static PyObject *__pyx_n_s__OverflowError; static PyObject *__pyx_n_s__PG; static PyObject *__pyx_n_s__PI; static PyObject *__pyx_n_s__PL; static PyObject *__pyx_n_s__PN; static PyObject *__pyx_n_s__PP; static PyObject *__pyx_n_s__PU; static PyObject *__pyx_n_s__PileupColumn; static PyObject *__pyx_n_s__PileupProxy; static PyObject *__pyx_n_s__PileupRead; static PyObject *__pyx_n_s__RG; static PyObject *__pyx_n_s__S; static PyObject *__pyx_n_s__SM; static PyObject *__pyx_n_s__SN; static PyObject *__pyx_n_s__SO; static PyObject *__pyx_n_s__SP; static PyObject *__pyx_n_s__SQ; static PyObject *__pyx_n_s__Samfile; static PyObject *__pyx_n_s__StderrStore; static PyObject *__pyx_n_s__StderrStoreWindows; static PyObject *__pyx_n_s__StopIteration; static PyObject *__pyx_n_s__TypeError; static PyObject *__pyx_n_s__UR; static PyObject *__pyx_n_s__UnicodeDecodeError; static PyObject *__pyx_n_s__VALID_HEADERS; static PyObject *__pyx_n_s__VALID_HEADER_FIELDS; static PyObject *__pyx_n_s__VALID_HEADER_ORDER; static PyObject *__pyx_n_s__VALID_HEADER_TYPES; static PyObject *__pyx_n_s__VN; static PyObject *__pyx_n_s__ValueError; static PyObject *__pyx_n_s__Windows; static PyObject *__pyx_n_s__Z; static PyObject *__pyx_n_s____all__; static PyObject *__pyx_n_s____del__; static PyObject *__pyx_n_s____dict__; static PyObject *__pyx_n_s____enter__; static PyObject *__pyx_n_s____exit__; static PyObject *__pyx_n_s____getattribute__; static PyObject *__pyx_n_s____init__; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____str__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___buildLine; static PyObject *__pyx_n_s___hasIndex; static PyObject *__pyx_n_s___isOpen; static PyObject *__pyx_n_s___open; static PyObject *__pyx_n_s___parseRegion; static PyObject *__pyx_n_s___samtools_dispatch; static PyObject *__pyx_n_s__a; static PyObject *__pyx_n_s__add_sq_text; static PyObject *__pyx_n_s__alignment; static PyObject *__pyx_n_s__all; static PyObject *__pyx_n_s__args; static PyObject *__pyx_n_s__ascii; static PyObject *__pyx_n_s__b; static PyObject *__pyx_n_s__beg; static PyObject *__pyx_n_s__bin; static PyObject *__pyx_n_s__bqual; static PyObject *__pyx_n_s__c; static PyObject *__pyx_n_s__calcsize; static PyObject *__pyx_n_s__callback; static PyObject *__pyx_n_s__cargs; static PyObject *__pyx_n_s__catch_stdout; static PyObject *__pyx_n_s__check_header; static PyObject *__pyx_n_s__check_sq; static PyObject *__pyx_n_s__chr; static PyObject *__pyx_n_s__cigar; static PyObject *__pyx_n_s__close; static PyObject *__pyx_n_s__collections; static PyObject *__pyx_n_s__compile; static PyObject *__pyx_n_s__consensus_quality; static PyObject *__pyx_n_s__coverage; static PyObject *__pyx_n_s__ctypes; static PyObject *__pyx_n_s__d; static PyObject *__pyx_n_s__data_len; static PyObject *__pyx_n_s__decode; static PyObject *__pyx_n_s__defaultdict; static PyObject *__pyx_n_s__dup; static PyObject *__pyx_n_s__dup2; static PyObject *__pyx_n_s__encode; static PyObject *__pyx_n_s__end; static PyObject *__pyx_n_s__enumerate; static PyObject *__pyx_n_s__exc_type; static PyObject *__pyx_n_s__exc_value; static PyObject *__pyx_n_s__exists; static PyObject *__pyx_n_s__extend; static PyObject *__pyx_n_s__f; static PyObject *__pyx_n_s__fastafile; static PyObject *__pyx_n_s__fd; static PyObject *__pyx_n_s__fetch; static PyObject *__pyx_n_s__fields; static PyObject *__pyx_n_s__filename; static PyObject *__pyx_n_s__fileno; static PyObject *__pyx_n_s__findall; static PyObject *__pyx_n_s__flag; static PyObject *__pyx_n_s__flush; static PyObject *__pyx_n_s__genotype; static PyObject *__pyx_n_s__getdefaultencoding; static PyObject *__pyx_n_s__gettid; static PyObject *__pyx_n_s__h; static PyObject *__pyx_n_s__header; static PyObject *__pyx_n_s__i; static PyObject *__pyx_n_s__id; static PyObject *__pyx_n_s__indel; static PyObject *__pyx_n_s__index; static PyObject *__pyx_n_s__inf; static PyObject *__pyx_n_s__is_del; static PyObject *__pyx_n_s__is_head; static PyObject *__pyx_n_s__is_tail; static PyObject *__pyx_n_s__isize; static PyObject *__pyx_n_s__islower; static PyObject *__pyx_n_s__isupper; static PyObject *__pyx_n_s__items; static PyObject *__pyx_n_s__itertools; static PyObject *__pyx_n_s__join; static PyObject *__pyx_n_s__l_aux; static PyObject *__pyx_n_s__l_qname; static PyObject *__pyx_n_s__l_qseq; static PyObject *__pyx_n_s__lengths; static PyObject *__pyx_n_s__level; static PyObject *__pyx_n_s__m_data; static PyObject *__pyx_n_s__map; static PyObject *__pyx_n_s__mapping_quality; static PyObject *__pyx_n_s__mapq; static PyObject *__pyx_n_s__mask; static PyObject *__pyx_n_s__max; static PyObject *__pyx_n_s__max_depth; static PyObject *__pyx_n_s__method; static PyObject *__pyx_n_s__min; static PyObject *__pyx_n_s__mkstemp; static PyObject *__pyx_n_s__mode; static PyObject *__pyx_n_s__mpos; static PyObject *__pyx_n_s__mrnm; static PyObject *__pyx_n_s__mtid; static PyObject *__pyx_n_s__n; static PyObject *__pyx_n_s__n_cigar; static PyObject *__pyx_n_s__nextiter; static PyObject *__pyx_n_s__nreferences; static PyObject *__pyx_n_s__object; static PyObject *__pyx_n_s__ofd; static PyObject *__pyx_n_s__offset; static PyObject *__pyx_n_s__open; static PyObject *__pyx_n_s__ord; static PyObject *__pyx_n_s__os; static PyObject *__pyx_n_s__out_stderr; static PyObject *__pyx_n_s__out_stdout; static PyObject *__pyx_n_s__pack_into; static PyObject *__pyx_n_s__path; static PyObject *__pyx_n_s__pileups; static PyObject *__pyx_n_s__platform; static PyObject *__pyx_n_s__port; static PyObject *__pyx_n_s__pos; static PyObject *__pyx_n_s__positions; static PyObject *__pyx_n_s__qname; static PyObject *__pyx_n_s__qpos; static PyObject *__pyx_n_s__qseq; static PyObject *__pyx_n_s__qual; static PyObject *__pyx_n_b__r; static PyObject *__pyx_n_s__r; static PyObject *__pyx_n_s__rU; static PyObject *__pyx_n_s__raw; static PyObject *__pyx_n_b__rb; static PyObject *__pyx_n_s__rb; static PyObject *__pyx_n_s__re; static PyObject *__pyx_n_s__read; static PyObject *__pyx_n_s__readAndRelease; static PyObject *__pyx_n_s__readlines; static PyObject *__pyx_n_s__record; static PyObject *__pyx_n_s__reference; static PyObject *__pyx_n_s__reference_base; static PyObject *__pyx_n_s__referencelengths; static PyObject *__pyx_n_s__referencenames; static PyObject *__pyx_n_s__references; static PyObject *__pyx_n_s__region; static PyObject *__pyx_n_s__release; static PyObject *__pyx_n_s__remove; static PyObject *__pyx_n_s__reopen; static PyObject *__pyx_n_s__restore; static PyObject *__pyx_n_s__retval; static PyObject *__pyx_n_s__rlen; 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static PySequenceMethods __pyx_tp_as_sequence_Fastafile = { __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_5pysam_9csamtools_Fastafile, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ __pyx_pw_5pysam_9csamtools_9Fastafile_19__contains__, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_Fastafile = { __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*mp_length*/ __pyx_pw_5pysam_9csamtools_9Fastafile_17__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Fastafile = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; 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if (!o) return 0; return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_FastqProxy(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_name(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10FastqProxy_4name_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_sequence(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10FastqProxy_8sequence_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_comment(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10FastqProxy_7comment_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_quality(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10FastqProxy_7quality_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_FastqProxy[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_FastqProxy[] = { {(char *)"name", __pyx_getprop_5pysam_9csamtools_10FastqProxy_name, 0, 0, 0}, {(char *)"sequence", __pyx_getprop_5pysam_9csamtools_10FastqProxy_sequence, 0, 0, 0}, {(char *)"comment", __pyx_getprop_5pysam_9csamtools_10FastqProxy_comment, 0, 0, 0}, {(char *)"quality", __pyx_getprop_5pysam_9csamtools_10FastqProxy_quality, 0, 0, 0}, {0, 0, 0, 0, 0} }; 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static PySequenceMethods __pyx_tp_as_sequence_FastqProxy = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_FastqProxy = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_FastqProxy = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_FastqProxy = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.FastqProxy"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_FastqProxy), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_FastqProxy, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_FastqProxy, /*tp_as_number*/ &__pyx_tp_as_sequence_FastqProxy, /*tp_as_sequence*/ &__pyx_tp_as_mapping_FastqProxy, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_FastqProxy, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("FastqProxy()"), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_FastqProxy, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_FastqProxy, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_9csamtools_10FastqProxy_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_FastqProxy, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile __pyx_vtable_5pysam_9csamtools_Fastqfile; static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastqfile(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_Fastqfile *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Fastqfile; p->_filename = Py_None; Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_9Fastqfile_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_Fastqfile(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_9Fastqfile_9__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->_filename); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_9csamtools_Fastqfile(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o; if (p->_filename) { e = (*v)(p->_filename, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_Fastqfile(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_Fastqfile *p = (struct __pyx_obj_5pysam_9csamtools_Fastqfile *)o; PyObject* tmp; tmp = ((PyObject*)p->_filename); p->_filename = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastqfile_filename(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_9Fastqfile_8filename_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_Fastqfile[] = { {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_2_isOpen)}, {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_5_open, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_4_open)}, {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_7close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_6close)}, {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastqfile_13__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastqfile_12__next__)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Fastqfile[] = { {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastqfile_filename, 0, __Pyx_DOCSTR(__pyx_k_198), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Fastqfile = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; 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(*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_query(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qend(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject 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__pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aend(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_alen(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_positions(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_inferred_length(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_15inferred_length_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_AlignedRead[] 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/*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_AlignedRead = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_AlignedRead = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.AlignedRead"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_AlignedRead), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_AlignedRead, /*tp_as_number*/ &__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/ &__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/ __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("AlignedRead()\n\n Class representing an aligned read. see SAM format specification for\n the meaning of fields (http://samtools.sourceforge.net/).\n\n This class stores a handle to the samtools C-structure representing\n an aligned read. Member read access is forwarded to the C-structure\n and converted into python objects. This implementation should be fast,\n as only the data needed is converted.\n\n For write access, the C-structure is updated in-place. This is\n not the most efficient way to build BAM entries, as the variable\n length data is concatenated and thus needs to resized if\n a field is updated. Furthermore, the BAM entry might be\n in an inconsistent state. The :meth:`~validate` method can\n be used to check if an entry is consistent.\n\n One issue to look out for is that the sequence should always\n be set *before* the quality scores. Setting the sequence will\n also erase any quality scores that were set previously.\n\n In Python 3, the fields containing sequence and quality\n (seq, query, qual and qqual) data are of type bytes. Other\n string data, such as the qname field and strings in the\n tags tuple, is represented as unicode strings. On assignment,\n both bytes and unicode objects are allowed, but unicode strings\n must contain only ASCII characters.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_AlignedRead, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_AlignedRead, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_AlignedRead, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile __pyx_vtable_5pysam_9csamtools_Samfile; static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_Samfile *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Samfile; p->_filename = Py_None; Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->_filename); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_9csamtools_Samfile(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o; if (p->_filename) { e = (*v)(p->_filename, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_Samfile(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_Samfile *p = (struct __pyx_obj_5pysam_9csamtools_Samfile *)o; PyObject* tmp; tmp = ((PyObject*)p->_filename); p->_filename = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_filename(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_nreferences(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_references(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_lengths(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_mapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_unmapped(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_text(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_header(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_Samfile[] = { {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen)}, {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex)}, {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_6_open)}, {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_8gettid)}, {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_10getrname)}, {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion)}, {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_14reset)}, {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_16seek)}, {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_18tell)}, {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_20fetch)}, {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_22mate)}, {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_24count)}, {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_26pileup)}, {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_28close)}, {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_32write)}, {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_34__enter__)}, {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_36__exit__)}, {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine)}, {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_42__next__)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Samfile[] = { {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_198), 0}, {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_200), 0}, {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_199), 0}, {(char *)"lengths", __pyx_getprop_5pysam_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_242), 0}, {(char *)"mapped", __pyx_getprop_5pysam_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_243), 0}, {(char *)"unmapped", __pyx_getprop_5pysam_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_244), 0}, {(char *)"text", __pyx_getprop_5pysam_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_245), 0}, {(char *)"header", __pyx_getprop_5pysam_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_246), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_Samfile = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_Samfile = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_Samfile = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_Samfile = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.Samfile"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_Samfile), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_Samfile, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_Samfile, /*tp_as_number*/ &__pyx_tp_as_sequence_Samfile, /*tp_as_sequence*/ &__pyx_tp_as_mapping_Samfile, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_Samfile, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,\n add_sq_text = False, check_header = True, check_sq = True )*\n\n A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened.\n\n *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary\n (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output.\n Use ``h`` to output header information in text (:term:`TAM`) mode.\n\n If ``b`` is present, it must immediately follow ``r`` or ``w``.\n Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open\n a :term:`BAM` formatted file for reading, type::\n\n f = pysam.Samfile('ex1.bam','rb')\n\n If mode is not specified, we will try to auto-detect in the order 'rb', 'r', thus both the following\n should work::\n\n f1 = pysam.Samfile('ex1.bam' )\n f2 = pysam.Samfile('ex1.sam' )\n\n If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random\n access to reads via :meth:`fetch` and :meth:`pileup` is disabled.\n\n For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several\n sources (see also the samtools format specification):\n\n 1. If *template* is given, the header is copied from a another *Samfile*\n (*template* must be of type *Samfile*).\n\n 2. If *header* is given, the header is built from a multi-level dictionary. The first level\n are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line\n being a list of tag-value pairs. The header is constructed first from all the defined fields,\n followed by user tags in alphabetical order.\n\n 3. If *text* is given, new header text is copied from raw text.\n\n 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. \n By default, 'SQ' and 'LN' tags will be added to the header text. This option can be\n changed by unsetting the flag *add_sq_text*. \n\n By default, if file a file is opened in mode 'r', it is checked for a valid header\n (*check_header* = True) and a definition of chromosome names (*check_sq* = True). \n \n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_Samfile, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_Samfile, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_7Samfile_41__iter__, /*tp_iter*/ __pyx_pw_5pysam_9csamtools_7Samfile_43__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_Samfile, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_Samfile, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_Samfile, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupProxy(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_tid(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(o); } static int __pyx_setprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) { if (v) { return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(o, v); } else { PyErr_SetString(PyExc_NotImplementedError, "__del__"); return -1; } } static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupProxy[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupProxy[] = { {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_247), 0}, {(char *)"n", __pyx_getprop_5pysam_9csamtools_11PileupProxy_n, __pyx_setprop_5pysam_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_248), 0}, {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pos, 0, 0, 0}, {(char *)"pileups", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_249), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_PileupProxy = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_PileupProxy = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_PileupProxy = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.PileupProxy"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_PileupProxy), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_PileupProxy, /*tp_as_number*/ &__pyx_tp_as_sequence_PileupProxy, /*tp_as_sequence*/ &__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("PileupProxy()\nA pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n\n This class is a proxy for results returned by the samtools pileup engine.\n If the underlying engine iterator advances, the results of this column\n will change.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_PileupProxy, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_PileupProxy, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_PileupProxy, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_9csamtools_PileupRead *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)o); p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_PileupRead(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->_alignment); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o; if (p->_alignment) { e = (*v)(((PyObject*)p->_alignment), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_PileupRead(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o; PyObject* tmp; tmp = ((PyObject*)p->_alignment); p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_alignment(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_qpos(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_indel(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_del(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_head(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(o); } static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_level(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupRead[] = { {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupRead[] = { {(char *)"alignment", __pyx_getprop_5pysam_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_250), 0}, {(char *)"qpos", __pyx_getprop_5pysam_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_251), 0}, {(char *)"indel", __pyx_getprop_5pysam_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_252), 0}, {(char *)"is_del", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_253), 0}, {(char *)"is_head", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_head, 0, 0, 0}, {(char *)"is_tail", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail, 0, 0, 0}, {(char *)"level", __pyx_getprop_5pysam_9csamtools_10PileupRead_level, 0, 0, 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_PileupRead = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_PileupRead = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_PileupRead = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_PileupRead = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.PileupRead"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_PileupRead), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_PileupRead, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_PileupRead, /*tp_as_number*/ &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/ &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ __pyx_pw_5pysam_9csamtools_10PileupRead_3__str__, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_PileupRead, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_PileupRead, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_PileupRead, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_PileupRead, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_PileupRead, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRow(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(PyObject *o) { (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRow[] = { {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorRow = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorRow"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRow), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference sequences.\n\n The method :meth:`Samfile.fetch` returns an IteratorRow.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorRow, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorRow, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion __pyx_vtable_5pysam_9csamtools_IteratorRowRegion; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion; p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->samfile); PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o); } static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o; e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion)); if (e) return e; if (p->samfile) { e = (*v)(((PyObject*)p->samfile), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o; PyObject* tmp; if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion); tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowRegion[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorRowRegion"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each iterator\n creates its own file handle by re-opening the\n file.\n\n Note that the index will be shared between\n samfile and the iterator.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorRowRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorRowRegion, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll __pyx_vtable_5pysam_9csamtools_IteratorRowAll; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll; if (__pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAll[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorRowAll"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/ __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n \n\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorRowAll, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorRowAll, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o; PyObject_GC_UnTrack(o); Py_CLEAR(p->samfile); Py_CLEAR(p->rowiter); PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o); } static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o; e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs)); if (e) return e; if (p->samfile) { e = (*v)(((PyObject*)p->samfile), a); if (e) return e; } if (p->rowiter) { e = (*v)(((PyObject*)p->rowiter), a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o; PyObject* tmp; if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs); tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->rowiter); p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs[] = { {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter)}, {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorRowAllRefs"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/ __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection __pyx_vtable_5pysam_9csamtools_IteratorRowSelection; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection; p->positions = Py_None; Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->positions); PyObject_GC_Track(o); __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o); } static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o; e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection)); if (e) return e; if (p->positions) { e = (*v)(p->positions, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o; PyObject* tmp; if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection); tmp = ((PyObject*)p->positions); p->positions = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowSelection[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorRowSelection"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/ __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorRowSelection, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorRowSelection, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_vtable_5pysam_9csamtools_IteratorColumn; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o); p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorColumn; p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); p->stepper = Py_None; Py_INCREF(Py_None); if (__pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->iter); Py_CLEAR(p->samfile); Py_CLEAR(p->fastafile); Py_CLEAR(p->stepper); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o; if (p->iter) { e = (*v)(((PyObject*)p->iter), a); if (e) return e; } if (p->samfile) { e = (*v)(((PyObject*)p->samfile), a); if (e) return e; } if (p->fastafile) { e = (*v)(((PyObject*)p->fastafile), a); if (e) return e; } if (p->stepper) { e = (*v)(p->stepper, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_IteratorColumn(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o; PyObject* tmp; tmp = ((PyObject*)p->iter); p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->fastafile); p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->stepper); p->stepper = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyObject *__pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len(PyObject *o, CYTHON_UNUSED void *x) { return __pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(o); } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumn[] = { {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference)}, {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference)}, {0, 0, 0, 0} }; static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_IteratorColumn[] = { {(char *)"seq_len", __pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_254), 0}, {0, 0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorColumn = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorColumn"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumn), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns,\n but each object in ``result`` will contain the same information.\n\n The desired behaviour can be achieved by list comprehension::\n\n result = [ x.pileups() for x in f.pileup() ]\n\n ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`.\n\n If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference`\n method, then the iterator will export the current sequence via the methods :meth:`getSequence`\n and :meth:`seq_len`.\n\n Optional kwargs to the iterator\n\n stepper\n The stepper controls how the iterator advances.\n Possible options for the stepper are\n\n all\n use all reads for pileup.\n samtools\n same filter and read processing as in :term:`csamtools` pileup\n\n The default is to use \"all\" if no stepper is given.\n\n fastafile\n A :class:`FastaFile` object\n mask\n Skip all reads with bits set in mask.\n max_depth\n maximum read depth. The default is 8000.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorColumn, /*tp_methods*/ 0, /*tp_members*/ __pyx_getsets_5pysam_9csamtools_IteratorColumn, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorColumn, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion; if (__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnRegion[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorColumnRegion"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorColumnRegion, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs; static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *p; PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)o); p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs; if (__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) { Py_DECREF(o); o = 0; } return o; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs[] = { {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IteratorColumnAllRefs"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/ &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ #if CYTHON_COMPILING_IN_PYPY __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/ #else 0, /*tp_iter*/ #endif __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_IndexedReads(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5pysam_9csamtools_IndexedReads *p; PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; p = ((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); p->index = Py_None; Py_INCREF(Py_None); return o; } static void __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o; PyObject_GC_UnTrack(o); { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } Py_CLEAR(p->samfile); Py_CLEAR(p->index); PyObject_GC_Track(o); (*Py_TYPE(o)->tp_free)(o); } static int __pyx_tp_traverse_5pysam_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) { int e; struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o; if (p->samfile) { e = (*v)(((PyObject*)p->samfile), a); if (e) return e; } if (p->index) { e = (*v)(p->index, a); if (e) return e; } return 0; } static int __pyx_tp_clear_5pysam_9csamtools_IndexedReads(PyObject *o) { struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o; PyObject* tmp; tmp = ((PyObject*)p->samfile); p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None); Py_XDECREF(tmp); tmp = ((PyObject*)p->index); p->index = Py_None; Py_INCREF(Py_None); Py_XDECREF(tmp); return 0; } static PyMethodDef __pyx_methods_5pysam_9csamtools_IndexedReads[] = { {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_2build)}, {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_4find)}, {0, 0, 0, 0} }; static PyNumberMethods __pyx_tp_as_number_IndexedReads = { 0, /*nb_add*/ 0, /*nb_subtract*/ 0, /*nb_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_divide*/ #endif 0, /*nb_remainder*/ 0, /*nb_divmod*/ 0, /*nb_power*/ 0, /*nb_negative*/ 0, /*nb_positive*/ 0, /*nb_absolute*/ 0, /*nb_nonzero*/ 0, /*nb_invert*/ 0, /*nb_lshift*/ 0, /*nb_rshift*/ 0, /*nb_and*/ 0, /*nb_xor*/ 0, /*nb_or*/ #if PY_MAJOR_VERSION < 3 0, /*nb_coerce*/ #endif 0, /*nb_int*/ #if PY_MAJOR_VERSION < 3 0, /*nb_long*/ #else 0, /*reserved*/ #endif 0, /*nb_float*/ #if PY_MAJOR_VERSION < 3 0, /*nb_oct*/ #endif #if PY_MAJOR_VERSION < 3 0, /*nb_hex*/ #endif 0, /*nb_inplace_add*/ 0, /*nb_inplace_subtract*/ 0, /*nb_inplace_multiply*/ #if PY_MAJOR_VERSION < 3 0, /*nb_inplace_divide*/ #endif 0, /*nb_inplace_remainder*/ 0, /*nb_inplace_power*/ 0, /*nb_inplace_lshift*/ 0, /*nb_inplace_rshift*/ 0, /*nb_inplace_and*/ 0, /*nb_inplace_xor*/ 0, /*nb_inplace_or*/ 0, /*nb_floor_divide*/ 0, /*nb_true_divide*/ 0, /*nb_inplace_floor_divide*/ 0, /*nb_inplace_true_divide*/ #if PY_VERSION_HEX >= 0x02050000 0, /*nb_index*/ #endif }; static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = { 0, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ 0, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ 0, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_IndexedReads = { 0, /*mp_length*/ 0, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = { #if PY_MAJOR_VERSION < 3 0, /*bf_getreadbuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getwritebuffer*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getsegcount*/ #endif #if PY_MAJOR_VERSION < 3 0, /*bf_getcharbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_getbuffer*/ #endif #if PY_VERSION_HEX >= 0x02060000 0, /*bf_releasebuffer*/ #endif }; static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("pysam.csamtools.IndexedReads"), /*tp_name*/ sizeof(struct __pyx_obj_5pysam_9csamtools_IndexedReads), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ &__pyx_tp_as_number_IndexedReads, /*tp_as_number*/ &__pyx_tp_as_sequence_IndexedReads, /*tp_as_sequence*/ &__pyx_tp_as_mapping_IndexedReads, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ &__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ __Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/ __pyx_tp_traverse_5pysam_9csamtools_IndexedReads, /*tp_traverse*/ __pyx_tp_clear_5pysam_9csamtools_IndexedReads, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5pysam_9csamtools_IndexedReads, /*tp_methods*/ 0, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5pysam_9csamtools_IndexedReads, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyObject *__pyx_tp_new_5pysam_9csamtools_SNPCall(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { PyObject *o = (*t->tp_alloc)(t, 0); if (!o) return 0; return o; } static void 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"pysam/csamtools.pyx":937 * ''' * convert numerical :term:`tid` into :term:`reference` name.''' * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not 0 <= tid < self.samfile.header.n_targets: * raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) */ __pyx_k_tuple_50 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_50)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_50); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_50)); /* "pysam/csamtools.pyx":987 * if len(parts) >= 3: rend = int(parts[2]) * * if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<< * * rtid = self.gettid( reference ) */ __pyx_k_tuple_52 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_0, __pyx_int_0, __pyx_int_0); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_52); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52)); /* "pysam/csamtools.pyx":1007 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not self.isbam: * raise NotImplementedError("seek only available in bam files") */ __pyx_k_tuple_55 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_55); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55)); /* "pysam/csamtools.pyx":1009 * raise ValueError( "I/O operation on closed file" ) * if not self.isbam: * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<< * if self.isstream: * raise OSError("seek no available in streams") */ __pyx_k_tuple_57 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_57); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57)); /* "pysam/csamtools.pyx":1011 * raise NotImplementedError("seek only available in bam files") * if self.isstream: * raise OSError("seek no available in streams") # <<<<<<<<<<<<<< * * return bam_seek( self.samfile.x.bam, offset, where ) */ __pyx_k_tuple_59 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_58)); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_59); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59)); /* "pysam/csamtools.pyx":1020 * ''' * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not self.isbam: * raise NotImplementedError("seek only available in bam files") */ __pyx_k_tuple_60 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_60)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_60); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_60)); /* "pysam/csamtools.pyx":1022 * raise ValueError( "I/O operation on closed file" ) * if not self.isbam: * raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<< * * return bam_tell( self.samfile.x.bam ) */ __pyx_k_tuple_61 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_61); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61)); /* "pysam/csamtools.pyx":1057 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) */ __pyx_k_tuple_63 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_63); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63)); /* "pysam/csamtools.pyx":1066 * if self.isbam: * if not until_eof and not self._hasIndex() and not self.isremote: * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<< * * if callback: */ __pyx_k_tuple_65 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1066; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_65); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65)); /* "pysam/csamtools.pyx":1069 * * if callback: * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<< * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) * return bam_fetch(self.samfile.x.bam, */ __pyx_k_tuple_67 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_66)); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1069; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_67); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67)); /* "pysam/csamtools.pyx":1070 * if callback: * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<< * return bam_fetch(self.samfile.x.bam, * self.index, */ __pyx_k_tuple_69 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_68)); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1070; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_69); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_69)); /* "pysam/csamtools.pyx":1090 * else: * if has_coord: * raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<< * * if callback: */ __pyx_k_tuple_71 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_70)); if (unlikely(!__pyx_k_tuple_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1090; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_71); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_71)); /* "pysam/csamtools.pyx":1093 * * if callback: * raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<< * * if self.samfile.header == NULL: */ __pyx_k_tuple_73 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_72)); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1093; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_73); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73)); /* "pysam/csamtools.pyx":1096 * * if self.samfile.header == NULL: * raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<< * * # check if targets are defined */ __pyx_k_tuple_75 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_74)); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1096; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_75); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75)); /* "pysam/csamtools.pyx":1101 * # give warning, sam_read1 segfaults * if self.samfile.header.n_targets == 0: * warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<< * * return IteratorRowAll( self, reopen=reopen ) */ __pyx_k_tuple_76 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_74)); if (unlikely(!__pyx_k_tuple_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1101; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_76); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_76)); /* "pysam/csamtools.pyx":1142 * * if mate_data.mate == NULL: * raise ValueError( "mate not found" ) # <<<<<<<<<<<<<< * * cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) */ __pyx_k_tuple_80 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_79)); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_80); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80)); /* "pysam/csamtools.pyx":1167 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) */ __pyx_k_tuple_82 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1167; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_82); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82)); /* "pysam/csamtools.pyx":1176 * if self.isbam: * if not until_eof and not self._hasIndex() and not self.isremote: * raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<< * * if not region: */ __pyx_k_tuple_83 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1176; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_83); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83)); /* "pysam/csamtools.pyx":1179 * * if not region: * raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<< * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) * bam_fetch(self.samfile.x.bam, */ __pyx_k_tuple_85 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_84)); if (unlikely(!__pyx_k_tuple_85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_85); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_85)); /* "pysam/csamtools.pyx":1180 * if not region: * raise ValueError( "counting functionality requires a region/reference" ) * if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<< * bam_fetch(self.samfile.x.bam, * self.index, */ __pyx_k_tuple_86 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_68)); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_86); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86)); /* "pysam/csamtools.pyx":1190 * return counter * else: * raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<< * * def pileup( self, */ __pyx_k_tuple_88 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_87)); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_88); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_88)); /* "pysam/csamtools.pyx":1249 * * if not self._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) */ __pyx_k_tuple_89 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_89); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89)); /* "pysam/csamtools.pyx":1254 * * if self.isbam: * if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<< * * if callback: */ __pyx_k_tuple_91 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_90)); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_91); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91)); /* "pysam/csamtools.pyx":1257 * * if callback: * if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<< * * buf = bam_plbuf_init( pileup_callback, callback ) */ __pyx_k_tuple_92 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_66)); if (unlikely(!__pyx_k_tuple_92)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_92); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_92)); /* "pysam/csamtools.pyx":1278 * * else: * raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<< * * def close( self ): */ __pyx_k_tuple_94 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_93)); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_94); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94)); /* "pysam/csamtools.pyx":1326 * '''number of :term:`reference` sequences in the file.''' * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * return self.samfile.header.n_targets * */ __pyx_k_tuple_95 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_95)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_95); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_95)); /* "pysam/csamtools.pyx":1332 * """tuple with the names of :term:`reference` sequences.""" * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * t = [] * for x from 0 <= x < self.samfile.header.n_targets: */ __pyx_k_tuple_96 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_96); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96)); /* "pysam/csamtools.pyx":1343 * """ * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * t = [] * for x from 0 <= x < self.samfile.header.n_targets: */ __pyx_k_tuple_97 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_97); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97)); /* "pysam/csamtools.pyx":1353 * """ * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) * if self.index == NULL: */ __pyx_k_tuple_98 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1353; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_98); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98)); /* "pysam/csamtools.pyx":1354 * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<< * if self.index == NULL: * raise ValueError( "mapping information not recorded in index or index not available") */ __pyx_k_tuple_100 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_99)); if (unlikely(!__pyx_k_tuple_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_100); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_100)); /* "pysam/csamtools.pyx":1356 * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) * if self.index == NULL: * raise ValueError( "mapping information not recorded in index or index not available") # <<<<<<<<<<<<<< * * cdef int tid */ __pyx_k_tuple_102 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_101)); if (unlikely(!__pyx_k_tuple_102)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_102); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_102)); /* "pysam/csamtools.pyx":1368 * """ * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) * cdef int tid */ __pyx_k_tuple_103 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_103); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103)); /* "pysam/csamtools.pyx":1369 * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) * if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<< * cdef int tid * cdef uint32_t total = 0 */ __pyx_k_tuple_105 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_104)); if (unlikely(!__pyx_k_tuple_105)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1369; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_105); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_105)); /* "pysam/csamtools.pyx":1381 * '''full contents of the :term:`sam file` header as a string.''' * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) * */ __pyx_k_tuple_106 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1381; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_106); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_106)); /* "pysam/csamtools.pyx":1389 * ''' * def __get__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * result = {} */ __pyx_k_tuple_107 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_107)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_107); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_107)); /* "pysam/csamtools.pyx":1396 * # convert to python string (note: call self.text to create 0-terminated string) * t = self.text * for line in t.split("\n"): # <<<<<<<<<<<<<< * if not line.strip(): continue * assert line.startswith("@"), "header line without '@': '%s'" % line */ __pyx_k_tuple_108 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_k_tuple_108)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_108); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_108)); /* "pysam/csamtools.pyx":1398 * for line in t.split("\n"): * if not line.strip(): continue * assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<< * fields = line[1:].split("\t") * record = fields[0] */ __pyx_k_tuple_110 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_109)); if (unlikely(!__pyx_k_tuple_110)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_110); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110)); /* "pysam/csamtools.pyx":1399 * if not line.strip(): continue * assert line.startswith("@"), "header line without '@': '%s'" % line * fields = line[1:].split("\t") # <<<<<<<<<<<<<< * record = fields[0] * assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) */ __pyx_k_tuple_112 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_5)); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_112); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112)); /* "pysam/csamtools.pyx":1412 * for field in fields[1:]: * if ":" not in field: * raise ValueError("malformatted header: no ':' in field" ) # <<<<<<<<<<<<<< * key, value = field.split(":",1) * # uppercase keys must be valid */ __pyx_k_tuple_116 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_115)); if (unlikely(!__pyx_k_tuple_116)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_116); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_116)); /* "pysam/csamtools.pyx":1413 * if ":" not in field: * raise ValueError("malformatted header: no ':' in field" ) * key, value = field.split(":",1) # <<<<<<<<<<<<<< * # uppercase keys must be valid * # lowercase are permitted for user fields */ __pyx_k_tuple_117 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_114), __pyx_int_1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_117); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117)); /* "pysam/csamtools.pyx":1511 * dest.text = calloc( len(text), sizeof(char)) * dest.l_text = len(text) * cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<< * strncpy( dest.text, btext, dest.l_text ) * */ __pyx_k_tuple_123 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1511; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_123); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_123)); /* "pysam/csamtools.pyx":1531 * seqname, seqlen = seqs[x] * dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) * bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<< * strncpy( dest.target_name[x], bseqname, len(seqname) + 1 ) * dest.target_len[x] = seqlen */ __pyx_k_tuple_125 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_125)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1531; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_125); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_125)); /* "pysam/csamtools.pyx":1546 * ############################################################### * def __iter__(self): * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * if not self.isbam and self.samfile.header.n_targets == 0: * raise NotImplementedError( "can not iterate over samfile without header") */ __pyx_k_tuple_126 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_126)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1546; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_126); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_126)); /* "pysam/csamtools.pyx":1548 * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) * if not self.isbam and self.samfile.header.n_targets == 0: * raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<< * return self * */ __pyx_k_tuple_128 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_127)); if (unlikely(!__pyx_k_tuple_128)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1548; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_128); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_128)); /* "pysam/csamtools.pyx":1628 * * if not samfile._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * if not samfile._hasIndex(): */ __pyx_k_tuple_129 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_129)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1628; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_129); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_129)); /* "pysam/csamtools.pyx":1631 * * if not samfile._hasIndex(): * raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<< * * # makes sure that samfile stays alive as long as the */ __pyx_k_tuple_131 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_130)); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_131); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131)); /* "pysam/csamtools.pyx":1703 * * if not samfile._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * if samfile.isbam: mode = b"rb" */ __pyx_k_tuple_132 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_132)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_132); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_132)); /* "pysam/csamtools.pyx":1758 * def __cinit__(self, Samfile samfile): * assert samfile._isOpen() * if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<< * self.samfile = samfile * self.tid = -1 */ __pyx_k_tuple_133 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_68)); if (unlikely(!__pyx_k_tuple_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1758; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_133); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_133)); /* "pysam/csamtools.pyx":1808 * * if not samfile._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * if not samfile._isOpen(): */ __pyx_k_tuple_134 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1808; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_134); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_134)); /* "pysam/csamtools.pyx":1811 * * if not samfile._isOpen(): * raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<< * * assert samfile.isbam, "can only use this iterator on bam files" */ __pyx_k_tuple_135 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_15)); if (unlikely(!__pyx_k_tuple_135)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1811; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_135); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_135)); /* "pysam/csamtools.pyx":2109 * self.cnext() * if self.n_plp < 0: * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<< * * if self.plp == NULL: */ __pyx_k_tuple_141 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_140)); if (unlikely(!__pyx_k_tuple_141)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2109; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_141); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_141)); /* "pysam/csamtools.pyx":2145 * * if self.n_plp < 0: * raise ValueError("error during iteration" ) # <<<<<<<<<<<<<< * * # return result, if within same reference */ __pyx_k_tuple_142 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_140)); if (unlikely(!__pyx_k_tuple_142)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_142); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_142)); /* "pysam/csamtools.pyx":2308 * qual = self.qual * else: * seq = self.seq.decode('ascii') # <<<<<<<<<<<<<< * qual = self.qual.decode('ascii') * return "\t".join(map(str, (self.qname, */ __pyx_k_tuple_144 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_144)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2308; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_144); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_144)); /* "pysam/csamtools.pyx":2309 * else: * seq = self.seq.decode('ascii') * qual = self.qual.decode('ascii') # <<<<<<<<<<<<<< * return "\t".join(map(str, (self.qname, * self.flag, */ __pyx_k_tuple_145 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_145)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2309; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_145); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_145)); /* "pysam/csamtools.pyx":2773 * for pytag, value in tags: * if not type(pytag) is bytes: * pytag = pytag.encode('ascii') # <<<<<<<<<<<<<< * t = type(value) * */ __pyx_k_tuple_150 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_150)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_150); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_150)); /* "pysam/csamtools.pyx":2801 * datafmt = "2sccI%i%s" % (len(value), datafmt) * args.extend( [pytag[:2], * pytype.encode('ascii'), # <<<<<<<<<<<<<< * datatype.encode('ascii'), * len(value)] + list(value) ) */ __pyx_k_tuple_153 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_153)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_153); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_153)); /* "pysam/csamtools.pyx":2802 * args.extend( [pytag[:2], * pytype.encode('ascii'), * datatype.encode('ascii'), # <<<<<<<<<<<<<< * len(value)] + list(value) ) * fmts.append( datafmt ) */ __pyx_k_tuple_154 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_154)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_154); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_154)); /* "pysam/csamtools.pyx":2825 * # Note: hex strings (H) are not supported yet * if t is not bytes: * value = value.encode('ascii') # <<<<<<<<<<<<<< * if len(value) == 1: * fmt, pytype = "2scc", 'A' */ __pyx_k_tuple_155 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_155)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_155); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_155)); /* "pysam/csamtools.pyx":2832 * * args.extend( [pytag[:2], * pytype.encode('ascii'), # <<<<<<<<<<<<<< * value ] ) * */ __pyx_k_tuple_157 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_157)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_157); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_157)); /* "pysam/csamtools.pyx":3271 * ''' * def __init__(self): * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<< * * def __str__(self): */ __pyx_k_tuple_183 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_182)); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_183); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183)); /* "pysam/csamtools.pyx":3297 * * if self.plp == NULL or self.plp[0] == NULL: * raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<< * * # warning: there could be problems if self.n and self.buf are */ __pyx_k_tuple_185 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_184)); if (unlikely(!__pyx_k_tuple_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3297; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_185); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_185)); /* "pysam/csamtools.pyx":3310 * * def __init__(self): * raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<< * * def __str__(self): */ __pyx_k_tuple_186 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_182)); if (unlikely(!__pyx_k_tuple_186)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3310; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_186); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_186)); /* "pysam/csamtools.pyx":3423 * # recover. 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if (unlikely(!__pyx_k_codeobj_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pysam/csamtools.pyx":340 * class StderrStoreWindows(): * '''does nothing. stderr can't be redirected on windows''' * def __init__(self): pass # <<<<<<<<<<<<<< * def readAndRelease(self): return [] * def release(self): pass */ __pyx_k_tuple_286 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_286)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_286); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_286)); __pyx_k_codeobj_287 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_286, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s____init__, 340, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pysam/csamtools.pyx":341 * '''does nothing. stderr can't be redirected on windows''' * def __init__(self): pass * def readAndRelease(self): return [] # <<<<<<<<<<<<<< * def release(self): pass * */ __pyx_k_tuple_289 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_289); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_289)); __pyx_k_codeobj_290 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_289, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s__readAndRelease, 341, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_290)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pysam/csamtools.pyx":342 * def __init__(self): pass * def readAndRelease(self): return [] * def release(self): pass # <<<<<<<<<<<<<< * * if platform.system()=='Windows': */ __pyx_k_tuple_292 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_292); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_292)); __pyx_k_codeobj_293 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_292, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s__release, 342, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_293)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /* "pysam/csamtools.pyx":360 * * # order of records within sam headers * VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<< * * # type conversions within sam header records */ __pyx_k_tuple_296 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_n_s__CO)); if (unlikely(!__pyx_k_tuple_296)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_296); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_296)); /* "pysam/csamtools.pyx":370 * * # output order of fields within records * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<< * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), */ __pyx_k_tuple_297 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__SO), ((PyObject *)__pyx_n_s__GO)); if (unlikely(!__pyx_k_tuple_297)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_297); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_297)); /* "pysam/csamtools.pyx":371 * # output order of fields within records * VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<< * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } */ __pyx_k_tuple_298 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__SN), ((PyObject *)__pyx_n_s__LN), ((PyObject *)__pyx_n_s__AS), ((PyObject *)__pyx_n_s__M5), ((PyObject *)__pyx_n_s__UR), ((PyObject *)__pyx_n_s__SP)); 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__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_299)); /* "pysam/csamtools.pyx":373 * "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), * "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), * "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<< * * */ __pyx_k_tuple_300 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__PN), ((PyObject *)__pyx_n_s__ID), ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__CL), ((PyObject *)__pyx_n_s__PP)); if (unlikely(!__pyx_k_tuple_300)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_300); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_300)); /* "pysam/csamtools.pyx":3343 * class Outs: * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html''' * def __init__(self, id = 1): # <<<<<<<<<<<<<< * self.streams = [] * self.id = id */ __pyx_k_tuple_301 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__id)); if (unlikely(!__pyx_k_tuple_301)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_301); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_301)); __pyx_k_codeobj_302 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_301, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s____init__, 3343, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_302)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_k_tuple_303 = PyTuple_Pack(1, ((PyObject *)__pyx_int_1)); if (unlikely(!__pyx_k_tuple_303)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3343; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_303); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_303)); /* "pysam/csamtools.pyx":3347 * self.id = id * * def setdevice(self, filename): # <<<<<<<<<<<<<< * '''open an existing file, like "/dev/null"''' * fd = os.open(filename, os.O_WRONLY) */ __pyx_k_tuple_305 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename), ((PyObject *)__pyx_n_s__fd)); 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__pyx_vtabptr_5pysam_9csamtools_Samfile = &__pyx_vtable_5pysam_9csamtools_Samfile; __pyx_vtable_5pysam_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *))__pyx_f_5pysam_9csamtools_7Samfile__buildHeader; __pyx_vtable_5pysam_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_getCurrent; __pyx_vtable_5pysam_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_cnext; __pyx_vtable_5pysam_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_5pysam_9csamtools_7Samfile_write; __pyx_vtable_5pysam_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int))__pyx_f_5pysam_9csamtools_7Samfile__getrname; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__.doc = __pyx_doc_5pysam_9csamtools_7Samfile_42__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__; } } #endif if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_Samfile = &__pyx_type_5pysam_9csamtools_Samfile; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3253; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_PileupProxy = &__pyx_type_5pysam_9csamtools_PileupProxy; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3305; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_PileupRead = &__pyx_type_5pysam_9csamtools_PileupRead; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1575; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorRow = &__pyx_type_5pysam_9csamtools_IteratorRow; __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion = &__pyx_vtable_5pysam_9csamtools_IteratorRowRegion; __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent; __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext; __pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__; } } #endif if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1600; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorRowRegion = &__pyx_type_5pysam_9csamtools_IteratorRowRegion; __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll = &__pyx_vtable_5pysam_9csamtools_IteratorRowAll; __pyx_vtable_5pysam_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent; __pyx_vtable_5pysam_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext; __pyx_type_5pysam_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__; } } #endif if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1684; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorRowAll = &__pyx_type_5pysam_9csamtools_IteratorRowAll; __pyx_type_5pysam_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__; } } #endif if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = &__pyx_type_5pysam_9csamtools_IteratorRowAllRefs; __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection = &__pyx_vtable_5pysam_9csamtools_IteratorRowSelection; __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent; __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext; __pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__; ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__; } } #endif if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorRowSelection = &__pyx_type_5pysam_9csamtools_IteratorRowSelection; __pyx_vtabptr_5pysam_9csamtools_IteratorColumn = &__pyx_vtable_5pysam_9csamtools_IteratorColumn; __pyx_vtable_5pysam_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_cnext; __pyx_vtable_5pysam_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence; __pyx_vtable_5pysam_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask; __pyx_vtable_5pysam_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData; __pyx_vtable_5pysam_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_reset; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1924; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5pysam_9csamtools_IteratorColumn = &__pyx_type_5pysam_9csamtools_IteratorColumn; __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion = &__pyx_vtable_5pysam_9csamtools_IteratorColumnRegion; __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn; __pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn; if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_CPYTHON { PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base; 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result = PyObject_GetAttr(dict, name); if (!result) { if (dict != __pyx_b) { PyErr_Clear(); result = PyObject_GetAttr(__pyx_b, name); } if (!result) { PyErr_SetObject(PyExc_NameError, name); } } return result; } #if CYTHON_PROFILE static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno) { if (*frame == NULL || !CYTHON_PROFILE_REUSE_FRAME) { if (*code == NULL) { *code = __Pyx_createFrameCodeObject(funcname, srcfile, firstlineno); if (*code == NULL) return 0; } *frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate*/ *code, /*PyCodeObject *code*/ PyModule_GetDict(__pyx_m), /*PyObject *globals*/ 0 /*PyObject *locals*/ ); if (*frame == NULL) return 0; } else { (*frame)->f_tstate = PyThreadState_GET(); } return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0; } static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) { PyObject *py_srcfile = 0; PyObject *py_funcname = 0; PyCodeObject *py_code = 0; #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); py_srcfile = PyString_FromString(srcfile); #else py_funcname = PyUnicode_FromString(funcname); py_srcfile = PyUnicode_FromString(srcfile); #endif if (!py_funcname | !py_srcfile) goto bad; py_code = PyCode_New( 0, /*int argcount,*/ #if PY_MAJOR_VERSION >= 3 0, /*int kwonlyargcount,*/ #endif 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ firstlineno, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return py_code; } #endif /* CYTHON_PROFILE */ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* cstring, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { Py_ssize_t length; if (unlikely((start < 0) | (stop < 0))) { length = strlen(cstring); if (start < 0) { start += length; if (start < 0) start = 0; } if (stop < 0) stop += length; } length = stop - start; if (unlikely(length <= 0)) return PyUnicode_FromUnicode(NULL, 0); cstring += start; if (decode_func) { return decode_func(cstring, length, errors); } else { return PyUnicode_Decode(cstring, length, encoding, errors); } } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; tstate->curexc_type = type; tstate->curexc_value = value; tstate->curexc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_Restore(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(type, value, tb); #endif } #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { Py_XINCREF(type); if (!value || value == Py_None) value = NULL; else Py_INCREF(value); if (!tb || tb == Py_None) tb = NULL; else { Py_INCREF(tb); if (!PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto raise_error; } } #if PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); value = Py_None; } #endif PyErr_NormalizeException(&type, &value, &tb); } else { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto raise_error; } value = type; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto raise_error; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { tb = 0; } else if (tb && !PyTraceBack_Check(tb)) { PyErr_SetString(PyExc_TypeError, "raise: arg 3 must be a traceback or None"); goto bad; } if (value == Py_None) value = 0; if (PyExceptionInstance_Check(type)) { if (value) { PyErr_SetString(PyExc_TypeError, "instance exception may not have a separate value"); goto bad; } value = type; type = (PyObject*) Py_TYPE(value); } else if (PyExceptionClass_Check(type)) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyEval_CallObject(type, args); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } if (cause && cause != Py_None) { PyObject *fixed_cause; if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { Py_INCREF(tb); tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } } bad: Py_XDECREF(owned_instance); return; } #endif static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (likely(PyObject_TypeCheck(obj, type))) return 1; PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", Py_TYPE(obj)->tp_name, type->tp_name); return 0; } static CYTHON_INLINE int __Pyx_CheckKeywordStrings( PyObject *kwdict, const char* function_name, int kw_allowed) { PyObject* key = 0; Py_ssize_t pos = 0; #if CPYTHON_COMPILING_IN_PYPY if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0)) goto invalid_keyword; return 1; #else while (PyDict_Next(kwdict, &pos, &key, 0)) { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) #endif if (unlikely(!PyUnicode_Check(key))) goto invalid_keyword_type; } if ((!kw_allowed) && unlikely(key)) goto invalid_keyword; return 1; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); return 0; #endif invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif return 0; } static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) { PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname); } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; #endif Py_INCREF(local_type); Py_INCREF(local_value); Py_INCREF(local_tb); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; /* Make sure tstate is in a consistent state when we XDECREF these objects (DECREF may run arbitrary code). */ Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (!type) { PyErr_Format(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (Py_TYPE(obj) == type) return 1; } else { if (PyObject_TypeCheck(obj, type)) return 1; } PyErr_Format(PyExc_TypeError, "Argument '%s' has incorrect type (expected %s, got %s)", name, type->tp_name, Py_TYPE(obj)->tp_name); return 0; } static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static CYTHON_INLINE long __Pyx_div_long(long a, long b) { long q = a / b; long r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE long __Pyx_mod_long(long a, long b) { long r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_traverse != current_tp_traverse) type = type->tp_base; while (type && type->tp_traverse == current_tp_traverse) type = type->tp_base; if (type && type->tp_traverse) return type->tp_traverse(obj, v, a); return 0; } static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { PyTypeObject* type = Py_TYPE(obj); while (type && type->tp_clear != current_tp_clear) type = type->tp_base; while (type && type->tp_clear == current_tp_clear) type = type->tp_base; if (type && type->tp_clear) type->tp_clear(obj); } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) { PyObject *metaclass; #if PY_MAJOR_VERSION < 3 if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = PyObject_GetAttrString(base, (char *)"__class__"); if (!metaclass) { PyErr_Clear(); metaclass = (PyObject*) Py_TYPE(base); } } else { metaclass = (PyObject *) &PyClass_Type; } #else if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) { PyObject *base = PyTuple_GET_ITEM(bases, 0); metaclass = (PyObject*) Py_TYPE(base); } else { metaclass = (PyObject *) &PyType_Type; } #endif Py_INCREF(metaclass); return metaclass; } static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name, PyObject *qualname, PyObject *modname) { PyObject *result; PyObject *metaclass; if (PyDict_SetItemString(dict, "__module__", modname) < 0) return NULL; if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0) return NULL; metaclass = PyDict_GetItemString(dict, "__metaclass__"); if (metaclass) { Py_INCREF(metaclass); } else { metaclass = __Pyx_FindPy2Metaclass(bases); } result = PyObject_CallFunctionObjArgs(metaclass, name, bases, dict, NULL); Py_DECREF(metaclass); return result; } static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { if (op->func.m_ml->ml_doc) { #if PY_MAJOR_VERSION >= 3 op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc); #else op->func_doc = PyString_FromString(op->func.m_ml->ml_doc); #endif if (unlikely(op->func_doc == NULL)) return NULL; } else { Py_INCREF(Py_None); return Py_None; } } Py_INCREF(op->func_doc); return op->func_doc; } static int __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp = op->func_doc; if (value == NULL) value = Py_None; /* Mark as deleted */ Py_INCREF(value); op->func_doc = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op) { if (unlikely(op->func_name == NULL)) { #if PY_MAJOR_VERSION >= 3 op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name); #else op->func_name = PyString_InternFromString(op->func.m_ml->ml_name); #endif if (unlikely(op->func_name == NULL)) return NULL; } Py_INCREF(op->func_name); return op->func_name; } static int __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__name__ must be set to a string object"); return -1; } tmp = op->func_name; Py_INCREF(value); op->func_name = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op) { Py_INCREF(op->func_qualname); return op->func_qualname; } static int __Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 if (unlikely(value == NULL || !PyUnicode_Check(value))) { #else if (unlikely(value == NULL || !PyString_Check(value))) { #endif PyErr_SetString(PyExc_TypeError, "__qualname__ must be set to a string object"); return -1; } tmp = op->func_qualname; Py_INCREF(value); op->func_qualname = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure) { PyObject *self; self = m->func_closure; if (self == NULL) self = Py_None; Py_INCREF(self); return self; } static PyObject * __Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op) { if (unlikely(op->func_dict == NULL)) { op->func_dict = PyDict_New(); if (unlikely(op->func_dict == NULL)) return NULL; } Py_INCREF(op->func_dict); return op->func_dict; } static int __Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value) { PyObject *tmp; if (unlikely(value == NULL)) { PyErr_SetString(PyExc_TypeError, "function's dictionary may not be deleted"); return -1; } if (unlikely(!PyDict_Check(value))) { PyErr_SetString(PyExc_TypeError, "setting function's dictionary to a non-dict"); return -1; } tmp = op->func_dict; Py_INCREF(value); op->func_dict = value; Py_XDECREF(tmp); return 0; } static PyObject * __Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op) { PyObject* dict = PyModule_GetDict(__pyx_m); Py_XINCREF(dict); return dict; } static PyObject * __Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op) { Py_INCREF(Py_None); return Py_None; } static PyObject * __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) { PyObject* result = (op->func_code) ? op->func_code : Py_None; Py_INCREF(result); return result; } static PyObject * __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) { if (op->defaults_tuple) { Py_INCREF(op->defaults_tuple); return op->defaults_tuple; } if (op->defaults_getter) { PyObject *res = op->defaults_getter((PyObject *) op); if (likely(res)) { Py_INCREF(res); op->defaults_tuple = res; } return res; } Py_INCREF(Py_None); return Py_None; } static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0}, {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0}, {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0}, {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0}, {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0}, {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0}, {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0}, {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0}, {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0}, {0, 0, 0, 0, 0} }; #ifndef PY_WRITE_RESTRICTED /* < Py2.5 */ #define PY_WRITE_RESTRICTED WRITE_RESTRICTED #endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} }; static PyObject * __Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromString(m->func.m_ml->ml_name); #else return PyString_FromString(m->func.m_ml->ml_name); #endif } static PyMethodDef __pyx_CyFunction_methods[] = { {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0}, {0, 0, 0, 0} }; static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname, PyObject *closure, PyObject *module, PyObject* code) { __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type); if (op == NULL) return NULL; op->flags = flags; op->func_weakreflist = NULL; op->func.m_ml = ml; op->func.m_self = (PyObject *) op; Py_XINCREF(closure); op->func_closure = closure; Py_XINCREF(module); op->func.m_module = module; op->func_dict = NULL; op->func_name = NULL; Py_INCREF(qualname); op->func_qualname = qualname; op->func_doc = NULL; op->func_classobj = NULL; Py_XINCREF(code); op->func_code = code; op->defaults_pyobjects = 0; op->defaults = NULL; op->defaults_tuple = NULL; op->defaults_getter = NULL; PyObject_GC_Track(op); return (PyObject *) op; } static int __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) { Py_CLEAR(m->func_closure); Py_CLEAR(m->func.m_module); Py_CLEAR(m->func_dict); Py_CLEAR(m->func_name); Py_CLEAR(m->func_qualname); Py_CLEAR(m->func_doc); Py_CLEAR(m->func_code); Py_CLEAR(m->func_classobj); Py_CLEAR(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_XDECREF(pydefaults[i]); PyMem_Free(m->defaults); m->defaults = NULL; } return 0; } static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m) { PyObject_GC_UnTrack(m); if (m->func_weakreflist != NULL) PyObject_ClearWeakRefs((PyObject *) m); __Pyx_CyFunction_clear(m); PyObject_GC_Del(m); } static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg) { Py_VISIT(m->func_closure); Py_VISIT(m->func.m_module); Py_VISIT(m->func_dict); Py_VISIT(m->func_name); Py_VISIT(m->func_qualname); Py_VISIT(m->func_doc); Py_VISIT(m->func_code); Py_VISIT(m->func_classobj); Py_VISIT(m->defaults_tuple); if (m->defaults) { PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m); int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_VISIT(pydefaults[i]); } return 0; } static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) { Py_INCREF(func); return func; } if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) { if (type == NULL) type = (PyObject *)(Py_TYPE(obj)); return PyMethod_New(func, type, (PyObject *)(Py_TYPE(type))); } if (obj == Py_None) obj = NULL; return PyMethod_New(func, obj, type); } static PyObject* __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) { #if PY_MAJOR_VERSION >= 3 return PyUnicode_FromFormat("", op->func_qualname, (void *)op); #else return PyString_FromFormat("", PyString_AsString(op->func_qualname), (void *)op); #endif } #if CYTHON_COMPILING_IN_PYPY static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyCFunctionObject* f = (PyCFunctionObject*)func; PyCFunction meth = PyCFunction_GET_FUNCTION(func); PyObject *self = PyCFunction_GET_SELF(func); Py_ssize_t size; switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { case METH_VARARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) return (*meth)(self, arg); break; case METH_VARARGS | METH_KEYWORDS: return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); case METH_NOARGS: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 0) return (*meth)(self, NULL); PyErr_Format(PyExc_TypeError, "%.200s() takes no arguments (%zd given)", f->m_ml->ml_name, size); return NULL; } break; case METH_O: if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); if (size == 1) return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); PyErr_Format(PyExc_TypeError, "%.200s() takes exactly one argument (%zd given)", f->m_ml->ml_name, size); return NULL; } break; default: PyErr_SetString(PyExc_SystemError, "Bad call flags in " "__Pyx_CyFunction_Call. METH_OLDARGS is no " "longer supported!"); return NULL; } PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments", f->m_ml->ml_name); return NULL; } #else static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { return PyCFunction_Call(func, arg, kw); } #endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ __Pyx_CyFunction_Call, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_CyFunction_methods, /*tp_methods*/ __pyx_CyFunction_members, /*tp_members*/ __pyx_CyFunction_getsets, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ __Pyx_CyFunction_descr_get, /*tp_descr_get*/ 0, /*tp_descr_set*/ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ 0, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static int __Pyx_CyFunction_init(void) { #if !CYTHON_COMPILING_IN_PYPY __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; #endif if (PyType_Ready(&__pyx_CyFunctionType_type) < 0) return -1; __pyx_CyFunctionType = &__pyx_CyFunctionType_type; return 0; } static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, sizeof(size)); m->defaults_pyobjects = pyobjects; return m->defaults; } static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; m->defaults_tuple = tuple; Py_INCREF(tuple); } static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) { const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint64_t) == sizeof(char)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint64_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint64_t) == sizeof(short)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint64_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint64_t) == sizeof(int)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint64_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint64_t) == sizeof(long)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint64_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else uint64_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (uint64_t)-1; } } static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint32_t) == sizeof(char)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint32_t) == sizeof(short)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint32_t) == sizeof(int)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint32_t) == sizeof(long)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else uint32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (uint32_t)-1; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t val) { const int8_t neg_one = (int8_t)-1, const_zero = (int8_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int8_t) == sizeof(char)) || (sizeof(int8_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int8_t) == sizeof(int)) || (sizeof(int8_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int8_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint8_t(uint8_t val) { const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint8_t) == sizeof(char)) || (sizeof(uint8_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint8_t) == sizeof(int)) || (sizeof(uint8_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint8_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int16_t(int16_t val) { const int16_t neg_one = (int16_t)-1, const_zero = (int16_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int16_t) == sizeof(char)) || (sizeof(int16_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int16_t) == sizeof(int)) || (sizeof(int16_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int16_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int16_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint16_t(uint16_t val) { const uint16_t neg_one = (uint16_t)-1, const_zero = (uint16_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint16_t) == sizeof(char)) || (sizeof(uint16_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint16_t) == sizeof(int)) || (sizeof(uint16_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint16_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint16_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t val) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int32_t) == sizeof(char)) || (sizeof(int32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int32_t) == sizeof(int)) || (sizeof(int32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int32_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) { const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint32_t) == sizeof(char)) || (sizeof(uint32_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint32_t) == sizeof(int)) || (sizeof(uint32_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint32_t), little, !is_unsigned); } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) { const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(int64_t) == sizeof(char)) || (sizeof(int64_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(int64_t) == sizeof(int)) || (sizeof(int64_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(int64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(int64_t), little, !is_unsigned); } } static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) { const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(uint8_t) == sizeof(char)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedChar(x); else return (uint8_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(uint8_t) == sizeof(short)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedShort(x); else return (uint8_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(uint8_t) == sizeof(int)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedInt(x); else return (uint8_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(uint8_t) == sizeof(long)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedLong(x); else return (uint8_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(uint8_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (uint8_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else uint8_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (uint8_t)-1; } } static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) { const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0; const int is_unsigned = const_zero < neg_one; if (sizeof(int32_t) == sizeof(char)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedChar(x); else return (int32_t)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(int32_t) == sizeof(short)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedShort(x); else return (int32_t)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(int32_t) == sizeof(int)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedInt(x); else return (int32_t)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(int32_t) == sizeof(long)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(int32_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (int32_t)__Pyx_PyInt_AsUnsignedLongLong(x); else return (int32_t)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else int32_t val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_VERSION_HEX < 0x03000000 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (int32_t)-1; } } static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint64_t(uint64_t val) { const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0; const int is_unsigned = const_zero < neg_one; if ((sizeof(uint64_t) == sizeof(char)) || (sizeof(uint64_t) == sizeof(short))) { return PyInt_FromLong((long)val); } else if ((sizeof(uint64_t) == sizeof(int)) || (sizeof(uint64_t) == sizeof(long))) { if (is_unsigned) return PyLong_FromUnsignedLong((unsigned long)val); else return PyInt_FromLong((long)val); } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG)val); else return PyLong_FromLongLong((PY_LONG_LONG)val); } else { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; return _PyLong_FromByteArray(bytes, sizeof(uint64_t), little, !is_unsigned); } } static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject* x) { const long neg_one = (long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_VERSION_HEX < 0x03000000 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)val; } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; #else PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); PyErr_SetExcInfo(*type, *value, *tb); #endif *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } static PyObject *__Pyx_Generator_Next(PyObject *self); static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); static PyObject *__Pyx_Generator_Close(PyObject *self); static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); static PyTypeObject *__pyx_GeneratorType = 0; #define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) #define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { PyObject *et, *ev, *tb; PyObject *value = NULL; __Pyx_ErrFetch(&et, &ev, &tb); if (!et) { Py_XDECREF(tb); Py_XDECREF(ev); Py_INCREF(Py_None); *pvalue = Py_None; return 0; } if (unlikely(et != PyExc_StopIteration) && unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) { __Pyx_ErrRestore(et, ev, tb); return -1; } if (likely(et == PyExc_StopIteration)) { if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) { if (!ev) { Py_INCREF(Py_None); ev = Py_None; } Py_XDECREF(tb); Py_DECREF(et); *pvalue = ev; return 0; } } PyErr_NormalizeException(&et, &ev, &tb); if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) { __Pyx_ErrRestore(et, ev, tb); return -1; } Py_XDECREF(tb); Py_DECREF(et); #if PY_VERSION_HEX >= 0x030300A0 value = ((PyStopIterationObject *)ev)->value; Py_INCREF(value); Py_DECREF(ev); #else { PyObject* args = PyObject_GetAttrString(ev, "args"); Py_DECREF(ev); if (likely(args)) { value = PyObject_GetItem(args, 0); Py_DECREF(args); } if (unlikely(!value)) { __Pyx_ErrRestore(NULL, NULL, NULL); Py_INCREF(Py_None); value = Py_None; } } #endif *pvalue = value; return 0; } #endif static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) { PyObject *exc_type = self->exc_type; PyObject *exc_value = self->exc_value; PyObject *exc_traceback = self->exc_traceback; self->exc_type = NULL; self->exc_value = NULL; self->exc_traceback = NULL; Py_XDECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_traceback); } static CYTHON_INLINE int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) { if (unlikely(gen->is_running)) { PyErr_SetString(PyExc_ValueError, "generator already executing"); return 1; } return 0; } static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) { PyObject *retval; assert(!self->is_running); if (unlikely(self->resume_label == 0)) { if (unlikely(value && value != Py_None)) { PyErr_SetString(PyExc_TypeError, "can't send non-None value to a " "just-started generator"); return NULL; } } if (unlikely(self->resume_label == -1)) { PyErr_SetNone(PyExc_StopIteration); return NULL; } if (value) { #if CYTHON_COMPILING_IN_PYPY #else /* Generators always return to their most recent caller, not * necessarily their creator. */ if (self->exc_traceback) { PyThreadState *tstate = PyThreadState_GET(); PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; PyFrameObject *f = tb->tb_frame; Py_XINCREF(tstate->frame); assert(f->f_back == NULL); f->f_back = tstate->frame; } #endif __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); } else { __Pyx_Generator_ExceptionClear(self); } self->is_running = 1; retval = self->body((PyObject *) self, value); self->is_running = 0; if (retval) { __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); #if CYTHON_COMPILING_IN_PYPY #else /* Don't keep the reference to f_back any longer than necessary. It * may keep a chain of frames alive or it could create a reference * cycle. */ if (self->exc_traceback) { PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; PyFrameObject *f = tb->tb_frame; Py_CLEAR(f->f_back); } #endif } else { __Pyx_Generator_ExceptionClear(self); } return retval; } static CYTHON_INLINE PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) { PyObject *ret; PyObject *val = NULL; __Pyx_Generator_Undelegate(gen); __Pyx_PyGen_FetchStopIterationValue(&val); ret = __Pyx_Generator_SendEx(gen, val); Py_XDECREF(val); return ret; } static PyObject *__Pyx_Generator_Next(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; PyObject *yf = gen->yieldfrom; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; gen->is_running = 1; ret = Py_TYPE(yf)->tp_iternext(yf); gen->is_running = 0; if (likely(ret)) { return ret; } return __Pyx_Generator_FinishDelegation(gen); } return __Pyx_Generator_SendEx(gen, Py_None); } static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; PyObject *yf = gen->yieldfrom; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; gen->is_running = 1; if (__Pyx_Generator_CheckExact(yf)) { ret = __Pyx_Generator_Send(yf, value); } else { if (value == Py_None) ret = PyIter_Next(yf); else ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value); } gen->is_running = 0; if (likely(ret)) { return ret; } return __Pyx_Generator_FinishDelegation(gen); } return __Pyx_Generator_SendEx(gen, value); } static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) { PyObject *retval = NULL; int err = 0; if (__Pyx_Generator_CheckExact(yf)) { retval = __Pyx_Generator_Close(yf); if (!retval) return -1; } else { PyObject *meth; gen->is_running = 1; meth = PyObject_GetAttrString(yf, "close"); if (unlikely(!meth)) { if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_WriteUnraisable(yf); } PyErr_Clear(); } else { retval = PyObject_CallFunction(meth, NULL); Py_DECREF(meth); if (!retval) err = -1; } gen->is_running = 0; } Py_XDECREF(retval); return err; } static PyObject *__Pyx_Generator_Close(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *retval, *raised_exception; PyObject *yf = gen->yieldfrom; int err = 0; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { Py_INCREF(yf); err = __Pyx_Generator_CloseIter(gen, yf); __Pyx_Generator_Undelegate(gen); Py_DECREF(yf); } if (err == 0) #if PY_VERSION_HEX < 0x02050000 PyErr_SetNone(PyExc_StopIteration); #else PyErr_SetNone(PyExc_GeneratorExit); #endif retval = __Pyx_Generator_SendEx(gen, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, "generator ignored GeneratorExit"); return NULL; } raised_exception = PyErr_Occurred(); if (!raised_exception || raised_exception == PyExc_StopIteration #if PY_VERSION_HEX >= 0x02050000 || raised_exception == PyExc_GeneratorExit || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit) #endif || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration)) { if (raised_exception) PyErr_Clear(); /* ignore these errors */ Py_INCREF(Py_None); return Py_None; } return NULL; } static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; PyObject *yf = gen->yieldfrom; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; Py_INCREF(yf); #if PY_VERSION_HEX >= 0x02050000 if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) { int err = __Pyx_Generator_CloseIter(gen, yf); Py_DECREF(yf); __Pyx_Generator_Undelegate(gen); if (err < 0) return __Pyx_Generator_SendEx(gen, NULL); goto throw_here; } #endif gen->is_running = 1; if (__Pyx_Generator_CheckExact(yf)) { ret = __Pyx_Generator_Throw(yf, args); } else { PyObject *meth = PyObject_GetAttrString(yf, "throw"); if (unlikely(!meth)) { Py_DECREF(yf); if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { gen->is_running = 0; return NULL; } PyErr_Clear(); __Pyx_Generator_Undelegate(gen); gen->is_running = 0; goto throw_here; } ret = PyObject_CallObject(meth, args); Py_DECREF(meth); } gen->is_running = 0; Py_DECREF(yf); if (!ret) { ret = __Pyx_Generator_FinishDelegation(gen); } return ret; } throw_here: __Pyx_Raise(typ, val, tb, NULL); return __Pyx_Generator_SendEx(gen, NULL); } static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_VISIT(gen->closure); Py_VISIT(gen->classobj); Py_VISIT(gen->yieldfrom); Py_VISIT(gen->exc_type); Py_VISIT(gen->exc_value); Py_VISIT(gen->exc_traceback); return 0; } static int __Pyx_Generator_clear(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_CLEAR(gen->closure); Py_CLEAR(gen->classobj); Py_CLEAR(gen->yieldfrom); Py_CLEAR(gen->exc_type); Py_CLEAR(gen->exc_value); Py_CLEAR(gen->exc_traceback); return 0; } static void __Pyx_Generator_dealloc(PyObject *self) { __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject_GC_UnTrack(gen); if (gen->gi_weakreflist != NULL) PyObject_ClearWeakRefs(self); PyObject_GC_Track(self); if (gen->resume_label > 0) { Py_TYPE(gen)->tp_del(self); if (self->ob_refcnt > 0) return; /* resurrected. :( */ } PyObject_GC_UnTrack(self); __Pyx_Generator_clear(self); PyObject_GC_Del(gen); } static void __Pyx_Generator_del(PyObject *self) { PyObject *res; PyObject *error_type, *error_value, *error_traceback; __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; if (gen->resume_label <= 0) return ; assert(self->ob_refcnt == 0); self->ob_refcnt = 1; __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); res = __Pyx_Generator_Close(self); if (res == NULL) PyErr_WriteUnraisable(self); else Py_DECREF(res); __Pyx_ErrRestore(error_type, error_value, error_traceback); /* Undo the temporary resurrection; can't use DECREF here, it would * cause a recursive call. */ assert(self->ob_refcnt > 0); if (--self->ob_refcnt == 0) return; /* this is the normal path out */ /* close() resurrected it! Make it look like the original Py_DECREF * never happened. */ { Py_ssize_t refcnt = self->ob_refcnt; _Py_NewReference(self); self->ob_refcnt = refcnt; } #if CYTHON_COMPILING_FOR_CPYTHON assert(PyType_IS_GC(self->ob_type) && _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED); /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so * we need to undo that. */ _Py_DEC_REFTOTAL; #endif /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object * chain, so no more to do there. * If COUNT_ALLOCS, the original decref bumped tp_frees, and * _Py_NewReference bumped tp_allocs: both of those need to be * undone. */ #ifdef COUNT_ALLOCS --Py_TYPE(self)->tp_frees; --Py_TYPE(self)->tp_allocs; #endif } static PyMemberDef __pyx_Generator_memberlist[] = { {(char *) "gi_running", #if PY_VERSION_HEX >= 0x02060000 T_BOOL, #else T_BYTE, #endif offsetof(__pyx_GeneratorObject, is_running), READONLY, NULL}, {0, 0, 0, 0, 0} }; static PyMethodDef __pyx_Generator_methods[] = { {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, {0, 0, 0, 0} }; static PyTypeObject __pyx_GeneratorType_type = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("generator"), /*tp_name*/ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/ 0, /*tp_itemsize*/ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/ 0, /*tp_print*/ 0, /*tp_getattr*/ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ #else 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ 0, /*tp_as_sequence*/ 0, /*tp_as_mapping*/ 0, /*tp_hash*/ 0, /*tp_call*/ 0, /*tp_str*/ 0, /*tp_getattro*/ 0, /*tp_setattro*/ 0, /*tp_as_buffer*/ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/ 0, /*tp_doc*/ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */ 0, /*tp_iter*/ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/ __pyx_Generator_methods, /*tp_methods*/ __pyx_Generator_memberlist, /*tp_members*/ 0, /*tp_getset*/ 0, /*tp_base*/ 0, /*tp_dict*/ 0, /*tp_descr_get*/ 0, /*tp_descr_set*/ 0, /*tp_dictoffset*/ 0, /*tp_init*/ 0, /*tp_alloc*/ 0, /*tp_new*/ 0, /*tp_free*/ 0, /*tp_is_gc*/ 0, /*tp_bases*/ 0, /*tp_mro*/ 0, /*tp_cache*/ 0, /*tp_subclasses*/ 0, /*tp_weaklist*/ __Pyx_Generator_del, /*tp_del*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, PyObject *closure) { __pyx_GeneratorObject *gen = PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type); if (gen == NULL) return NULL; gen->body = body; gen->closure = closure; Py_XINCREF(closure); gen->is_running = 0; gen->resume_label = 0; gen->classobj = NULL; gen->yieldfrom = NULL; gen->exc_type = NULL; gen->exc_value = NULL; gen->exc_traceback = NULL; gen->gi_weakreflist = NULL; PyObject_GC_Track(gen); return gen; } static int __pyx_Generator_init(void) { __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr; __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter; if (PyType_Ready(&__pyx_GeneratorType_type)) { return -1; } __pyx_GeneratorType = &__pyx_GeneratorType_type; return 0; } static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); #if PY_MAJOR_VERSION < 3 ctx = PyString_FromString(name); #else ctx = PyUnicode_FromString(name); #endif __Pyx_ErrRestore(old_exc, old_val, old_tb); if (!ctx) { PyErr_WriteUnraisable(Py_None); } else { PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } } static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } return 0; } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) PyObject *ob = PyCapsule_New(vtable, 0, 0); #else PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); #endif if (!ob) goto bad; if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) goto bad; Py_DECREF(ob); return 0; bad: Py_XDECREF(ob); return -1; } #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; PyObject *py_module = 0; py_name = __Pyx_PyIdentifier_FromString(name); if (!py_name) goto bad; py_module = PyImport_Import(py_name); Py_DECREF(py_name); return py_module; bad: Py_XDECREF(py_name); return 0; } #endif #ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) { PyObject *py_module = 0; PyObject *result = 0; PyObject *py_name = 0; char warning[200]; Py_ssize_t basicsize; #ifdef Py_LIMITED_API PyObject *py_basicsize; #endif py_module = __Pyx_ImportModule(module_name); if (!py_module) goto bad; py_name = __Pyx_PyIdentifier_FromString(class_name); if (!py_name) goto bad; result = PyObject_GetAttr(py_module, py_name); Py_DECREF(py_name); py_name = 0; Py_DECREF(py_module); py_module = 0; if (!result) goto bad; if (!PyType_Check(result)) { PyErr_Format(PyExc_TypeError, "%s.%s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { start = mid + 1; } else { return mid; } } if (code_line <= entries[mid].code_line) { return mid; } else { return mid + 1; } } static PyCodeObject *__pyx_find_code_object(int code_line) { PyCodeObject* code_object; int pos; if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { return NULL; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { return NULL; } code_object = __pyx_code_cache.entries[pos].code_object; Py_INCREF(code_object); return code_object; } static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { int pos, i; __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; if (unlikely(!code_line)) { return; } if (unlikely(!entries)) { entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); if (likely(entries)) { __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = 64; __pyx_code_cache.count = 1; entries[0].code_line = code_line; entries[0].code_object = code_object; Py_INCREF(code_object); } return; } pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { PyCodeObject* tmp = entries[pos].code_object; entries[pos].code_object = code_object; Py_DECREF(tmp); return; } if (__pyx_code_cache.count == __pyx_code_cache.max_count) { int new_max = __pyx_code_cache.max_count + 64; entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __pyx_empty_bytes, /*PyObject *code,*/ __pyx_empty_tuple, /*PyObject *consts,*/ __pyx_empty_tuple, /*PyObject *names,*/ __pyx_empty_tuple, /*PyObject *varnames,*/ __pyx_empty_tuple, /*PyObject *freevars,*/ __pyx_empty_tuple, /*PyObject *cellvars,*/ py_srcfile, /*PyObject *filename,*/ py_funcname, /*PyObject *name,*/ py_line, /*int firstlineno,*/ __pyx_empty_bytes /*PyObject *lnotab*/ ); Py_DECREF(py_srcfile); Py_DECREF(py_funcname); return py_code; bad: Py_XDECREF(py_srcfile); Py_XDECREF(py_funcname); return NULL; } static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_globals = 0; PyFrameObject *py_frame = 0; py_code = __pyx_find_code_object(c_line ? c_line : py_line); if (!py_code) { py_code = __Pyx_CreateCodeObjectForTraceback( funcname, c_line, py_line, filename); if (!py_code) goto bad; __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } py_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*PyObject *globals,*/ 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); } else if (t->intern) { *t->p = PyString_InternFromString(t->s); } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } #else /* Python 3+ has unicode identifiers */ if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); } else if (t->encoding) { *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); } else { *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); } } else { *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); } #endif if (!*t->p) return -1; ++t; } return 0; } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_VERSION_HEX < 0x03000000 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_VERSION_HEX < 0x03000000 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_VERSION_HEX < 0x03000000 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%s__ returned non-%s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); if (!x) return -1; ival = PyInt_AsSsize_t(x); Py_DECREF(x); return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) { return (size_t)-1; } else if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */ pysam-0.7.7/pysam/tabix_util.h0000664000076400007650000000044112241337202016146 0ustar andreasandreas/* See issue 122 On some MACOSX systems getline is not defined. */ #include #include "kseq.h" #if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700) #include "unistd.h" ssize_t getline(char **line, size_t *linelen, FILE *fp); #endif KSTREAM_INIT( gzFile, gzread, 16384) pysam-0.7.7/pysam/Pileup.py0000664000076400007650000002016112075076733015460 0ustar andreasandreas'''Tools for working with files in the samtools pileup -c format.''' import collections import pysam PileupSubstitution = collections.namedtuple( "PileupSubstitution", " ".join( (\ "chromosome", "pos", "reference_base", "genotype", "consensus_quality", "snp_quality", "mapping_quality", "coverage", "read_bases", "base_qualities" ) ) ) PileupIndel = collections.namedtuple( "PileupIndel", " ".join( (\ "chromosome", "pos", "reference_base", "genotype", "consensus_quality", "snp_quality", "mapping_quality", "coverage", "first_allele", "second_allele", "reads_first", "reads_second", "reads_diff" ) ) ) def iterate( infile ): '''iterate over ``samtools pileup -c`` formatted file. *infile* can be any iterator over a lines. The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution` or :class:`pysam.Pileup.PileupIndel`. .. note:: The parser converts to 0-based coordinates ''' conv_subst = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str) conv_indel = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str,int,int,int) for line in infile: d = line[:-1].split() if d[2] == "*": try: yield PileupIndel( *[x(y) for x,y in zip(conv_indel,d) ] ) except TypeError: raise pysam.SamtoolsError( "parsing error in line: `%s`" % line) else: try: yield PileupSubstitution( *[x(y) for x,y in zip(conv_subst,d) ] ) except TypeError: raise pysam.SamtoolsError( "parsing error in line: `%s`" % line) ENCODE_GENOTYPE = { 'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'AA': 'A', 'CC': 'C', 'GG': 'G', 'TT': 'T', 'UU': 'U', 'AG': 'r', 'GA': 'R', 'CT': 'y', 'TC': 'Y', 'AC': 'm', 'CA': 'M', 'GT': 'k', 'TG': 'K', 'CG': 's', 'GC': 'S', 'AT': 'w', 'TA': 'W', } DECODE_GENOTYPE = { 'A': 'AA', 'C': 'CC', 'G': 'GG', 'T': 'TT', 'r': 'AG', 'R': 'AG', 'y': 'CT', 'Y': 'CT', 'm': 'AC', 'M': 'AC', 'k': 'GT', 'K': 'GT', 's': 'CG', 'S': 'CG', 'w': 'AT', 'W': 'AT', } ##------------------------------------------------------------ def encodeGenotype( code ): '''encode genotypes like GG, GA into a one-letter code. The returned code is lower case if code[0] < code[1], otherwise it is uppercase. ''' return ENCODE_GENOTYPE[ code.upper() ] def decodeGenotype( code ): '''decode single letter genotypes like m, M into two letters. This is the reverse operation to :meth:`encodeGenotype`. ''' return DECODE_GENOTYPE[ code ] def translateIndelGenotypeFromVCF( vcf_genotypes, ref ): '''translate indel from vcf to pileup format.''' # indels def getPrefix( s1, s2 ): '''get common prefix of strings s1 and s2.''' n = min( len( s1), len( s2 ) ) for x in range( n ): if s1[x] != s2[x]: return s1[:x] return s1[:n] def getSuffix( s1, s2 ): '''get common sufix of strings s1 and s2.''' n = min( len( s1), len( s2 ) ) if s1[-1] != s2[-1]: return "" for x in range( -2, -n - 1, -1 ): if s1[x] != s2[x]: return s1[x+1:] return s1[-n:] def getGenotype( variant, ref ): if variant == ref: return "*", 0 if len(ref) > len(variant): # is a deletion if ref.startswith(variant): return "-%s" % ref[len(variant):], len(variant) - 1 elif ref.endswith( variant ): return "-%s" % ref[:-len(variant)], -1 else: prefix = getPrefix( ref, variant ) suffix = getSuffix( ref, variant ) shared = len(prefix) + len(suffix) - len(variant) # print "-", prefix, suffix, ref, variant, shared, len(prefix), len(suffix), len(ref) if shared < 0: raise ValueError() return "-%s" % ref[len(prefix):-(len(suffix)-shared)], len(prefix) - 1 elif len(ref) < len(variant): # is an insertion if variant.startswith(ref): return "+%s" % variant[len(ref):], len(ref) - 1 elif variant.endswith(ref): return "+%s" % variant[:len(ref)], 0 else: prefix = getPrefix( ref, variant ) suffix = getSuffix( ref, variant ) shared = len(prefix) + len(suffix) - len(ref) if shared < 0: raise ValueError() return "+%s" % variant[len(prefix):-(len(suffix)-shared)], len(prefix) else: assert 0, "snp?" # in pileup, the position refers to the base # after the coordinate, hence subtract 1 #pos -= 1 genotypes, offsets = [], [] is_error = True for variant in vcf_genotypes: try: g, offset = getGenotype( variant, ref ) except ValueError: break genotypes.append( g ) if g != "*": offsets.append( offset ) else: is_error = False if is_error: raise ValueError() assert len(set(offsets )) == 1, "multiple offsets for indel" offset = offsets[0] genotypes = "/".join( genotypes ) return genotypes, offset def vcf2pileup( vcf, sample ): '''convert vcf record to pileup record.''' chromosome = vcf.contig pos = vcf.pos reference = vcf.ref allelles = [reference] + vcf.alt data = vcf[sample] # get genotype genotypes = data["GT"] if len(genotypes) > 1: raise ValueError( "only single genotype per position, %s" % (str(vcf))) genotypes = genotypes[0] # not a variant if genotypes[0] == ".": return None genotypes = [ allelles[int(x)] for x in genotypes if x != "/" ] # snp_quality is "genotype quality" snp_quality = consensus_quality = data.get( "GQ", [0])[0] mapping_quality = vcf.info.get( "MQ", [0])[0] coverage = data.get( "DP", 0) if len(reference) > 1 or max([len(x) for x in vcf.alt] ) > 1: # indel genotype, offset = translateIndelGenotypeFromVCF( genotypes, reference ) return PileupIndel( chromosome, pos + offset, "*", genotype, consensus_quality, snp_quality, mapping_quality, coverage, genotype, "<" * len(genotype), 0, 0, 0 ) else: genotype = encodeGenotype( "".join(genotypes) ) read_bases = "" base_qualities = "" return PileupSubstitution( chromosome, pos, reference, genotype, consensus_quality, snp_quality, mapping_quality, coverage, read_bases, base_qualities ) def iterate_from_vcf( infile, sample ): '''iterate over a vcf-formatted file. *infile* can be any iterator over a lines. The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution` or :class:`pysam.Pileup.PileupIndel`. Positions without a snp will be skipped. This method is wasteful and written to support same legacy code that expects samtools pileup output. Better use the vcf parser directly. ''' vcf = pysam.VCF() vcf.connect( infile ) if sample not in vcf.getsamples(): raise KeyErorr( "sample %s not vcf file" ) for row in vcf.fetch(): result = vcf2pileup( row, sample ) if result: yield result pysam-0.7.7/pysam/namedtuple.py0000664000076400007650000001170011700526652016351 0ustar andreasandreasfrom operator import itemgetter as _itemgetter from keyword import iskeyword as _iskeyword import sys as _sys def namedtuple(typename, field_names, verbose=False, rename=False): """Returns a new subclass of tuple with named fields. >>> Point = namedtuple('Point', 'x y') >>> Point.__doc__ # docstring for the new class 'Point(x, y)' >>> p = Point(11, y=22) # instantiate with positional args or keywords >>> p[0] + p[1] # indexable like a plain tuple 33 >>> x, y = p # unpack like a regular tuple >>> x, y (11, 22) >>> p.x + p.y # fields also accessable by name 33 >>> d = p._asdict() # convert to a dictionary >>> d['x'] 11 >>> Point(**d) # convert from a dictionary Point(x=11, y=22) >>> p._replace(x=100) # _replace() is like str.replace() but targets named fields Point(x=100, y=22) """ # Parse and validate the field names. Validation serves two purposes, # generating informative error messages and preventing template injection attacks. if isinstance(field_names, basestring): field_names = field_names.replace(',', ' ').split() # names separated by whitespace and/or commas field_names = tuple(map(str, field_names)) if rename: names = list(field_names) seen = set() for i, name in enumerate(names): if (not min(c.isalnum() or c=='_' for c in name) or _iskeyword(name) or not name or name[0].isdigit() or name.startswith('_') or name in seen): names[i] = '_%d' % i seen.add(name) field_names = tuple(names) for name in (typename,) + field_names: if not min(c.isalnum() or c=='_' for c in name): raise ValueError('Type names and field names can only contain alphanumeric characters and underscores: %r' % name) if _iskeyword(name): raise ValueError('Type names and field names cannot be a keyword: %r' % name) if name[0].isdigit(): raise ValueError('Type names and field names cannot start with a number: %r' % name) seen_names = set() for name in field_names: if name.startswith('_') and not rename: raise ValueError('Field names cannot start with an underscore: %r' % name) if name in seen_names: raise ValueError('Encountered duplicate field name: %r' % name) seen_names.add(name) # Create and fill-in the class template numfields = len(field_names) argtxt = repr(field_names).replace("'", "")[1:-1] # tuple repr without parens or quotes reprtxt = ', '.join('%s=%%r' % name for name in field_names) template = '''class %(typename)s(tuple): '%(typename)s(%(argtxt)s)' \n __slots__ = () \n _fields = %(field_names)r \n def __new__(_cls, %(argtxt)s): return _tuple.__new__(_cls, (%(argtxt)s)) \n @classmethod def _make(cls, iterable, new=tuple.__new__, len=len): 'Make a new %(typename)s object from a sequence or iterable' result = new(cls, iterable) if len(result) != %(numfields)d: raise TypeError('Expected %(numfields)d arguments, got %%d' %% len(result)) return result \n def __repr__(self): return '%(typename)s(%(reprtxt)s)' %% self \n def _asdict(self): 'Return a new dict which maps field names to their values' return dict(zip(self._fields, self)) \n def _replace(_self, **kwds): 'Return a new %(typename)s object replacing specified fields with new values' result = _self._make(map(kwds.pop, %(field_names)r, _self)) if kwds: raise ValueError('Got unexpected field names: %%r' %% kwds.keys()) return result \n def __getnewargs__(self): return tuple(self) \n\n''' % locals() for i, name in enumerate(field_names): template += ' %s = _property(_itemgetter(%d))\n' % (name, i) if verbose: print template # Execute the template string in a temporary namespace namespace = dict(_itemgetter=_itemgetter, __name__='namedtuple_%s' % typename, _property=property, _tuple=tuple) try: exec template in namespace except SyntaxError, e: raise SyntaxError(e.message + ':\n' + template) result = namespace[typename] # For pickling to work, the __module__ variable needs to be set to the frame # where the named tuple is created. Bypass this step in enviroments where # sys._getframe is not defined (Jython for example) or sys._getframe is not # defined for arguments greater than 0 (IronPython). try: result.__module__ = _sys._getframe(1).f_globals.get('__name__', '__main__') except (AttributeError, ValueError): pass return result pysam-0.7.7/pysam/__init__.py0000664000076400007650000001163312163100634015747 0ustar andreasandreasfrom pysam.csamtools import * from pysam.ctabix import * import pysam.csamtools as csamtools import pysam.ctabix as ctabix from pysam.cvcf import * import pysam.cvcf as cvcf import pysam.Pileup as Pileup import sys import os class SamtoolsError( Exception ): '''exception raised in case of an error incurred in the samtools library.''' def __init__(self, value): self.value = value def __str__(self): return repr(self.value) class SamtoolsDispatcher(object): '''samtools dispatcher. Emulates the samtools command line as module calls. Captures stdout and stderr. Raises a :class:`pysam.SamtoolsError` exception in case samtools exits with an error code other than 0. Some command line options are associated with parsers. For example, the samtools command "pileup -c" creates a tab-separated table on standard output. In order to associate parsers with options, an optional list of parsers can be supplied. The list will be processed in order checking for the presence of each option. If no parser is given or no appropriate parser is found, the stdout output of samtools commands will be returned. ''' dispatch=None parsers=None def __init__(self,dispatch, parsers): self.dispatch = dispatch self.parsers = parsers self.stderr = [] def __call__(self, *args, **kwargs): '''execute a samtools command ''' retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch, args ) if retval: raise SamtoolsError( 'csamtools returned with error %i: %s' % (retval, "\n".join( stderr ) )) self.stderr = stderr # samtools commands do not propagate the return code correctly. # I have thus added this patch to throw if there is output on stderr. # Note that there is sometimes output on stderr that is not an error, # for example: [sam_header_read2] 2 sequences loaded. # Ignore messages like these stderr = [ x for x in stderr \ if not (x.startswith( "[sam_header_read2]" ) or \ x.startswith("[bam_index_load]") or \ x.startswith("[bam_sort_core]") or \ x.startswith("[samopen] SAM header is present") ) ] if stderr: raise SamtoolsError( "\n".join( stderr ) ) # call parser for stdout: if not kwargs.get("raw") and stdout and self.parsers: for options, parser in self.parsers: for option in options: if option not in args: break else: return parser(stdout) return stdout def getMessages( self ): return self.stderr def usage(self): '''return the samtools usage information for this command''' retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch ) return "".join(stderr) # # samtools command line options to export in python # # import is a python reserved word. SAMTOOLS_DISPATCH = { # samtools 'documented' commands "view" : ( "view", None ), "sort" : ( "sort", None), "mpileup" : ( "mpileup", None), "depth" : ("depth", None), "faidx" : ("faidx", None), "tview" : ("tview", None), "index" : ("index", None), "idxstats" : ("idxstats", None), "fixmate" : ("fixmate", None), "flagstat" : ("flagstat", None), "calmd" : ("calmd", None), "merge" : ("merge", None), "rmdup" : ("rmdup", None), "reheader" : ("reheader", None), "cat" : ("cat", None), "targetcut" : ("targetcut", None), "phase" : ("phase", None), # others "samimport": ( "import", None), "bam2fq" : ("bam2fq", None), "pad2unpad" : ("pad2unpad", None), "depad" : ("pad2unpad", None), "bedcov" : ("bedcov", None), "bamshuf" : ("bamshuf", None), # obsolete # "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ), } # instantiate samtools commands as python functions for key, options in SAMTOOLS_DISPATCH.items(): cmd, parser = options globals()[key] = SamtoolsDispatcher(cmd, parser) # hack to export all the symbols from csamtools __all__ = \ csamtools.__all__ + \ ctabix.__all__ + \ cvcf.__all__ +\ [ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\ ["Pileup" ] from pysam.version import __version__, __samtools_version__ ########################################################### # Utility functions for compilation def get_include(): '''return a list of include directories.''' dirname = os.path.abspath(os.path.join(os.path.dirname(__file__))) return [ dirname, os.path.join(dirname, 'include', 'samtools'), os.path.join(dirname, 'include', 'tabix') ] def get_defines(): '''return a list of defined compilation parameters.''' return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')] pysam-0.7.7/pysam/csamtools.pyx0000664000076400007650000043111112241543147016410 0ustar andreasandreas# cython: embedsignature=True # cython: profile=True # adds doc-strings for sphinx import tempfile import os import sys import types import itertools import struct import ctypes import collections import re import platform import warnings from cpython cimport PyErr_SetString, PyBytes_Check, PyUnicode_Check, PyBytes_FromStringAndSize from cpython.version cimport PY_MAJOR_VERSION ######################################################################## ######################################################################## ######################################################################## ## Python 3 compatibility functions ######################################################################## IS_PYTHON3 = PY_MAJOR_VERSION >= 3 cdef from_string_and_size(char* s, size_t length): if PY_MAJOR_VERSION < 3: return s[:length] else: return s[:length].decode("ascii") # filename encoding (copied from lxml.etree.pyx) cdef str _FILENAME_ENCODING _FILENAME_ENCODING = sys.getfilesystemencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = sys.getdefaultencoding() if _FILENAME_ENCODING is None: _FILENAME_ENCODING = 'ascii' #cdef char* _C_FILENAME_ENCODING #_C_FILENAME_ENCODING = _FILENAME_ENCODING cdef bytes _encodeFilename(object filename): """Make sure a filename is 8-bit encoded (or None).""" if filename is None: return None elif PyBytes_Check(filename): return filename elif PyUnicode_Check(filename): return filename.encode(_FILENAME_ENCODING) else: raise TypeError, u"Argument must be string or unicode." cdef bytes _force_bytes(object s): u"""convert string or unicode object to bytes, assuming ascii encoding. """ if PY_MAJOR_VERSION < 3: return s elif s is None: return None elif PyBytes_Check(s): return s elif PyUnicode_Check(s): return s.encode('ascii') else: raise TypeError, u"Argument must be string, bytes or unicode." cdef inline bytes _force_cmdline_bytes(object s): return _force_bytes(s) cdef _charptr_to_str(char* s): if PY_MAJOR_VERSION < 3: return s else: return s.decode("ascii") cdef _force_str(object s): """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)""" if s is None: return None if PY_MAJOR_VERSION < 3: return s elif PyBytes_Check(s): return s.decode('ascii') else: # assume unicode return s ######################################################################## ######################################################################## ######################################################################## ## Constants and global variables ######################################################################## # defines imported from samtools DEF SEEK_SET = 0 DEF SEEK_CUR = 1 DEF SEEK_END = 2 ## These are bits set in the flag. ## have to put these definitions here, in csamtools.pxd they got ignored ## @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */ DEF BAM_FPAIRED =1 ## @abstract the read is mapped in a proper pair */ DEF BAM_FPROPER_PAIR =2 ## @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */ DEF BAM_FUNMAP =4 ## @abstract the mate is unmapped */ DEF BAM_FMUNMAP =8 ## @abstract the read is mapped to the reverse strand */ DEF BAM_FREVERSE =16 ## @abstract the mate is mapped to the reverse strand */ DEF BAM_FMREVERSE =32 ## @abstract this is read1 */ DEF BAM_FREAD1 =64 ## @abstract this is read2 */ DEF BAM_FREAD2 =128 ## @abstract not primary alignment */ DEF BAM_FSECONDARY =256 ## @abstract QC failure */ DEF BAM_FQCFAIL =512 ## @abstract optical or PCR duplicate */ DEF BAM_FDUP =1024 ##################################################################### # CIGAR operations DEF BAM_CIGAR_SHIFT=4 DEF BAM_CIGAR_MASK=((1 << BAM_CIGAR_SHIFT) - 1) DEF BAM_CMATCH = 0 DEF BAM_CINS = 1 DEF BAM_CDEL = 2 DEF BAM_CREF_SKIP = 3 DEF BAM_CSOFT_CLIP = 4 DEF BAM_CHARD_CLIP = 5 DEF BAM_CPAD = 6 DEF BAM_CEQUAL = 7 DEF BAM_CDIFF = 8 cdef char* CODE2CIGAR= "MIDNSHP=X" if IS_PYTHON3: CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) else: CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" ) ##################################################################### ## set pysam stderr to /dev/null pysam_unset_stderr() ##################################################################### # hard-coded constants cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN" cdef int max_pos = 2 << 29 ##################################################################### ##################################################################### ##################################################################### ## private factory methods ##################################################################### cdef class AlignedRead cdef makeAlignedRead(bam1_t * src): '''enter src into AlignedRead.''' cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) dest._delegate = bam_dup1(src) return dest cdef class PileupProxy cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ): cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) dest.plp = plp dest.tid = tid dest.pos = pos dest.n = n return dest cdef class PileupRead cdef makePileupRead( bam_pileup1_t * src ): '''fill a PileupRead object from a bam_pileup1_t * object.''' cdef PileupRead dest = PileupRead.__new__(PileupRead) dest._alignment = makeAlignedRead( src.b ) dest._qpos = src.qpos dest._indel = src.indel dest._level = src.level dest._is_del = src.is_del dest._is_head = src.is_head dest._is_tail = src.is_tail return dest cdef class FastqProxy cdef makeFastqProxy( kseq_t * src): '''enter src into AlignedRead.''' cdef FastqProxy dest = FastqProxy.__new__(FastqProxy) dest._delegate = src return dest cdef convertBinaryTagToList( uint8_t * s ): """return bytesize, number of values list of values in s.""" cdef char auxtype cdef uint8_t byte_size cdef int32_t nvalues # get byte size auxtype = s[0] byte_size = bam_aux_type2size( auxtype ) s += 1 # get number of values in array nvalues = (s)[0] s += 4 # get values values = [] if auxtype == 'c': for x from 0 <= x < nvalues: values.append((s)[0]) s += 1 elif auxtype == 'C': for x from 0 <= x < nvalues: values.append((s)[0]) s += 1 elif auxtype == 's': for x from 0 <= x < nvalues: values.append((s)[0]) s += 2 elif auxtype == 'S': for x from 0 <= x < nvalues: values.append((s)[0]) s += 2 elif auxtype == 'i': for x from 0 <= x < nvalues: values.append((s)[0]) s += 4 elif auxtype == 'I': for x from 0 <= x < nvalues: values.append((s)[0]) s += 4 elif auxtype == 'f': for x from 0 <= x < nvalues: values.append((s)[0]) s += 4 return byte_size, nvalues, values ##################################################################### ##################################################################### ##################################################################### ## Generic callbacks for inserting python callbacks. ##################################################################### cdef int fetch_callback( bam1_t *alignment, void *f): '''callback for bam_fetch. calls function in *f* with a new :class:`AlignedRead` object as parameter. ''' a = makeAlignedRead( alignment ) (f)(a) class PileupColumn(object): '''A pileup column. A pileup column contains all the reads that map to a certain target base. tid chromosome ID as is defined in the header pos the target base coordinate (0-based) n number of reads mapping to this column pileups list of reads (:class:`pysam.PileupRead`) aligned to this column ''' def __str__(self): return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ "\n" + "\n".join( map(str, self.pileups) ) cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f): '''callback for pileup. calls function in *f* with a new :class:`Pileup` object as parameter. tid chromosome ID as is defined in the header pos start coordinate of the alignment, 0-based n number of elements in pl array pl array of alignments data user provided data ''' p = PileupColumn() p.tid = tid p.pos = pos p.n = n pileups = [] cdef int x for x from 0 <= x < n: pileups.append( makePileupRead( &(pl[x]) ) ) p.pileups = pileups (f)(p) cdef int pileup_fetch_callback( bam1_t *b, void *data): '''callback for bam_fetch. Fetches reads and submits them to pileup. ''' cdef bam_plbuf_t * buf buf = data bam_plbuf_push(b, buf) return 0 class StderrStore(): ''' stderr is captured. ''' def __init__(self): return self.stderr_h, self.stderr_f = tempfile.mkstemp() self.stderr_save = Outs( sys.stderr.fileno() ) self.stderr_save.setfd( self.stderr_h ) def readAndRelease( self ): return [] self.stderr_save.restore() lines = [] if os.path.exists(self.stderr_f): lines = open( self.stderr_f, "r" ).readlines() os.remove( self.stderr_f ) return lines def release(self): return self.stderr_save.restore() if os.path.exists(self.stderr_f): os.remove( self.stderr_f ) def __del__(self): self.release() class StderrStoreWindows(): '''does nothing. stderr can't be redirected on windows''' def __init__(self): pass def readAndRelease(self): return [] def release(self): pass if platform.system()=='Windows': del StderrStore StderrStore = StderrStoreWindows ###################################################################### ###################################################################### ###################################################################### # valid types for sam headers VALID_HEADER_TYPES = { "HD" : dict, "SQ" : list, "RG" : list, "PG" : list, "CO" : list } # order of records within sam headers VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # type conversions within sam header records VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # output order of fields within records VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } ###################################################################### ###################################################################### ###################################################################### ## Public methods ###################################################################### cdef class Fastafile: '''*(filename)* A *FASTA* file. The file is automatically opened. The file expects an indexed fasta file. TODO: add automatic indexing. add function to get sequence names. ''' def __cinit__(self, *args, **kwargs ): self.fastafile = NULL self._filename = None self._references = None self._lengths = None self.reference2length = None self._open( *args, **kwargs ) def _isOpen( self ): '''return true if samfile has been opened.''' return self.fastafile != NULL def __len__(self): if self.fastafile == NULL: raise ValueError( "calling len() on closed file" ) return faidx_fetch_nseq(self.fastafile) def _open(self, filename): '''open an indexed fasta file. This method expects an indexed fasta file. ''' # close a previously opened file if self.fastafile != NULL: self.close() self._filename = _encodeFilename(filename) self.fastafile = fai_load(self._filename) if self.fastafile == NULL: raise IOError("could not open file `%s`" % filename) # read index if not os.path.exists( self._filename + b".fai" ): raise ValueError("could not locate index file") with open( self._filename + b".fai" ) as inf: data = [ x.split("\t") for x in inf ] self._references = tuple(x[0] for x in data) self._lengths = tuple(int(x[1]) for x in data) self.reference2length = dict(zip(self._references, self._lengths)) def close( self ): if self.fastafile != NULL: fai_destroy( self.fastafile ) self.fastafile = NULL def __dealloc__(self): self.close() property filename: '''number of :term:`filename` associated with this object.''' def __get__(self): return self._filename property references: '''tuple with the names of :term:`reference` sequences.''' def __get__(self): return self._references property nreferences: '''number of :term:`reference` sequences in the file.''' def __get__(self): return len(self._references) if self.references else None property lengths: '''tuple with the lengths of :term:`reference` sequences.''' def __get__(self): return self._lengths def fetch( self, reference = None, start = None, end = None, region = None): '''*(reference = None, start = None, end = None, region = None)* fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing. The region is specified by :term:`reference`, *start* and *end*. fetch returns an empty string if the region is out of range or addresses an unknown *reference*. If *reference* is given and *start* is None, the sequence from the first base is returned. Similarly, if *end* is None, the sequence until the last base is returned. Alternatively, a samtools :term:`region` string can be supplied. ''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) cdef int length cdef char * seq if not region: if reference is None: raise ValueError( 'no sequence/region supplied.' ) if start is None: start = 0 if end is None: end = max_pos -1 if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) if start == end: return b"" # valid ranges are from 0 to 2^29-1 if not 0 <= start < max_pos: raise IndexError( 'start out of range (%i)' % start ) if not 0 <= end < max_pos: raise IndexError( 'end out of range (%i)' % end ) # note: faidx_fetch_seq has a bug such that out-of-range access # always returns the last residue. Hence do not use faidx_fetch_seq, # but use fai_fetch instead # seq = faidx_fetch_seq(self.fastafile, # reference, # start, # end-1, # &length) region = "%s:%i-%i" % (reference, start+1, end) if PY_MAJOR_VERSION >= 3: region = region.encode('ascii') seq = fai_fetch( self.fastafile, region, &length ) else: # samtools adds a '\0' at the end seq = fai_fetch( self.fastafile, region, &length ) # copy to python if seq == NULL: return b"" else: try: py_seq = seq[:length] finally: free(seq) return py_seq cdef char * _fetch( self, char * reference, int start, int end, int * length ): '''fetch sequence for reference, start and end''' return faidx_fetch_seq(self.fastafile, reference, start, end-1, length ) def getReferenceLength( self, reference ): '''return the length of reference.''' return self.reference2length[reference] def __getitem__(self, reference): return self.fetch(reference) def __contains__( self, reference ): '''return true if reference in fasta file.''' return reference in self.reference2length ###################################################################### ###################################################################### ###################################################################### ## Fastq file ###################################################################### cdef class FastqProxy: def __init__(self): pass property name: def __get__(self): return self._delegate.name.s property sequence: def __get__(self): return self._delegate.seq.s property comment: def __get__(self): if self._delegate.comment.l: return self._delegate.comment.s else: return None property quality: def __get__(self): if self._delegate.qual.l: return self._delegate.qual.s else: return None cdef class Fastqfile: '''*(filename)* A *FASTQ* file. The file is automatically opened. ''' def __cinit__(self, *args, **kwargs ): # self.fastqfile = NULL self._filename = None self.entry = NULL self._open( *args, **kwargs ) def _isOpen( self ): '''return true if samfile has been opened.''' return self.entry != NULL def _open(self, filename): '''open an indexed fasta file. This method expects an indexed fasta file. ''' self.close() if not os.path.exists( filename ): raise IOError( "No such file or directory: %s" % filename ) filename = _encodeFilename(filename) self.fastqfile = gzopen( filename, "r" ) self.entry = kseq_init( self.fastqfile ) self._filename = filename def close( self ): '''close file.''' if self.entry != NULL: gzclose( self.fastqfile ) if self.entry: kseq_destroy(self.entry) self.entry = NULL def __dealloc__(self): self.close() property filename: '''number of :term:`filename` associated with this object.''' def __get__(self): return self._filename def __iter__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) return self cdef kseq_t * getCurrent( self ): return self.entry cdef int cnext(self): '''C version of iterator ''' return kseq_read(self.entry) def __next__(self): """ python version of next(). """ cdef int l l = kseq_read( self.entry) if (l > 0): return makeFastqProxy( self.entry ) else: raise StopIteration #------------------------------------------------------------------------ #------------------------------------------------------------------------ #------------------------------------------------------------------------ cdef int count_callback( bam1_t *alignment, void *f): '''callback for bam_fetch - count number of reads. ''' cdef int* counter = (f) counter[0] += 1; ctypedef struct MateData: char * name bam1_t * mate uint32_t flag #------------------------------------------------------------------------ #------------------------------------------------------------------------ #------------------------------------------------------------------------ cdef int mate_callback( bam1_t *alignment, void *f): '''callback for bam_fetch = filter mate ''' cdef MateData * d = (f) # printf("mate = %p, name1 = %s, name2=%s\t%i\t%i\t%i\n", # d.mate, d.name, bam1_qname(alignment), # d.flag, alignment.core.flag, alignment.core.flag & d.flag) if d.mate == NULL: # could be sped up by comparing the lengths of query strings first # using l_qname # # also, make sure that we get the other read by comparing # the flags if alignment.core.flag & d.flag != 0 and \ strcmp( bam1_qname( alignment ), d.name ) == 0: d.mate = bam_dup1( alignment ) cdef class Samfile: '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None, add_sq_text = False, check_header = True, check_sq = True )* A :term:`SAM`/:term:`BAM` formatted file. The file is automatically opened. *mode* should be ``r`` for reading or ``w`` for writing. The default is text mode (:term:`SAM`). For binary (:term:`BAM`) I/O you should append ``b`` for compressed or ``u`` for uncompressed :term:`BAM` output. Use ``h`` to output header information in text (:term:`TAM`) mode. If ``b`` is present, it must immediately follow ``r`` or ``w``. Valid modes are ``r``, ``w``, ``wh``, ``rb``, ``wb`` and ``wbu``. For instance, to open a :term:`BAM` formatted file for reading, type:: f = pysam.Samfile('ex1.bam','rb') If mode is not specified, we will try to auto-detect in the order 'rb', 'r', thus both the following should work:: f1 = pysam.Samfile('ex1.bam' ) f2 = pysam.Samfile('ex1.sam' ) If an index for a BAM file exists (.bai), it will be opened automatically. Without an index random access to reads via :meth:`fetch` and :meth:`pileup` is disabled. For writing, the header of a :term:`SAM` file/:term:`BAM` file can be constituted from several sources (see also the samtools format specification): 1. If *template* is given, the header is copied from a another *Samfile* (*template* must be of type *Samfile*). 2. If *header* is given, the header is built from a multi-level dictionary. The first level are the four types ('HD', 'SQ', ...). The second level are a list of lines, with each line being a list of tag-value pairs. The header is constructed first from all the defined fields, followed by user tags in alphabetical order. 3. If *text* is given, new header text is copied from raw text. 4. The names (*referencenames*) and lengths (*referencelengths*) are supplied directly as lists. By default, 'SQ' and 'LN' tags will be added to the header text. This option can be changed by unsetting the flag *add_sq_text*. By default, if file a file is opened in mode 'r', it is checked for a valid header (*check_header* = True) and a definition of chromosome names (*check_sq* = True). ''' def __cinit__(self, *args, **kwargs ): self.samfile = NULL self._filename = None self.isbam = False self.isstream = False self._open( *args, **kwargs ) # allocate memory for iterator self.b = calloc(1, sizeof(bam1_t)) def _isOpen( self ): '''return true if samfile has been opened.''' return self.samfile != NULL def _hasIndex( self ): '''return true if samfile has an existing (and opened) index.''' return self.index != NULL def _open( self, filename, mode = None, Samfile template = None, referencenames = None, referencelengths = None, text = None, header = None, port = None, add_sq_text = True, check_header = True, check_sq = True, ): '''open a sam/bam file. If _open is called on an existing bamfile, the current file will be closed and a new file will be opened. ''' # read mode autodetection if mode is None: try: self._open(filename, 'rb', template=template, referencenames=referencenames, referencelengths=referencelengths, text=text, header=header, port=port, check_header=check_header, check_sq=check_sq) return except ValueError, msg: pass self._open(filename, 'r', template=template, referencenames=referencenames, referencelengths=referencelengths, text=text, header=header, port=port, check_header=check_header, check_sq=check_sq) return assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode # close a previously opened file if self.samfile != NULL: self.close() cdef bam_header_t * header_to_write header_to_write = NULL cdef bytes bmode = mode.encode('ascii') self._filename = filename = _encodeFilename(filename) self.isstream = filename == b"-" self.isbam = len(mode) > 1 and mode[1] == 'b' self.isremote = filename.startswith(b"http:") or filename.startswith(b"ftp:") cdef char * ctext ctext = NULL if mode[0] == 'w': # open file for writing # header structure (used for writing) if template: # copy header from another file header_to_write = template.samfile.header elif header: header_to_write = self._buildHeader( header ) else: # build header from a target names and lengths assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # allocate and fill header referencenames = [ _force_bytes(ref) for ref in referencenames ] header_to_write = bam_header_init() header_to_write.n_targets = len(referencenames) n = 0 for x in referencenames: n += len(x) + 1 header_to_write.target_name = calloc(n, sizeof(char*)) header_to_write.target_len = calloc(n, sizeof(uint32_t)) for x from 0 <= x < header_to_write.n_targets: header_to_write.target_len[x] = referencelengths[x] name = referencenames[x] header_to_write.target_name[x] = calloc(len(name)+1, sizeof(char)) strncpy( header_to_write.target_name[x], name, len(name) ) # Optionally, if there is no text, add a SAM compatible header to output # file. if text is None and add_sq_text: text = [] for x from 0 <= x < header_to_write.n_targets: text.append( "@SQ\tSN:%s\tLN:%s\n" % \ (_force_str(referencenames[x]), referencelengths[x] ) ) text = ''.join(text) if text != None: # copy without \0 text = _force_bytes(text) ctext = text header_to_write.l_text = strlen(ctext) header_to_write.text = calloc( strlen(ctext), sizeof(char) ) memcpy( header_to_write.text, ctext, strlen(ctext) ) header_to_write.hash = NULL header_to_write.rg2lib = NULL # open file. Header gets written to file at the same time for bam files # and sam files (in the latter case, the mode needs to be wh) store = StderrStore() self.samfile = samopen( filename, bmode, header_to_write ) store.release() # bam_header_destroy takes care of cleaning up of all the members if not template and header_to_write != NULL: bam_header_destroy( header_to_write ) elif mode[0] == "r": # open file for reading if filename != b"-" and not self.isremote and not os.path.exists( filename ): raise IOError( "file `%s` not found" % filename) # try to detect errors self.samfile = samopen( filename, bmode, NULL ) if self.samfile == NULL: raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) # bam files require a valid header if self.isbam: if self.samfile.header == NULL: raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) else: # in sam files it is optional (samfile full of unmapped reads) if check_header and self.samfile.header == NULL: raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode ) # disabled for autodetection to work # needs to be disabled so that reading from sam-files without headers works if check_sq and self.samfile.header.n_targets == 0: raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) if self.samfile == NULL: raise IOError("could not open file `%s`" % filename ) # check for index and open if present if mode[0] == "r" and self.isbam: if not self.isremote: if not os.path.exists(filename + b".bai") \ and not os.path.exists( filename[:-4] + b".bai"): self.index = NULL else: # returns NULL if there is no index or index could not be opened self.index = bam_index_load(filename) if self.index == NULL: raise IOError("error while opening index `%s` " % filename ) else: self.index = bam_index_load(filename) if self.index == NULL: raise IOError("error while opening index `%s` " % filename ) if not self.isstream: self.start_offset = bam_tell( self.samfile.x.bam ) def gettid( self, reference ): ''' convert :term:`reference` name into numerical :term:`tid` returns -1 if reference is not known. ''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) reference = _force_bytes(reference) return pysam_reference2tid( self.samfile.header, reference ) def getrname( self, tid ): ''' convert numerical :term:`tid` into :term:`reference` name.''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not 0 <= tid < self.samfile.header.n_targets: raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) return _charptr_to_str(self.samfile.header.target_name[tid]) cdef char * _getrname( self, int tid ): # TODO unused ''' convert numerical :term:`tid` into :term:`reference` name.''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not 0 <= tid < self.samfile.header.n_targets: raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) return self.samfile.header.target_name[tid] def _parseRegion( self, reference = None, start = None, end = None, region = None ): ''' parse region information. raise ValueError for for invalid regions. returns a tuple of flag, tid, start and end. Flag indicates whether some coordinates were supplied. Note that regions are 1-based, while start,end are python coordinates. ''' # This method's main objective is to translate from a reference to a tid. # For now, it calls bam_parse_region, which is clumsy. Might be worth # implementing it all in pysam (makes use of khash). cdef int rtid cdef long long rstart cdef long long rend rtid = -1 rstart = 0 rend = max_pos if start != None: try: rstart = start except OverflowError: raise ValueError( 'start out of range (%i)' % start ) if end != None: try: rend = end except OverflowError: raise ValueError( 'end out of range (%i)' % end ) if region: region = _force_str(region) parts = re.split( "[:-]", region ) reference = parts[0] if len(parts) >= 2: rstart = int(parts[1]) - 1 if len(parts) >= 3: rend = int(parts[2]) if not reference: return 0, 0, 0, 0 rtid = self.gettid( reference ) if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) return 1, rtid, rstart, rend def reset( self ): '''reset file position to beginning of read section.''' return self.seek( self.start_offset, 0 ) def seek( self, uint64_t offset, int where = 0): ''' move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`. ''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not self.isbam: raise NotImplementedError("seek only available in bam files") if self.isstream: raise OSError("seek no available in streams") return bam_seek( self.samfile.x.bam, offset, where ) def tell( self ): ''' return current file position ''' if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not self.isbam: raise NotImplementedError("seek only available in bam files") return bam_tell( self.samfile.x.bam ) def fetch( self, reference = None, start = None, end = None, region = None, callback = None, until_eof = False ): ''' fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied. Without *reference* or *region* all mapped reads will be fetched. The reads will be returned ordered by reference sequence, which will not necessarily be the order within the file. If *until_eof* is given, all reads from the current file position will be returned in order as they are within the file. Using this option will also fetch unmapped reads. If only *reference* is set, all reads aligned to *reference* will be fetched. The method returns an iterator of type :class:`pysam.IteratorRow` unless a *callback is provided. If *callback* is given, the callback will be executed for each position within the :term:`region`. Note that callbacks currently work only, if *region* or *reference* is given. Note that a :term:`SAM` file does not allow random access. If *region* or *reference* are given, an exception is raised. ''' cdef int rtid, rstart, rend, has_coord if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) if self.isstream: reopen = False else: reopen = True if self.isbam: if not until_eof and not self._hasIndex() and not self.isremote: raise ValueError( "fetch called on bamfile without index" ) if callback: if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) if not self._hasIndex(): raise ValueError( "no index available for fetch" ) return bam_fetch(self.samfile.x.bam, self.index, rtid, rstart, rend, callback, fetch_callback ) else: if has_coord: return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen ) else: if until_eof: return IteratorRowAll( self, reopen=reopen ) else: # AH: check - reason why no reopen for AllRefs? return IteratorRowAllRefs(self ) # , reopen=reopen ) else: if has_coord: raise ValueError ("fetching by region is not available for sam files" ) if callback: raise NotImplementedError( "callback not implemented yet" ) if self.samfile.header == NULL: raise ValueError( "fetch called for samfile without header") # check if targets are defined # give warning, sam_read1 segfaults if self.samfile.header.n_targets == 0: warnings.warn( "fetch called for samfile without header") return IteratorRowAll( self, reopen=reopen ) def mate( self, AlignedRead read ): '''return the mate of :class:`AlignedRead` *read*. Throws a ValueError if read is unpaired or the mate is unmapped. .. note:: Calling this method will change the file position. This might interfere with any iterators that have not re-opened the file. ''' cdef uint32_t flag = read._delegate.core.flag if flag & BAM_FPAIRED == 0: raise ValueError( "read %s: is unpaired" % (read.qname)) if flag & BAM_FMUNMAP != 0: raise ValueError( "mate %s: is unmapped" % (read.qname)) cdef MateData mate_data mate_data.name = bam1_qname(read._delegate) mate_data.mate = NULL # xor flags to get the other mate cdef int x = BAM_FREAD1 + BAM_FREAD2 mate_data.flag = ( flag ^ x) & x bam_fetch(self.samfile.x.bam, self.index, read._delegate.core.mtid, read._delegate.core.mpos, read._delegate.core.mpos + 1, &mate_data, mate_callback ) if mate_data.mate == NULL: raise ValueError( "mate not found" ) cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) dest._delegate = mate_data.mate return dest def count( self, reference = None, start = None, end = None, region = None, until_eof = False ): '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)* count reads :term:`region` using 0-based indexing. The region is specified by :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied. Note that a :term:`TAM` file does not allow random access. If *region* or *reference* are given, an exception is raised. ''' cdef int rtid cdef int rstart cdef int rend if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) cdef int counter counter = 0; if self.isbam: if not until_eof and not self._hasIndex() and not self.isremote: raise ValueError( "fetch called on bamfile without index" ) if not region: raise ValueError( "counting functionality requires a region/reference" ) if not self._hasIndex(): raise ValueError( "no index available for fetch" ) bam_fetch(self.samfile.x.bam, self.index, rtid, rstart, rend, &counter, count_callback ) return counter else: raise ValueError ("count for a region is not available for sam files" ) def pileup( self, reference = None, start = None, end = None, region = None, callback = None, **kwargs ): ''' perform a :term:`pileup` within a :term:`region`. The region is specified by :term:`reference`, *start* and *end* (using 0-based indexing). Alternatively, a samtools *region* string can be supplied. Without *reference* or *region* all reads will be used for the pileup. The reads will be returned ordered by :term:`reference` sequence, which will not necessarily be the order within the file. The method returns an iterator of type :class:`pysam.IteratorColumn` unless a *callback is provided. If a *callback* is given, the callback will be executed for each column within the :term:`region`. Note that :term:`SAM` formatted files do not allow random access. In these files, if a *region* or *reference* are given an exception is raised. Optional *kwargs* to the iterator: stepper The stepper controlls how the iterator advances. Possible options for the stepper are ``all`` use all reads for pileup. ``samtools`` same filter and read processing as in :term:`csamtools` pileup fastafile A :class:`FastaFile` object mask Skip all reads with bits set in mask if mask=True. max_depth Maximum read depth permitted. The default limit is *8000*. truncate By default, the samtools pileup engine outputs all reads overlapping a region (see note below). If truncate is True and a region is given, only output columns in the exact region specificied. .. note:: *all* reads which overlap the region are returned. The first base returned will be the first base of the first read *not* necessarily the first base of the region used in the query. ''' cdef int rtid, rstart, rend, has_coord cdef bam_plbuf_t *buf if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) if self.isbam: if not self._hasIndex(): raise ValueError( "no index available for pileup" ) if callback: if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) buf = bam_plbuf_init( pileup_callback, callback ) bam_fetch(self.samfile.x.bam, self.index, rtid, rstart, rend, buf, pileup_fetch_callback ) # finalize pileup bam_plbuf_push( NULL, buf) bam_plbuf_destroy(buf) else: if has_coord: return IteratorColumnRegion( self, tid = rtid, start = rstart, end = rend, **kwargs ) else: return IteratorColumnAllRefs(self, **kwargs ) else: raise NotImplementedError( "pileup of samfiles not implemented yet" ) def close( self ): ''' closes the :class:`pysam.Samfile`.''' if self.samfile != NULL: samclose( self.samfile ) bam_index_destroy(self.index); self.samfile = NULL def __dealloc__( self ): # remember: dealloc cannot call other methods # note: no doc string # note: __del__ is not called. self.close() bam_destroy1(self.b) cpdef int write( self, AlignedRead read ) except -1: ''' write a single :class:`pysam.AlignedRead` to disk. returns the number of bytes written. ''' if not self._isOpen(): return 0 return samwrite( self.samfile, read._delegate ) def __enter__(self): return self def __exit__(self, exc_type, exc_value, traceback): self.close() return False ############################################################### ############################################################### ############################################################### ## properties ############################################################### property filename: '''number of :term:`filename` associated with this object.''' def __get__(self): return self._filename property nreferences: '''number of :term:`reference` sequences in the file.''' def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) return self.samfile.header.n_targets property references: """tuple with the names of :term:`reference` sequences.""" def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) t = [] for x from 0 <= x < self.samfile.header.n_targets: t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) return tuple(t) property lengths: """tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as :attr:`pysam.Samfile.references` """ def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) t = [] for x from 0 <= x < self.samfile.header.n_targets: t.append( self.samfile.header.target_len[x] ) return tuple(t) property mapped: """total number of mapped reads in file. """ def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) if self.index == NULL: raise ValueError( "mapping information not recorded in index or index not available") cdef int tid cdef uint32_t total = 0 for tid from 0 <= tid < self.samfile.header.n_targets: total += pysam_get_mapped( self.index, tid ) return total property unmapped: """total number of unmapped reads in file. """ def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) cdef int tid cdef uint32_t total = 0 for tid from 0 <= tid < self.samfile.header.n_targets: total += pysam_get_unmapped( self.index, tid ) # get unmapped reads without coordinates total += pysam_get_unmapped( self.index, -1 ) return total property text: '''full contents of the :term:`sam file` header as a string.''' def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) property header: '''header information within the :term:`sam file`. The records and fields are returned as a two-level dictionary. ''' def __get__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) result = {} if self.samfile.header.text != NULL: # convert to python string (note: call self.text to create 0-terminated string) t = self.text for line in t.split("\n"): if not line.strip(): continue assert line.startswith("@"), "header line without '@': '%s'" % line fields = line[1:].split("\t") record = fields[0] assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) # treat comments if record == "CO": if record not in result: result[record] = [] result[record].append( "\t".join( fields[1:] ) ) continue # the following is clumsy as generators do not work? x = {} for field in fields[1:]: if ":" not in field: raise ValueError("malformatted header: no ':' in field" ) key, value = field.split(":",1) # uppercase keys must be valid # lowercase are permitted for user fields if key in VALID_HEADER_FIELDS[record]: x[key] = VALID_HEADER_FIELDS[record][key](value) elif not key.isupper(): x[key] = value else: raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) if VALID_HEADER_TYPES[record] == dict: if record in result: raise ValueError( "multiple '%s' lines are not permitted" % record ) result[record] = x elif VALID_HEADER_TYPES[record] == list: if record not in result: result[record] = [] result[record].append( x ) # if there are no SQ lines in the header, add the reference names # from the information in the bam file. # Background: c-samtools keeps the textual part of the header separate from # the list of reference names and lengths. Thus, if a header contains only # SQ lines, the SQ information is not part of the textual header and thus # are missing from the output. See issue 84. if "SQ" not in result: sq = [] for ref, length in zip( self.references, self.lengths ): sq.append( {'LN': length, 'SN': ref } ) result["SQ"] = sq return result def _buildLine( self, fields, record ): '''build a header line from *fields* dictionary for *record*''' # TODO: add checking for field and sort order line = ["@%s" % record ] # comment if record == "CO": line.append( fields ) # user tags elif record.islower(): for key in sorted(fields): line.append( "%s:%s" % (key, str(fields[key]))) # defined tags else: # write fields of the specification for key in VALID_HEADER_ORDER[record]: if key in fields: line.append( "%s:%s" % (key, str(fields[key]))) # write user fields for key in fields: if not key.isupper(): line.append( "%s:%s" % (key, str(fields[key]))) return "\t".join( line ) cdef bam_header_t * _buildHeader( self, new_header ): '''return a new header built from a dictionary in *new_header*. This method inserts the text field, target_name and target_len. ''' lines = [] # check if hash exists # create new header and copy old data cdef bam_header_t * dest dest = bam_header_init() # first: defined tags for record in VALID_HEADERS: if record in new_header: ttype = VALID_HEADER_TYPES[record] data = new_header[record] if type( data ) != type( ttype() ): raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) if type( data ) is dict: lines.append( self._buildLine( data, record ) ) else: for fields in new_header[record]: lines.append( self._buildLine( fields, record ) ) # then: user tags (lower case), sorted alphabetically for record, data in sorted(new_header.items()): if record in VALID_HEADERS: continue if type( data ) is dict: lines.append( self._buildLine( data, record ) ) else: for fields in new_header[record]: lines.append( self._buildLine( fields, record ) ) text = "\n".join(lines) + "\n" if dest.text != NULL: free( dest.text ) dest.text = calloc( len(text), sizeof(char)) dest.l_text = len(text) cdef bytes btext = text.encode('ascii') strncpy( dest.text, btext, dest.l_text ) cdef bytes bseqname # collect targets if "SQ" in new_header: seqs = [] for fields in new_header["SQ"]: try: seqs.append( (fields["SN"], fields["LN"] ) ) except KeyError: raise KeyError( "incomplete sequence information in '%s'" % str(fields)) dest.n_targets = len(seqs) dest.target_name = calloc( dest.n_targets, sizeof(char*) ) dest.target_len = calloc( dest.n_targets, sizeof(uint32_t) ) for x from 0 <= x < dest.n_targets: seqname, seqlen = seqs[x] dest.target_name[x] = calloc( len( seqname ) + 1, sizeof(char) ) bseqname = seqname.encode('ascii') strncpy( dest.target_name[x], bseqname, len(seqname) + 1 ) dest.target_len[x] = seqlen return dest ############################################################### ############################################################### ############################################################### ## file-object like iterator access ## note: concurrent access will cause errors (see IteratorRow ## and reopen) ## Possible solutions: deprecate or open new file handle ############################################################### def __iter__(self): if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) if not self.isbam and self.samfile.header.n_targets == 0: raise NotImplementedError( "can not iterate over samfile without header") return self cdef bam1_t * getCurrent( self ): return self.b cdef int cnext(self): ''' cversion of iterator. Used by :class:`pysam.Samfile.IteratorColumn`. ''' cdef int ret return samread(self.samfile, self.b) def __next__(self): """ python version of next(). """ cdef int ret ret = samread(self.samfile, self.b) if (ret > 0): return makeAlignedRead( self.b ) else: raise StopIteration ##------------------------------------------------------------------- ##------------------------------------------------------------------- ##------------------------------------------------------------------- cdef class IteratorRow: '''abstract base class for iterators over mapped reads. Various iterators implement different behaviours for wrapping around contig boundaries. Examples include: :class:`pysam.IteratorRowRegion` iterate within a single contig and a defined region. :class:`pysam.IteratorRowAll` iterate until EOF. This iterator will also include unmapped reads. :class:`pysam.IteratorRowAllRefs` iterate over all reads in all reference sequences. The method :meth:`Samfile.fetch` returns an IteratorRow. .. note:: It is usually not necessary to create an object of this class explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`. ''' pass cdef class IteratorRowRegion(IteratorRow): """*(Samfile samfile, int tid, int beg, int end, int reopen = True )* iterate over mapped reads in a region. By default, the file is re-openend to avoid conflicts between multiple iterators working on the same file. Set *reopen* = False to not re-open *samfile*. The samtools iterators assume that the file position between iterations do not change. As a consequence, no two iterators can work on the same file. To permit this, each iterator creates its own file handle by re-opening the file. Note that the index will be shared between samfile and the iterator. .. note:: It is usually not necessary to create an object of this class explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`. """ def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): if not samfile._isOpen(): raise ValueError( "I/O operation on closed file" ) if not samfile._hasIndex(): raise ValueError( "no index available for iteration" ) # makes sure that samfile stays alive as long as the # iterator is alive self.samfile = samfile if samfile.isbam: mode = b"rb" else: mode = b"r" # reopen the file - note that this makes the iterator # slow and causes pileup to slow down significantly. if reopen: store = StderrStore() self.fp = samopen( samfile._filename, mode, NULL ) store.release() assert self.fp != NULL self.owns_samfile = True else: self.fp = self.samfile.samfile self.owns_samfile = False self.retval = 0 self.iter = bam_iter_query(self.samfile.index, tid, beg, end) self.b = bam_init1() def __iter__(self): return self cdef bam1_t * getCurrent( self ): return self.b cdef int cnext(self): '''cversion of iterator. Used by IteratorColumn''' self.retval = bam_iter_read( self.fp.x.bam, self.iter, self.b) def __next__(self): """python version of next(). """ self.cnext() if self.retval < 0: raise StopIteration return makeAlignedRead( self.b ) def __dealloc__(self): bam_destroy1(self.b) bam_iter_destroy( self.iter ) if self.owns_samfile: samclose( self.fp ) cdef class IteratorRowAll(IteratorRow): """*(Samfile samfile, int reopen = True)* iterate over all reads in *samfile* By default, the file is re-openend to avoid conflicts between multiple iterators working on the same file. Set *reopen* = False to not re-open *samfile*. .. note:: It is usually not necessary to create an object of this class explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`. """ def __cinit__(self, Samfile samfile, int reopen = True ): if not samfile._isOpen(): raise ValueError( "I/O operation on closed file" ) if samfile.isbam: mode = b"rb" else: mode = b"r" # reopen the file to avoid iterator conflict if reopen: store = StderrStore() self.fp = samopen( samfile._filename, mode, NULL ) store.release() assert self.fp != NULL self.owns_samfile = True else: self.fp = samfile.samfile self.owns_samfile = False # allocate memory for alignment self.b = calloc(1, sizeof(bam1_t)) def __iter__(self): return self cdef bam1_t * getCurrent( self ): return self.b cdef int cnext(self): '''cversion of iterator. Used by IteratorColumn''' return samread(self.fp, self.b) def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef int ret ret = samread(self.fp, self.b) if (ret > 0): return makeAlignedRead( self.b ) else: raise StopIteration def __dealloc__(self): bam_destroy1(self.b) if self.owns_samfile: samclose( self.fp ) cdef class IteratorRowAllRefs(IteratorRow): """iterates over all mapped reads by chaining iterators over each reference .. note:: It is usually not necessary to create an object of this class explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`. """ def __cinit__(self, Samfile samfile): assert samfile._isOpen() if not samfile._hasIndex(): raise ValueError("no index available for fetch") self.samfile = samfile self.tid = -1 def nextiter(self): self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) def __iter__(self): return self def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ # Create an initial iterator if self.tid==-1: if not self.samfile.nreferences: raise StopIteration self.tid = 0 self.nextiter() while 1: self.rowiter.cnext() # If current iterator is not exhausted, return aligned read if self.rowiter.retval>0: return makeAlignedRead(self.rowiter.b) self.tid += 1 # Otherwise, proceed to next reference or stop if self.tidcalloc(1, sizeof(bam1_t)) self.positions = positions self.current_pos = 0 def __iter__(self): return self cdef bam1_t * getCurrent( self ): return self.b cdef int cnext(self): '''cversion of iterator''' # end iteration if out of positions if self.current_pos >= len(self.positions): return -1 bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) self.current_pos += 1 return samread(self.fp, self.b) def __next__(self): """python version of next(). pyrex uses this non-standard name instead of next() """ cdef int ret = self.cnext() if (ret > 0): return makeAlignedRead( self.b ) else: raise StopIteration def __dealloc__(self): bam_destroy1(self.b) if self.owns_samfile: samclose( self.fp ) ##------------------------------------------------------------------- ##------------------------------------------------------------------- ##------------------------------------------------------------------- cdef int __advance_all( void * data, bam1_t * b ): '''advance without any read filtering. ''' cdef __iterdata * d d = <__iterdata*>data return bam_iter_read( d.samfile.x.bam, d.iter, b ) cdef int __advance_snpcalls( void * data, bam1_t * b ): '''advance using same filter and read processing as in the samtools pileup. ''' cdef __iterdata * d d = <__iterdata*>data cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) cdef int skip = 0 cdef int q cdef int is_cns = 1 cdef int is_nobaq = 0 cdef int capQ_thres = 0 # reload sequence if d.fastafile != NULL and b.core.tid != d.tid: if d.seq != NULL: free(d.seq) d.tid = b.core.tid d.seq = faidx_fetch_seq(d.fastafile, d.samfile.header.target_name[d.tid], 0, max_pos, &d.seq_len) if d.seq == NULL: raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \ (d.samfile.header.target_name[d.tid], d.tid)) while ret >= 0: skip = 0 # realign read - changes base qualities if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) if d.seq != NULL and capQ_thres > 10: q = bam_cap_mapQ(b, d.seq, capQ_thres) if q < 0: skip = 1 elif b.core.qual > q: b.core.qual = q if b.core.flag & BAM_FUNMAP: skip = 1 elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 if not skip: break # additional filters ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) return ret cdef class IteratorColumn: '''abstract base class for iterators over columns. IteratorColumn objects wrap the pileup functionality of samtools. For reasons of efficiency, the iterator points to the current pileup buffer. The pileup buffer is updated at every iteration. This might cause some unexpected behavious. For example, consider the conversion to a list:: f = Samfile("file.bam", "rb") result = list( f.pileup() ) Here, ``result`` will contain ``n`` objects of type :class:`PileupProxy` for ``n`` columns, but each object in ``result`` will contain the same information. The desired behaviour can be achieved by list comprehension:: result = [ x.pileups() for x in f.pileup() ] ``result`` will be a list of ``n`` lists of objects of type :class:`PileupRead`. If the iterator is associated with a :class:`Fastafile` using the :meth:`addReference` method, then the iterator will export the current sequence via the methods :meth:`getSequence` and :meth:`seq_len`. Optional kwargs to the iterator stepper The stepper controls how the iterator advances. Possible options for the stepper are all use all reads for pileup. samtools same filter and read processing as in :term:`csamtools` pileup The default is to use "all" if no stepper is given. fastafile A :class:`FastaFile` object mask Skip all reads with bits set in mask. max_depth maximum read depth. The default is 8000. ''' def __cinit__( self, Samfile samfile, **kwargs ): self.samfile = samfile self.mask = kwargs.get("mask", BAM_DEF_MASK ) self.fastafile = kwargs.get( "fastafile", None ) self.stepper = kwargs.get( "stepper", None ) self.max_depth = kwargs.get( "max_depth", 8000 ) self.iterdata.seq = NULL self.tid = 0 self.pos = 0 self.n_plp = 0 self.plp = NULL self.pileup_iter = NULL def __iter__(self): return self cdef int cnext(self): '''perform next iteration. ''' self.plp = bam_plp_auto( self.pileup_iter, &self.tid, &self.pos, &self.n_plp ) cdef char * getSequence( self ): '''return current reference sequence underlying the iterator. ''' return self.iterdata.seq property seq_len: '''current sequence length.''' def __get__(self): return self.iterdata.seq_len def addReference( self, Fastafile fastafile ): ''' add reference sequences in *fastafile* to iterator.''' self.fastafile = fastafile if self.iterdata.seq != NULL: free(self.iterdata.seq) self.iterdata.tid = -1 self.iterdata.fastafile = self.fastafile.fastafile def hasReference( self ): ''' return true if iterator is associated with a reference''' return self.fastafile cdef setMask( self, mask ): '''set masking flag in iterator. reads with bits set in *mask* will be skipped. ''' self.mask = mask bam_plp_set_mask( self.pileup_iter, self.mask ) cdef setupIteratorData( self, int tid, int start, int end, int reopen = 0 ): '''setup the iterator structure''' self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen ) self.iterdata.samfile = self.samfile.samfile self.iterdata.iter = self.iter.iter self.iterdata.seq = NULL self.iterdata.tid = -1 if self.fastafile != None: self.iterdata.fastafile = self.fastafile.fastafile else: self.iterdata.fastafile = NULL if self.stepper == None or self.stepper == "all": self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata ) elif self.stepper == "samtools": self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata ) else: raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) if self.max_depth: bam_plp_set_maxcnt( self.pileup_iter, self.max_depth ) bam_plp_set_mask( self.pileup_iter, self.mask ) cdef reset( self, tid, start, end ): '''reset iterator position. This permits using the iterator multiple times without having to incur the full set-up costs. ''' self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 ) self.iterdata.iter = self.iter.iter # invalidate sequence if different tid if self.tid != tid: if self.iterdata.seq != NULL: free( self.iterdata.seq ) self.iterdata.seq = NULL self.iterdata.tid = -1 # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata ) bam_plp_reset(self.pileup_iter) def __dealloc__(self): # reset in order to avoid memory leak messages for iterators # that have not been fully consumed if self.pileup_iter != NULL: bam_plp_reset(self.pileup_iter) bam_plp_destroy(self.pileup_iter) self.pileup_iter = NULL self.plp = NULL if self.iterdata.seq != NULL: free(self.iterdata.seq) self.iterdata.seq = NULL cdef class IteratorColumnRegion(IteratorColumn): '''iterates over a region only. ''' def __cinit__(self, Samfile samfile, int tid = 0, int start = 0, int end = max_pos, int truncate = False, **kwargs ): # initialize iterator self.setupIteratorData( tid, start, end, 1 ) self.start = start self.end = end self.truncate = truncate def __next__(self): """python version of next(). """ while 1: self.cnext() if self.n_plp < 0: raise ValueError("error during iteration" ) if self.plp == NULL: raise StopIteration if self.truncate: if self.start > self.pos: continue if self.pos >= self.end: raise StopIteration return makePileupProxy( &self.plp, self.tid, self.pos, self.n_plp ) cdef class IteratorColumnAllRefs(IteratorColumn): """iterates over all columns by chaining iterators over each reference """ def __cinit__(self, Samfile samfile, **kwargs ): # no iteration over empty files if not samfile.nreferences: raise StopIteration # initialize iterator self.setupIteratorData( self.tid, 0, max_pos, 1 ) def __next__(self): """python version of next(). """ while 1: self.cnext() if self.n_plp < 0: raise ValueError("error during iteration" ) # return result, if within same reference if self.plp != NULL: return makePileupProxy( &self.plp, self.tid, self.pos, self.n_plp ) # otherwise, proceed to next reference or stop self.tid += 1 if self.tid < self.samfile.nreferences: self.setupIteratorData( self.tid, 0, max_pos, 0 ) else: raise StopIteration ##------------------------------------------------------------------- ##------------------------------------------------------------------- ##------------------------------------------------------------------- cdef inline int32_t query_start(bam1_t *src) except -1: cdef uint32_t * cigar_p, op cdef uint32_t k cdef uint32_t start_offset = 0 if src.core.n_cigar: cigar_p = bam1_cigar(src); for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK if op==BAM_CHARD_CLIP: if start_offset!=0 and start_offset!=src.core.l_qseq: PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') return -1 elif op==BAM_CSOFT_CLIP: start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT else: break return start_offset ##------------------------------------------------------------------- ##------------------------------------------------------------------- ##------------------------------------------------------------------- cdef inline int32_t query_end(bam1_t *src) except -1: cdef uint32_t * cigar_p, op cdef uint32_t k cdef uint32_t end_offset = src.core.l_qseq if src.core.n_cigar>1: cigar_p = bam1_cigar(src); for k from src.core.n_cigar > k >= 1: op = cigar_p[k] & BAM_CIGAR_MASK if op==BAM_CHARD_CLIP: if end_offset!=0 and end_offset!=src.core.l_qseq: PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') return -1 elif op==BAM_CSOFT_CLIP: end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT else: break if end_offset==0: end_offset = src.core.l_qseq return end_offset cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): cdef uint8_t * p cdef uint32_t k cdef char * s if not src.core.l_qseq: return None seq = PyBytes_FromStringAndSize(NULL, end - start) s = seq p = bam1_seq(src) for k from start <= k < end: # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c) # note: do not use string literal as it will be a python string s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] return seq cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): cdef uint8_t * p cdef uint32_t k cdef char * q p = bam1_qual(src) if p[0] == 0xff: return None qual = PyBytes_FromStringAndSize(NULL, end - start) q = qual for k from start <= k < end: ## equivalent to t[i] + 33 (see bam.c) q[k-start] = p[k] + 33 return qual cdef class AlignedRead: ''' Class representing an aligned read. see SAM format specification for the meaning of fields (http://samtools.sourceforge.net/). This class stores a handle to the samtools C-structure representing an aligned read. Member read access is forwarded to the C-structure and converted into python objects. This implementation should be fast, as only the data needed is converted. For write access, the C-structure is updated in-place. This is not the most efficient way to build BAM entries, as the variable length data is concatenated and thus needs to resized if a field is updated. Furthermore, the BAM entry might be in an inconsistent state. The :meth:`~validate` method can be used to check if an entry is consistent. One issue to look out for is that the sequence should always be set *before* the quality scores. Setting the sequence will also erase any quality scores that were set previously. In Python 3, the fields containing sequence and quality (seq, query, qual and qqual) data are of type bytes. Other string data, such as the qname field and strings in the tags tuple, is represented as unicode strings. On assignment, both bytes and unicode objects are allowed, but unicode strings must contain only ASCII characters. ''' # Now only called when instances are created from Python def __init__(self): # see bam_init1 self._delegate = calloc( 1, sizeof( bam1_t) ) # allocate some memory # If size is 0, calloc does not return a pointer that can be passed to free() # so allocate 40 bytes for a new read self._delegate.m_data = 40 self._delegate.data = calloc( self._delegate.m_data, 1 ) self._delegate.data_len = 0 def __dealloc__(self): bam_destroy1(self._delegate) def __str__(self): """return string representation of alignment. The representation is an approximate :term:`sam` format. An aligned read might not be associated with a :term:`Samfile`. As a result :term:`tid` is shown instead of the reference name. Similarly, the tags field is returned in its parsed state. """ # sam-parsing is done in sam.c/bam_format1_core which # requires a valid header. if sys.version_info[0] < 3: seq = self.seq qual = self.qual else: seq = self.seq.decode('ascii') qual = self.qual.decode('ascii') return "\t".join(map(str, (self.qname, self.flag, self.rname, self.pos, self.mapq, self.cigar, self.mrnm, self.mpos, self.rlen, seq, qual, self.tags ))) def compare(self, AlignedRead other): '''return -1,0,1, if contents in this are binary <,=,> to *other*''' cdef int retval, x cdef bam1_t *t, *o t = self._delegate o = other._delegate # uncomment for debugging purposes # cdef unsigned char * oo, * tt # tt = (&t.core) # oo = (&o.core) # for x from 0 <= x < sizeof( bam1_core_t): print x, tt[x], oo[x] # tt = (t.data) # oo = (o.data) # for x from 0 <= x < max(t.data_len, o.data_len): print x, tt[x], oo[x], chr(tt[x]), chr(oo[x]) # Fast-path test for object identity if t==o: return 0 retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) if retval: return retval retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len) if retval: return retval return memcmp(t.data, o.data, t.data_len) # Disabled so long as __cmp__ is a special method def __hash__(self): return _Py_HashPointer(self) ####################################################################### ####################################################################### ## Basic properties ####################################################################### property qname: """the query name (None if not present)""" def __get__(self): cdef bam1_t * src src = self._delegate if src.core.l_qname == 0: return None return _charptr_to_str(bam1_qname( src )) def __set__(self, qname ): if qname == None or len(qname) == 0: return qname = _force_bytes(qname) cdef bam1_t * src cdef int l cdef char * p src = self._delegate p = bam1_qname( src ) # the qname is \0 terminated l = len(qname) + 1 pysam_bam_update( src, src.core.l_qname, l, p ) src.core.l_qname = l # re-acquire pointer to location in memory # as it might have moved p = bam1_qname(src) strncpy( p, qname, l ) property cigar: """the :term:`cigar` alignment (None if not present). The alignment is returned as a list of tuples of (operation, length). The operations are: +-----+--------------+-----+ |M |BAM_CMATCH |0 | +-----+--------------+-----+ |I |BAM_CINS |1 | +-----+--------------+-----+ |D |BAM_CDEL |2 | +-----+--------------+-----+ |N |BAM_CREF_SKIP |3 | +-----+--------------+-----+ |S |BAM_CSOFT_CLIP|4 | +-----+--------------+-----+ |H |BAM_CHARD_CLIP|5 | +-----+--------------+-----+ |P |BAM_CPAD |6 | +-----+--------------+-----+ |= |BAM_CEQUAL |7 | +-----+--------------+-----+ |X |BAM_CDIFF |8 | +-----+--------------+-----+ .. note:: The output is a list of (operation, length) tuples, such as ``[ (0, 30) ]``. This is different from the SAM specification and the the :meth:`cigarstring` property, which uses a (length,operation order, for example: ``30M``. """ def __get__(self): cdef uint32_t * cigar_p cdef bam1_t * src cdef op, l, cigar cdef int k src = self._delegate if src.core.n_cigar == 0: return None cigar = [] cigar_p = bam1_cigar(src); for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT cigar.append((op, l)) return cigar def __set__(self, values ): if values == None or len(values) == 0: return cdef uint32_t * p cdef bam1_t * src cdef op, l cdef int k k = 0 src = self._delegate # get location of cigar string p = bam1_cigar(src) # create space for cigar data within src.data pysam_bam_update( src, src.core.n_cigar * 4, len(values) * 4, p ) # length is number of cigar operations, not bytes src.core.n_cigar = len(values) # re-acquire pointer to location in memory # as it might have moved p = bam1_cigar(src) # insert cigar operations for op, l in values: p[k] = l << BAM_CIGAR_SHIFT | op k += 1 ## setting the cigar string also updates the "bin" attribute src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) property cigarstring: '''the :term:`cigar` alignment as a string. The cigar string is a string of alternating integers and characters denoting the length and the type of an operation. .. note:: The order length,operation is specified in the SAM format. It is different from the order of the :meth:`cigar` property. Returns the empty string if not present. ''' def __get__(self): c = self.cigar if c == None: return "" # reverse order else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c]) def __set__(self, cigar): if cigar == None or len(cigar) == 0: self.cigar = [] parts = CIGAR_REGEX.findall( cigar ) # reverse order self.cigar = [ (CIGAR2CODE[ord(y)], int(x)) for x,y in parts ] property seq: """read sequence bases, including :term:`soft clipped` bases (None if not present). In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient. Note that assigning to seq will invalidate any quality scores. Thus, to in-place edit the sequence and quality scores, copies of the quality scores need to be taken. Consider trimming for example:: q = read.qual read.seq = read.seq[5:10] read.qual = q[5:10] """ def __get__(self): cdef bam1_t * src cdef char * s src = self._delegate if src.core.l_qseq == 0: return None return get_seq_range(src, 0, src.core.l_qseq) def __set__(self,seq): # samtools manages sequence and quality length memory together # if no quality information is present, the first byte says 0xff. cdef bam1_t * src cdef uint8_t * p cdef char * s cdef int l, k, nbytes_new, nbytes_old if seq == None: l = 0 else: l = len(seq) seq = _force_bytes(seq) src = self._delegate # as the sequence is stored in half-bytes, the total length (sequence # plus quality scores) is (l+1)/2 + l nbytes_new = (l+1)/2 + l nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # acquire pointer to location in memory p = bam1_seq( src ) src.core.l_qseq = l # change length of data field pysam_bam_update( src, nbytes_old, nbytes_new, p) if l > 0: # re-acquire pointer to location in memory # as it might have moved p = bam1_seq( src ) for k from 0 <= k < nbytes_new: p[k] = 0 # convert to C string s = seq for k from 0 <= k < l: p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # erase qualities p = bam1_qual( src ) p[0] = 0xff property qual: """read sequence base qualities, including :term:`soft clipped` bases (None if not present). In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient. Note that to set quality scores the sequence has to be set previously as this will determine the permitted length of the quality score array. This method raises a ValueError if the length of the quality scores and the sequence are not the same. """ def __get__(self): cdef bam1_t * src cdef char * q src = self._delegate if src.core.l_qseq == 0: return None return get_qual_range(src, 0, src.core.l_qseq) def __set__(self,qual): # note that space is already allocated via the sequences cdef bam1_t * src cdef uint8_t * p cdef char * q cdef int k src = self._delegate p = bam1_qual( src ) if qual == None or len(qual) == 0: # if absent - set to 0xff p[0] = 0xff return qual = _force_bytes(qual) cdef int l # convert to C string q = qual l = len(qual) if src.core.l_qseq != l: raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) assert src.core.l_qseq == l for k from 0 <= k < l: p[k] = q[k] - 33 property query: """aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present). In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient. SAM/BAM files may included extra flanking bases sequences that were not part of the alignment. These bases may be the result of the Smith-Waterman or other algorithms, which may not require alignments that begin at the first residue or end at the last. In addition, extra sequencing adapters, multiplex identifiers, and low-quality bases that were not considered for alignment may have been retained.""" def __get__(self): cdef bam1_t * src cdef uint32_t start, end cdef char * s src = self._delegate if src.core.l_qseq == 0: return None start = query_start(src) end = query_end(src) return get_seq_range(src, start, end) property qqual: """aligned query sequence quality values (None if not present). This property is read-only. In Python 3, this property is of type bytes.""" def __get__(self): cdef bam1_t * src cdef uint32_t start, end src = self._delegate if src.core.l_qseq == 0: return None start = query_start(src) end = query_end(src) return get_qual_range(src, start, end) property qstart: """start index of the aligned query portion of the sequence (0-based, inclusive)""" def __get__(self): return query_start(self._delegate) property qend: """end index of the aligned query portion of the sequence (0-based, exclusive)""" def __get__(self): return query_end(self._delegate) property qlen: """Length of the aligned query sequence""" def __get__(self): cdef bam1_t * src src = self._delegate return query_end(src)-query_start(src) property tags: """the tags in the AUX field. This property permits convenience access to the tags. Changes it the returned list will not update the tags automatically. Instead, the following is required for adding a new tag:: read.tags = read.tags + [("RG",0)] This method will happily write the same tag multiple times. """ def __get__(self): cdef char * ctag cdef bam1_t * src cdef uint8_t * s cdef char auxtag[3] cdef char auxtype cdef uint8_t byte_size cdef int32_t nvalues src = self._delegate if src.l_aux == 0: return [] s = bam1_aux( src ) result = [] auxtag[2] = 0 while s < (src.data + src.data_len): # get tag auxtag[0] = s[0] auxtag[1] = s[1] s += 2 auxtype = s[0] if auxtype in ('c', 'C'): value = bam_aux2i(s) s += 1 elif auxtype in ('s', 'S'): value = bam_aux2i(s) s += 2 elif auxtype in ('i', 'I'): value = bam_aux2i(s) s += 4 elif auxtype == 'f': value = bam_aux2f(s) s += 4 elif auxtype == 'd': value = bam_aux2d(s) s += 8 elif auxtype == 'A': value = "%c" % bam_aux2A(s) s += 1 elif auxtype in ('Z', 'H'): value = _charptr_to_str(bam_aux2Z(s)) # +1 for NULL terminated string s += len(value) + 1 elif auxtype == 'B': s += 1 byte_size, nvalues, value = convertBinaryTagToList( s ) # 5 for 1 char and 1 int s += 5 + ( nvalues * byte_size) - 1 s += 1 result.append( (_charptr_to_str(auxtag), value) ) return result def __set__(self, tags): cdef bam1_t * src cdef uint8_t * s cdef uint8_t * new_data cdef char * temp src = self._delegate fmts, args = ["<"], [] if tags != None: # map samtools code to python.struct code and byte size for pytag, value in tags: if not type(pytag) is bytes: pytag = pytag.encode('ascii') t = type(value) if t is tuple or t is list: # binary tags - treat separately pytype = 'B' # get data type - first value determines type if type(value[0]) is float: datafmt, datatype = "f", "f" else: mi, ma = min(value), max(value) absmax = max( abs(mi), abs(ma) ) # signed ints if mi < 0: if mi >= -127: datafmt, datatype = "b", 'c' elif mi >= -32767: datafmt, datatype = "h", 's' elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) else: datafmt, datatype = "i", 'i' # unsigned ints else: if absmax <= 255: datafmt, datatype = "B", 'C' elif absmax <= 65535: datafmt, datatype = "H", 'S' elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) else: datafmt, datatype = "I", 'I' datafmt = "2sccI%i%s" % (len(value), datafmt) args.extend( [pytag[:2], pytype.encode('ascii'), datatype.encode('ascii'), len(value)] + list(value) ) fmts.append( datafmt ) continue if t is float: fmt, pytype = "2scf", 'f' elif t is int: # negative values if value < 0: if value >= -127: fmt, pytype = "2scb", 'c' elif value >= -32767: fmt, pytype = "2sch", 's' elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) else: fmt, pytype = "2sci", 'i' # positive values else: if value <= 255: fmt, pytype = "2scB", 'C' elif value <= 65535: fmt, pytype = "2scH", 'S' elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) else: fmt, pytype = "2scI", 'I' else: # Note: hex strings (H) are not supported yet if t is not bytes: value = value.encode('ascii') if len(value) == 1: fmt, pytype = "2scc", 'A' else: fmt, pytype = "2sc%is" % (len(value)+1), 'Z' args.extend( [pytag[:2], pytype.encode('ascii'), value ] ) fmts.append( fmt ) fmt = "".join(fmts) total_size = struct.calcsize(fmt) buffer = ctypes.create_string_buffer(total_size) struct.pack_into( fmt, buffer, 0, *args ) # delete the old data and allocate new space. # If total_size == 0, the aux field will be # empty pysam_bam_update( src, src.l_aux, total_size, bam1_aux( src ) ) src.l_aux = total_size # copy data only if there is any if total_size != 0: # get location of new data s = bam1_aux( src ) # check if there is direct path from buffer.raw to tmp p = buffer.raw # create handle to make sure buffer stays alive long # enough for memcpy, see issue 129 temp = p memcpy( s, temp, total_size ) property flag: """properties flag""" def __get__(self): return self._delegate.core.flag def __set__(self, flag): self._delegate.core.flag = flag property rname: """ :term:`target` ID DEPRECATED from pysam-0.4 - use tid in the future. The rname field caused a lot of confusion as it returns the :term:`target` ID instead of the reference sequence name. .. note:: This field contains the index of the reference sequence in the sequence dictionary. To obtain the name of the reference sequence, use :meth:`pysam.Samfile.getrname()` """ def __get__(self): return self._delegate.core.tid def __set__(self, tid): self._delegate.core.tid = tid property tid: """ :term:`target` ID .. note:: This field contains the index of the reference sequence in the sequence dictionary. To obtain the name of the reference sequence, use :meth:`pysam.Samfile.getrname()` """ def __get__(self): return self._delegate.core.tid def __set__(self, tid): self._delegate.core.tid = tid property pos: """0-based leftmost coordinate""" def __get__(self): return self._delegate.core.pos def __set__(self, pos): ## setting the cigar string also updates the "bin" attribute cdef bam1_t * src src = self._delegate if src.core.n_cigar: src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) ) else: src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1) self._delegate.core.pos = pos property bin: """properties bin""" def __get__(self): return self._delegate.core.bin def __set__(self, bin): self._delegate.core.bin = bin property rlen: '''length of the read (read only). Returns 0 if not given.''' def __get__(self): return self._delegate.core.l_qseq property aend: '''aligned reference position of the read on the reference genome. aend points to one past the last aligned residue. Returns None if not available.''' def __get__(self): cdef bam1_t * src src = self._delegate if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: return None return bam_calend(&src.core, bam1_cigar(src)) property alen: '''aligned length of the read on the reference genome. Returns None if not available.''' def __get__(self): cdef bam1_t * src src = self._delegate if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: return None return bam_calend(&src.core, bam1_cigar(src)) - \ self._delegate.core.pos property mapq: """mapping quality""" def __get__(self): return self._delegate.core.qual def __set__(self, qual): self._delegate.core.qual = qual property mrnm: """the :term:`reference` id of the mate deprecated, use RNEXT instead. """ def __get__(self): return self._delegate.core.mtid def __set__(self, mtid): self._delegate.core.mtid = mtid property rnext: """the :term:`reference` id of the mate """ def __get__(self): return self._delegate.core.mtid def __set__(self, mtid): self._delegate.core.mtid = mtid property mpos: """the position of the mate deprecated, use PNEXT instead.""" def __get__(self): return self._delegate.core.mpos def __set__(self, mpos): self._delegate.core.mpos = mpos property pnext: """the position of the mate""" def __get__(self): return self._delegate.core.mpos def __set__(self, mpos): self._delegate.core.mpos = mpos ####################################################################### ####################################################################### ## Flags ####################################################################### property isize: """the insert size deprecated: use tlen instead""" def __get__(self): return self._delegate.core.isize def __set__(self, isize): self._delegate.core.isize = isize property tlen: """the insert size""" def __get__(self): return self._delegate.core.isize def __set__(self, isize): self._delegate.core.isize = isize property is_paired: """true if read is paired in sequencing""" def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FPAIRED else: self._delegate.core.flag &= ~BAM_FPAIRED property is_proper_pair: """true if read is mapped in a proper pair""" def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FPROPER_PAIR else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR property is_unmapped: """true if read itself is unmapped""" def __get__(self): return (self.flag & BAM_FUNMAP) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FUNMAP else: self._delegate.core.flag &= ~BAM_FUNMAP property mate_is_unmapped: """true if the mate is unmapped""" def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FMUNMAP else: self._delegate.core.flag &= ~BAM_FMUNMAP property is_reverse: """true if read is mapped to reverse strand""" def __get__(self): return (self.flag & BAM_FREVERSE) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FREVERSE else: self._delegate.core.flag &= ~BAM_FREVERSE property mate_is_reverse: """true is read is mapped to reverse strand""" def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FMREVERSE else: self._delegate.core.flag &= ~BAM_FMREVERSE property is_read1: """true if this is read1""" def __get__(self): return (self.flag & BAM_FREAD1) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FREAD1 else: self._delegate.core.flag &= ~BAM_FREAD1 property is_read2: """true if this is read2""" def __get__(self): return (self.flag & BAM_FREAD2) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FREAD2 else: self._delegate.core.flag &= ~BAM_FREAD2 property is_secondary: """true if not primary alignment""" def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FSECONDARY else: self._delegate.core.flag &= ~BAM_FSECONDARY property is_qcfail: """true if QC failure""" def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FQCFAIL else: self._delegate.core.flag &= ~BAM_FQCFAIL property is_duplicate: """true if optical or PCR duplicate""" def __get__(self): return (self.flag & BAM_FDUP) != 0 def __set__(self,val): if val: self._delegate.core.flag |= BAM_FDUP else: self._delegate.core.flag &= ~BAM_FDUP ####################################################################### ####################################################################### ## Derived properties ####################################################################### property positions: """a list of reference positions that this read aligns to.""" def __get__(self): cdef uint32_t k, i, pos cdef int op cdef uint32_t * cigar_p cdef bam1_t * src src = self._delegate if src.core.n_cigar == 0: return [] result = [] pos = src.core.pos cigar_p = bam1_cigar(src) for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH: for i from pos <= i < pos + l: result.append( i ) if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: pos += l return result property inferred_length: """inferred read length from CIGAR string. Returns 0 if CIGAR string is not present. """ def __get__(self): cdef uint32_t k, qpos cdef int op cdef uint32_t * cigar_p cdef bam1_t * src src = self._delegate if src.core.n_cigar == 0: return 0 qpos = 0 cigar_p = bam1_cigar(src) for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK if op == BAM_CMATCH or op == BAM_CINS or op == BAM_CSOFT_CLIP: qpos += cigar_p[k] >> BAM_CIGAR_SHIFT return qpos property aligned_pairs: """a list of aligned read and reference positions. Unaligned position are marked by None. """ def __get__(self): cdef uint32_t k, i, pos, qpos cdef int op cdef uint32_t * cigar_p cdef bam1_t * src src = self._delegate if src.core.n_cigar == 0: return [] result = [] pos = src.core.pos qpos = 0 cigar_p = bam1_cigar(src) for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH: for i from pos <= i < pos + l: result.append( (qpos, i) ) qpos += 1 pos += l elif op == BAM_CINS: for i from pos <= i < pos + l: result.append( (qpos, None) ) qpos += 1 elif op == BAM_CDEL or op == BAM_CREF_SKIP: for i from pos <= i < pos + l: result.append( (None, i) ) pos += l return result ####################################################################### ####################################################################### ## ####################################################################### def overlap( self, uint32_t start, uint32_t end ): """return number of aligned bases of read overlapping the interval *start* and *end* on the reference sequence. """ cdef uint32_t k, i, pos, overlap cdef int op, o cdef uint32_t * cigar_p cdef bam1_t * src overlap = 0 src = self._delegate if src.core.n_cigar == 0: return 0 pos = src.core.pos o = 0 cigar_p = bam1_cigar(src) for k from 0 <= k < src.core.n_cigar: op = cigar_p[k] & BAM_CIGAR_MASK l = cigar_p[k] >> BAM_CIGAR_SHIFT if op == BAM_CMATCH: o = min( pos + l, end) - max( pos, start ) if o > 0: overlap += o if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: pos += l return overlap def opt(self, tag): """retrieves optional data given a two-letter *tag*""" #see bam_aux.c: bam_aux_get() and bam_aux2i() etc cdef uint8_t * v cdef int nvalues btag = _force_bytes(tag) v = bam_aux_get(self._delegate, btag) if v == NULL: raise KeyError( "tag '%s' not present" % tag ) auxtype = chr(v[0]) if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S': return bam_aux2i(v) elif auxtype == 'i' or auxtype == 'I': return bam_aux2i(v) elif auxtype == 'f' or auxtype == 'F': return bam_aux2f(v) elif auxtype == 'd' or auxtype == 'D': return bam_aux2d(v) elif auxtype == 'A': # there might a more efficient way # to convert a char into a string return '%c' % bam_aux2A(v) elif auxtype == 'Z': return _charptr_to_str(bam_aux2Z(v)) elif auxtype == 'B': bytesize, nvalues, values = convertBinaryTagToList( v + 1 ) return values else: raise ValueError("unknown auxilliary type '%s'" % auxtype) def fancy_str (self): """returns list of fieldnames/values in pretty format for debugging """ ret_string = [] field_names = { "tid": "Contig index", "pos": "Mapped position on contig", "mtid": "Contig index for mate pair", "mpos": "Position of mate pair", "isize": "Insert size", "flag": "Binary flag", "n_cigar": "Count of cigar entries", "cigar": "Cigar entries", "qual": "Mapping quality", "bin": "Bam index bin number", "l_qname": "Length of query name", "qname": "Query name", "l_qseq": "Length of query sequence", "qseq": "Query sequence", "bqual": "Quality scores", "l_aux": "Length of auxilary data", "m_data": "Maximum data length", "data_len": "Current data length", } fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", "n_cigar", "cigar", "qual", "bin", "l_qname", "qname", "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"] for f in fields_names_in_order: if not f in self.__dict__: continue ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f))) for f in self.__dict__: if not f in field_names: ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) return ret_string cdef class PileupProxy: '''A pileup column. A pileup column contains all the reads that map to a certain target base. tid chromosome ID as is defined in the header pos the target base coordinate (0-based) n number of reads mapping to this column pileups list of reads (:class:`pysam.PileupRead`) aligned to this column This class is a proxy for results returned by the samtools pileup engine. If the underlying engine iterator advances, the results of this column will change. ''' def __init__(self): raise TypeError("This class cannot be instantiated from Python") def __str__(self): return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ "\n" +\ "\n".join( map(str, self.pileups) ) property tid: '''the chromosome ID as is defined in the header''' def __get__(self): return self.tid property n: '''number of reads mapping to this column.''' def __get__(self): return self.n_pu def __set__(self, n): self.n_pu = n property pos: def __get__(self): return self.pos property pileups: '''list of reads (:class:`pysam.PileupRead`) aligned to this column''' def __get__(self): cdef int x pileups = [] if self.plp == NULL or self.plp[0] == NULL: raise ValueError("PileupProxy accessed after iterator finished") # warning: there could be problems if self.n and self.buf are # out of sync. for x from 0 <= x < self.n_pu: pileups.append( makePileupRead( &(self.plp[0][x])) ) return pileups cdef class PileupRead: '''A read aligned to a column. ''' def __init__(self): raise TypeError("This class cannot be instantiated from Python") def __str__(self): return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) ) property alignment: """a :class:`pysam.AlignedRead` object of the aligned read""" def __get__(self): return self._alignment property qpos: """position of the read base at the pileup site, 0-based""" def __get__(self): return self._qpos property indel: """indel length; 0 for no indel, positive for ins and negative for del""" def __get__(self): return self._indel property is_del: """1 iff the base on the padded read is a deletion""" def __get__(self): return self._is_del property is_head: def __get__(self): return self._is_head property is_tail: def __get__(self): return self._is_tail property level: def __get__(self): return self._level class Outs: '''http://mail.python.org/pipermail/python-list/2000-June/038406.html''' def __init__(self, id = 1): self.streams = [] self.id = id def setdevice(self, filename): '''open an existing file, like "/dev/null"''' fd = os.open(filename, os.O_WRONLY) self.setfd(fd) def setfile(self, filename): '''open a new file.''' fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); self.setfd(fd) def setfd(self, fd): ofd = os.dup(self.id) # Save old stream on new unit. self.streams.append(ofd) sys.stdout.flush() # Buffered data goes to old stream. sys.stderr.flush() # Buffered data goes to old stream. os.dup2(fd, self.id) # Open unit 1 on new stream. os.close(fd) # Close other unit (look out, caller.) def restore(self): '''restore previous output stream''' if self.streams: # the following was not sufficient, hence flush both stderr and stdout # os.fsync( self.id ) sys.stdout.flush() sys.stderr.flush() os.dup2(self.streams[-1], self.id) os.close(self.streams[-1]) del self.streams[-1] def _samtools_dispatch( method, args = (), catch_stdout = True ): '''call ``method`` in samtools providing arguments in args. .. note:: This method redirects stdout to capture it from samtools. If for some reason stdout disappears the reason might be in this method. .. note:: The current implementation might only work on linux. .. note:: This method captures stdout and stderr using temporary files, which are then read into memory in their entirety. This method is slow and might cause large memory overhead. See http://bytes.com/topic/c/answers/487231-how-capture-stdout-temporarily on the topic of redirecting stderr/stdout. ''' # note that debugging this module can be a problem # as stdout/stderr will not appear on the terminal # some special cases if method == "index": if not os.path.exists( args[0] ): raise IOError( "No such file or directory: '%s'" % args[0] ) # redirect stderr and stdout to file stderr_h, stderr_f = tempfile.mkstemp() pysam_set_stderr( stderr_h ) if catch_stdout: stdout_h, stdout_f = tempfile.mkstemp() try: stdout_save = Outs( sys.stdout.fileno() ) stdout_save.setfd( stdout_h ) except AttributeError: # stdout has already been redirected catch_stdout = False # patch for `samtools view` # samtools `view` closes stdout, from which I can not # recover. Thus redirect output to file with -o option. if method == "view": if "-o" in args: raise ValueError("option -o is forbidden in samtools view") args = ( "-o", stdout_f ) + args # do the function call to samtools cdef char ** cargs cdef int i, n, retval n = len(args) method = _force_cmdline_bytes(method) args = [ _force_cmdline_bytes(a) for a in args ] # allocate two more for first (dummy) argument (contains command) cargs = calloc( n+2, sizeof( char *) ) cargs[0] = "samtools" cargs[1] = method for i from 0 <= i < n: cargs[i+2] = args[i] retval = pysam_dispatch(n+2, cargs) free( cargs ) # restore stdout/stderr. This will also flush, so # needs to be before reading back the file contents if catch_stdout: stdout_save.restore() try: with open( stdout_f, "r") as inf: out_stdout = inf.readlines() except UnicodeDecodeError: with open( stdout_f, "rb") as inf: # read binary output out_stdout = inf.read() os.remove( stdout_f ) else: out_stdout = [] # get error messages pysam_unset_stderr() try: with open( stderr_f, "r") as inf: out_stderr = inf.readlines() except UnicodeDecodeError: with open( stderr_f, "rb") as inf: # read binary output out_stderr = inf.read() else: out_stderr = [] finally: os.remove( stderr_f ) return retval, out_stderr, out_stdout cdef class SNPCall: '''the results of a SNP call.''' cdef int _tid cdef int _pos cdef char _reference_base cdef char _genotype cdef int _consensus_quality cdef int _snp_quality cdef int _rms_mapping_quality cdef int _coverage property tid: '''the chromosome ID as is defined in the header''' def __get__(self): return self._tid property pos: '''nucleotide position of SNP.''' def __get__(self): return self._pos property reference_base: '''reference base at pos. ``N`` if no reference sequence supplied.''' def __get__(self): return from_string_and_size( &self._reference_base, 1 ) property genotype: '''the genotype called.''' def __get__(self): return from_string_and_size( &self._genotype, 1 ) property consensus_quality: '''the genotype quality (Phred-scaled).''' def __get__(self): return self._consensus_quality property snp_quality: '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.''' def __get__(self): return self._snp_quality property mapping_quality: '''the root mean square (rms) of the mapping quality of all reads involved in the call.''' def __get__(self): return self._rms_mapping_quality property coverage: '''coverage or read depth - the number of reads involved in the call.''' def __get__(self): return self._coverage def __str__(self): return "\t".join( map(str, ( self.tid, self.pos, self.reference_base, self.genotype, self.consensus_quality, self.snp_quality, self.mapping_quality, self.coverage ) ) ) # cdef class SNPCallerBase: # '''Base class for SNP callers. # *min_baseQ* # minimum base quality (possibly capped by BAQ) # *capQ_threshold* # coefficient for adjusting mapQ of poor mappings # *theta* # theta in maq consensus calling model # *n_haplotypes* # number of haplotypes in the sample # *het_rate* # prior of a difference between two haplotypes # ''' # cdef bam_maqcns_t * c # cdef IteratorColumn iter # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # self.iter = iterator_column # self.c = bam_maqcns_init() # # set the default parameterization according to # # samtools # # new default mode for samtools >0.1.10 # self.c.errmod = kwargs.get( "errmod", BAM_ERRMOD_MAQ2 ) # self.c.min_baseQ = kwargs.get( "min_baseQ", 13 ) # # self.c.capQ_thres = kwargs.get( "capQ_threshold", 60 ) # self.c.n_hap = kwargs.get( "n_haplotypes", 2 ) # self.c.het_rate = kwargs.get( "het_rate", 0.001 ) # self.c.theta = kwargs.get( "theta", 0.83 ) # if self.c.errmod != BAM_ERRMOD_MAQ2: # self.c.theta += 0.02 # # call prepare AFTER setting parameters # bam_maqcns_prepare( self.c ) # def __dealloc__(self): # bam_maqcns_destroy( self.c ) # cdef __dump( self, glf1_t * g, uint32_t cns, int rb ): # '''debugging output.''' # pysam_dump_glf( g, self.c ); # print "" # for x in range(self.iter.n_plp): # print "--> read %i %s %i" % (x, # bam1_qname(self.iter.plp[x].b), # self.iter.plp[x].qpos, # ) # print "pos=%i, cns=%i, q_r = %f, depth=%i, n=%i, rb=%i, cns-cq=%i %i %i %i" \ # % (self.iter.pos, # cns, # self.c.q_r, # self.iter.n_plp, # self.iter.n_plp, # rb, # cns >> 8 & 0xff, # cns >> 16 & 0xff, # cns & 0xff, # cns >> 28, # ) # printf("-------------------------------------\n"); # sys.stdout.flush() # cdef class IteratorSNPCalls( SNPCallerBase ): # """*(IteratorColumn iterator)* # call SNPs within a region. # *iterator* is a pileup iterator. SNPs will be called # on all positions returned by this iterator. # This caller is fast if SNPs are called over large continuous # regions. It is slow, if instantiated frequently and in random # order as the sequence will have to be reloaded. # """ # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # assert self.iter.hasReference(), "IteratorSNPCalls requires an pileup iterator with reference sequence" # def __iter__(self): # return self # def __next__(self): # """python version of next(). # """ # # the following code was adapted from bam_plcmd.c:pileup_func() # self.iter.cnext() # if self.iter.n_plp < 0: # raise ValueError("error during iteration" ) # if self.iter.plp == NULL: # raise StopIteration # cdef char * seq = self.iter.getSequence() # cdef int seq_len = self.iter.seq_len # assert seq != NULL # # reference base # if self.iter.pos >= seq_len: # raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # cdef int rb = seq[self.iter.pos] # cdef uint32_t cns # cdef glf1_t * g # g = bam_maqcns_glfgen( self.iter.n_plp, # self.iter.plp, # bam_nt16_table[rb], # self.c ) # if pysam_glf_depth( g ) == 0: # cns = 0xfu << 28 | 0xf << 24 # else: # cns = glf2cns(g, (self.c.q_r + .499)) # free(g) # cdef SNPCall call # call = SNPCall() # call._tid = self.iter.tid # call._pos = self.iter.pos # call._reference_base = rb # call._genotype = bam_nt16_rev_table[cns>>28] # call._consensus_quality = cns >> 8 & 0xff # call._snp_quality = cns & 0xff # call._rms_mapping_quality = cns >> 16&0xff # call._coverage = self.iter.n_plp # return call # cdef class SNPCaller( SNPCallerBase ): # '''*(IteratorColumn iterator_column )* # The samtools SNP caller. # This object will call SNPs in *samfile* against the reference # sequence in *fasta*. # This caller is fast for calling few SNPs in selected regions. # It is slow, if called over large genomic regions. # ''' # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # pass # def call(self, reference, int pos ): # """call a snp on chromosome *reference* # and position *pos*. # returns a :class:`SNPCall` object. # """ # cdef int tid = self.iter.samfile.gettid( reference ) # self.iter.reset( tid, pos, pos + 1 ) # while 1: # self.iter.cnext() # if self.iter.n_plp < 0: # raise ValueError("error during iteration" ) # if self.iter.plp == NULL: # raise ValueError( "no reads in region - no call" ) # if self.iter.pos == pos: break # cdef char * seq = self.iter.getSequence() # cdef int seq_len = self.iter.seq_len # assert seq != NULL # # reference base # if self.iter.pos >= seq_len: # raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # cdef int rb = seq[self.iter.pos] # cdef uint32_t cns # # cdef glf1_t * g # # # # g = bam_maqcns_glfgen( self.iter.n_plp, # # self.iter.plp, # # bam_nt16_table[rb], # # self.c ) # ## # # # # if pysam_glf_depth( g ) == 0: # # cns = 0xfu << 28 | 0xf << 24 # # else: # # cns = glf2cns(g, (self.c.q_r + .499)) # # # # free(g) # cdef SNPCall call # call = SNPCall() # call._tid = self.iter.tid # call._pos = self.iter.pos # call._reference_base = rb # call._genotype = bam_nt16_rev_table[cns>>28] # call._consensus_quality = cns >> 8 & 0xff # call._snp_quality = cns & 0xff # call._rms_mapping_quality = cns >> 16&0xff # call._coverage = self.iter.n_plp # return call # cdef class IndelCall: # '''the results of an indel call.''' # cdef int _tid # cdef int _pos # cdef int _coverage # cdef int _rms_mapping_quality # cdef bam_maqindel_ret_t * _r # def __cinit__(self): # #assert r != NULL # #self._r = r # pass # property tid: # '''the chromosome ID as is defined in the header''' # def __get__(self): # return self._tid # property pos: # '''nucleotide position of SNP.''' # def __get__(self): return self._pos # property genotype: # '''the genotype called.''' # def __get__(self): # if self._r.gt == 0: # s = PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1) # return "%s/%s" % (s,s) # elif self._r.gt == 1: # s = PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1) # return "%s/%s" % (s,s) # else: # return "%s/%s" % (self.first_allele, self.second_allele ) # property consensus_quality: # '''the genotype quality (Phred-scaled).''' # def __get__(self): return self._r.q_cns # property snp_quality: # '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.''' # def __get__(self): return self._r.q_ref # property mapping_quality: # '''the root mean square (rms) of the mapping quality of all reads involved in the call.''' # def __get__(self): return self._rms_mapping_quality # property coverage: # '''coverage or read depth - the number of reads involved in the call.''' # def __get__(self): return self._coverage # property first_allele: # '''sequence of first allele.''' # def __get__(self): return PyString_FromStringAndSize( self._r.s[0], self._r.indel1 + 1) # property second_allele: # '''sequence of second allele.''' # def __get__(self): return PyString_FromStringAndSize( self._r.s[1], self._r.indel2 + 1) # property reads_first: # '''reads supporting first allele.''' # def __get__(self): return self._r.cnt1 # property reads_second: # '''reads supporting first allele.''' # def __get__(self): return self._r.cnt2 # property reads_diff: # '''reads supporting first allele.''' # def __get__(self): return self._r.cnt_anti # def __str__(self): # return "\t".join( map(str, ( # self.tid, # self.pos, # self.genotype, # self.consensus_quality, # self.snp_quality, # self.mapping_quality, # self.coverage, # self.first_allele, # self.second_allele, # self.reads_first, # self.reads_second, # self.reads_diff ) ) ) # def __dealloc__(self ): # bam_maqindel_ret_destroy(self._r) # cdef class IndelCallerBase: # '''Base class for SNP callers. # *min_baseQ* # minimum base quality (possibly capped by BAQ) # *capQ_threshold* # coefficient for adjusting mapQ of poor mappings # *theta* # theta in maq consensus calling model # *n_haplotypes* # number of haplotypes in the sample # *het_rate* # prior of a difference between two haplotypes # ''' # cdef bam_maqindel_opt_t * options # cdef IteratorColumn iter # cdef int cap_mapQ # cdef int max_depth # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # self.iter = iterator_column # assert iterator_column.hasReference(), "IndelCallerBase requires an pileup iterator with reference sequence" # self.options = bam_maqindel_opt_init() # # set the default parameterization according to # # samtools # self.options.r_indel = kwargs.get( "r_indel", 0.00015 ) # self.options.q_indel = kwargs.get( "q_indel", 40 ) # self.cap_mapQ = kwargs.get( "cap_mapQ", 60 ) # self.max_depth = kwargs.get( "max_depth", 1024 ) # def __dealloc__(self): # free( self.options ) # def _call( self ): # cdef char * seq = self.iter.getSequence() # cdef int seq_len = self.iter.seq_len # assert seq != NULL # # reference base # if self.iter.pos >= seq_len: # raise ValueError( "position %i out of bounds on reference sequence (len=%i)" % (self.iter.pos, seq_len) ) # cdef bam_maqindel_ret_t * r # cdef int m = min( self.max_depth, self.iter.n_plp ) # # printf("pysam: m=%i, q_indel=%i, r_indel=%f, r_snp=%i, mm_penalty=%i, indel_err=%i, ambi_thres=%i\n", # # m, self.options.q_indel, self.options.r_indel, self.options.r_snp, self.options.mm_penalty, # # self.options.indel_err, self.options.ambi_thres ); # r = bam_maqindel(m, # self.iter.pos, # self.options, # self.iter.plp, # seq, # 0, # NULL) # if r == NULL: return None # cdef IndelCall call # call = IndelCall() # call._r = r # call._tid = self.iter.tid # call._pos = self.iter.pos # call._coverage = self.iter.n_plp # cdef uint64_t rms_aux = 0 # cdef int i = 0 # cdef bam_pileup1_t * p # cdef int tmp # for i from 0 <= i < self.iter.n_plp: # p = self.iter.plp + i # if p.b.core.qual < self.cap_mapQ: # tmp = p.b.core.qual # else: # tmp = self.cap_mapQ # rms_aux += tmp * tmp # call._rms_mapping_quality = (sqrt(rms_aux / self.iter.n_plp) + .499) # return call # cdef class IndelCaller( IndelCallerBase ): # '''*(IteratorColumn iterator_column )* # The samtools SNP caller. # This object will call SNPs in *samfile* against the reference # sequence in *fasta*. # This caller is fast for calling few SNPs in selected regions. # It is slow, if called over large genomic regions. # ''' # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # pass # def call(self, reference, int pos ): # """call a snp on chromosome *reference* # and position *pos*. # returns a :class:`SNPCall` object or None, if no indel call could be made. # """ # cdef int tid = self.iter.samfile.gettid( reference ) # self.iter.reset( tid, pos, pos + 1 ) # while 1: # self.iter.cnext() # if self.iter.n_plp < 0: # raise ValueError("error during iteration" ) # if self.iter.plp == NULL: # raise ValueError( "no reads in region - no call" ) # if self.iter.pos == pos: break # return self._call() # cdef class IteratorIndelCalls( IndelCallerBase ): # """*(IteratorColumn iterator)* # call indels within a region. # *iterator* is a pileup iterator. SNPs will be called # on all positions returned by this iterator. # This caller is fast if SNPs are called over large continuous # regions. It is slow, if instantiated frequently and in random # order as the sequence will have to be reloaded. # """ # def __cinit__(self, # IteratorColumn iterator_column, # **kwargs ): # pass # def __iter__(self): # return self # def __next__(self): # """python version of next(). # """ # # the following code was adapted from bam_plcmd.c:pileup_func() # self.iter.cnext() # if self.iter.n_plp < 0: # raise ValueError("error during iteration" ) # if self.iter.plp == NULL: # raise StopIteration # return self._call() cdef class IndexedReads: """index a bamfile by read. The index is kept in memory. By default, the file is re-openend to avoid conflicts if multiple operators work on the same file. Set *reopen* = False to not re-open *samfile*. """ def __init__(self, Samfile samfile, int reopen = True ): self.samfile = samfile if samfile.isbam: mode = b"rb" else: mode = b"r" # reopen the file - note that this makes the iterator # slow and causes pileup to slow down significantly. if reopen: store = StderrStore() self.fp = samopen( samfile._filename, mode, NULL ) store.release() assert self.fp != NULL self.owns_samfile = True else: self.fp = samfile.samfile self.owns_samfile = False assert samfile.isbam, "can only IndexReads on bam files" def build( self ): '''build index.''' self.index = collections.defaultdict( list ) # this method will start indexing from the current file position # if you decide cdef int ret = 1 cdef bam1_t * b = calloc(1, sizeof( bam1_t) ) cdef uint64_t pos while ret > 0: pos = bam_tell( self.fp.x.bam ) ret = samread( self.fp, b) if ret > 0: qname = _charptr_to_str(bam1_qname( b )) self.index[qname].append( pos ) bam_destroy1( b ) def find( self, qname ): if qname in self.index: return IteratorRowSelection( self.samfile, self.index[qname], reopen = False ) else: raise KeyError( "read %s not found" % qname ) def __dealloc__(self): if self.owns_samfile: samclose( self.fp ) __all__ = ["Samfile", "Fastafile", "Fastqfile", "IteratorRow", "IteratorColumn", "AlignedRead", "PileupColumn", "PileupProxy", "PileupRead", # "IteratorSNPCalls", # "SNPCaller", # "IndelCaller", # "IteratorIndelCalls", "IndexedReads" ] pysam-0.7.7/setup.cfg0000664000076400007650000000032212241575073014331 0ustar andreasandreas[bdist_rpm] vendor = TDB doc_files = README doc/*.html ChangeLog distribution-name = Red Hat Linux packager = TDB requires = python [egg_info] tag_build = tag_date = 0 tag_svn_revision = 0 pysam-0.7.7/PKG-INFO0000664000076400007650000000044112241575073013607 0ustar andreasandreasMetadata-Version: 1.1 Name: pysam Version: 0.7.7 Summary: pysam Home-page: http://code.google.com/p/pysam/ Author: Andreas Heger Author-email: andreas.heger@gmail.com License: MIT Description: pysam ***** Platform: ALL Requires: cython (>=0.17) pysam-0.7.7/THANKS0000664000076400007650000000040112007666010013411 0ustar andreasandreasWe would like to thank Heng Li and the other samtools contributors for their support and their hard work. As a wrapper, pysam merely tries to make their code accessible to the python community - the heavy lifting has been done by the samtools developers. pysam-0.7.7/samtools/0000775000076400007650000000000012241575073014354 5ustar andreasandreaspysam-0.7.7/samtools/bam_sort.c.pysam.c0000664000076400007650000004452712162637166017717 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include #include "bam.h" #include "ksort.h" static int g_is_by_qname = 0; static int strnum_cmp(const char *_a, const char *_b) { const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b; const unsigned char *pa = a, *pb = b; while (*pa && *pb) { if (isdigit(*pa) && isdigit(*pb)) { while (*pa == '0') ++pa; while (*pb == '0') ++pb; while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb; if (isdigit(*pa) && isdigit(*pb)) { int i = 0; while (isdigit(pa[i]) && isdigit(pb[i])) ++i; return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb; } else if (isdigit(*pa)) return 1; else if (isdigit(*pb)) return -1; else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1; } else { if (*pa != *pb) return (int)*pa - (int)*pb; ++pa; ++pb; } } return *pa? 1 : *pb? -1 : 0; } #define HEAP_EMPTY 0xffffffffffffffffull typedef struct { int i; uint64_t pos, idx; bam1_t *b; } heap1_t; #define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx)))) static inline int heap_lt(const heap1_t a, const heap1_t b) { if (g_is_by_qname) { int t; if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0; t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b)); return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0))); } else return __pos_cmp(a, b); } KSORT_INIT(heap, heap1_t, heap_lt) static void swap_header_targets(bam_header_t *h1, bam_header_t *h2) { bam_header_t t; t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets; t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name; t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len; } static void swap_header_text(bam_header_t *h1, bam_header_t *h2) { int tempi; char *temps; tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi; temps = h1->text, h1->text = h2->text, h2->text = temps; } #define MERGE_RG 1 #define MERGE_UNCOMP 2 #define MERGE_LEVEL1 4 #define MERGE_FORCE 8 /*! @abstract Merge multiple sorted BAM. @param is_by_qname whether to sort by query name @param out output BAM file name @param headers name of SAM file from which to copy '@' header lines, or NULL to copy them from the first file to be merged @param n number of files to be merged @param fn names of files to be merged @discussion Padding information may NOT correctly maintained. This function is NOT thread safe. */ int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level) { bamFile fpout, *fp; heap1_t *heap; bam_header_t *hout = 0; bam_header_t *hheaders = NULL; int i, j, *RG_len = 0; uint64_t idx = 0; char **RG = 0, mode[8]; bam_iter_t *iter = 0; if (headers) { tamFile fpheaders = sam_open(headers); if (fpheaders == 0) { const char *message = strerror(errno); fprintf(pysamerr, "[bam_merge_core] cannot open '%s': %s\n", headers, message); return -1; } hheaders = sam_header_read(fpheaders); sam_close(fpheaders); } g_is_by_qname = by_qname; fp = (bamFile*)calloc(n, sizeof(bamFile)); heap = (heap1_t*)calloc(n, sizeof(heap1_t)); iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t)); // prepare RG tag if (flag & MERGE_RG) { RG = (char**)calloc(n, sizeof(void*)); RG_len = (int*)calloc(n, sizeof(int)); for (i = 0; i != n; ++i) { int l = strlen(fn[i]); const char *s = fn[i]; if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4; for (j = l - 1; j >= 0; --j) if (s[j] == '/') break; ++j; l -= j; RG[i] = calloc(l + 1, 1); RG_len[i] = l; strncpy(RG[i], s + j, l); } } // read the first for (i = 0; i != n; ++i) { bam_header_t *hin; fp[i] = bam_open(fn[i], "r"); if (fp[i] == 0) { int j; fprintf(pysamerr, "[bam_merge_core] fail to open file %s\n", fn[i]); for (j = 0; j < i; ++j) bam_close(fp[j]); free(fp); free(heap); // FIXME: possible memory leak return -1; } hin = bam_header_read(fp[i]); if (i == 0) { // the first BAM hout = hin; } else { // validate multiple baf int min_n_targets = hout->n_targets; if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets; for (j = 0; j < min_n_targets; ++j) if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) { fprintf(pysamerr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n", hout->target_name[j], hin->target_name[j], fn[i]); return -1; } // If this input file has additional target reference sequences, // add them to the headers to be output if (hin->n_targets > hout->n_targets) { swap_header_targets(hout, hin); // FIXME Possibly we should also create @SQ text headers // for the newly added reference sequences } bam_header_destroy(hin); } } if (hheaders) { // If the text headers to be swapped in include any @SQ headers, // check that they are consistent with the existing binary list // of reference information. if (hheaders->n_targets > 0) { if (hout->n_targets != hheaders->n_targets) { fprintf(pysamerr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers); if (!reg) return -1; } for (j = 0; j < hout->n_targets; ++j) if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) { fprintf(pysamerr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers); if (!reg) return -1; } } swap_header_text(hout, hheaders); bam_header_destroy(hheaders); } if (reg) { int tid, beg, end; if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) { fprintf(pysamerr, "[%s] Malformated region string or undefined reference name\n", __func__); return -1; } for (i = 0; i < n; ++i) { bam_index_t *idx; idx = bam_index_load(fn[i]); iter[i] = bam_iter_query(idx, tid, beg, end); bam_index_destroy(idx); } } for (i = 0; i < n; ++i) { heap1_t *h = heap + i; h->i = i; h->b = (bam1_t*)calloc(1, sizeof(bam1_t)); if (bam_iter_read(fp[i], iter[i], h->b) >= 0) { h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b); h->idx = idx++; } else h->pos = HEAP_EMPTY; } if (flag & MERGE_UNCOMP) level = 0; else if (flag & MERGE_LEVEL1) level = 1; strcpy(mode, "w"); if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9); if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) { fprintf(pysamerr, "[%s] fail to create the output file.\n", __func__); return -1; } bam_header_write(fpout, hout); bam_header_destroy(hout); if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256); ks_heapmake(heap, n, heap); while (heap->pos != HEAP_EMPTY) { bam1_t *b = heap->b; if (flag & MERGE_RG) { uint8_t *rg = bam_aux_get(b, "RG"); if (rg) bam_aux_del(b, rg); bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]); } bam_write1_core(fpout, &b->core, b->data_len, b->data); if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) { heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b); heap->idx = idx++; } else if (j == -1) { heap->pos = HEAP_EMPTY; free(heap->b->data); free(heap->b); heap->b = 0; } else fprintf(pysamerr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]); ks_heapadjust(heap, 0, n, heap); } if (flag & MERGE_RG) { for (i = 0; i != n; ++i) free(RG[i]); free(RG); free(RG_len); } for (i = 0; i != n; ++i) { bam_iter_destroy(iter[i]); bam_close(fp[i]); } bam_close(fpout); free(fp); free(heap); free(iter); return 0; } int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg) { return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1); } int bam_merge(int argc, char *argv[]) { int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1; char *fn_headers = NULL, *reg = 0; while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) { switch (c) { case 'r': flag |= MERGE_RG; break; case 'f': flag |= MERGE_FORCE; break; case 'h': fn_headers = strdup(optarg); break; case 'n': is_by_qname = 1; break; case '1': flag |= MERGE_LEVEL1; break; case 'u': flag |= MERGE_UNCOMP; break; case 'R': reg = strdup(optarg); break; case 'l': level = atoi(optarg); break; case '@': n_threads = atoi(optarg); break; } } if (optind + 2 >= argc) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools merge [-nr] [-h inh.sam] [...]\n\n"); fprintf(pysamerr, "Options: -n sort by read names\n"); fprintf(pysamerr, " -r attach RG tag (inferred from file names)\n"); fprintf(pysamerr, " -u uncompressed BAM output\n"); fprintf(pysamerr, " -f overwrite the output BAM if exist\n"); fprintf(pysamerr, " -1 compress level 1\n"); fprintf(pysamerr, " -l INT compression level, from 0 to 9 [-1]\n"); fprintf(pysamerr, " -@ INT number of BAM compression threads [0]\n"); fprintf(pysamerr, " -R STR merge file in the specified region STR [all]\n"); fprintf(pysamerr, " -h FILE copy the header in FILE to [in1.bam]\n\n"); fprintf(pysamerr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n"); fprintf(pysamerr, " must provide the correct header with -h, or uses Picard which properly maintains\n"); fprintf(pysamerr, " the header dictionary in merging.\n\n"); return 1; } if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) { FILE *fp = fopen(argv[optind], "rb"); if (fp != NULL) { fclose(fp); fprintf(pysamerr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]); return 1; } } if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1; free(reg); free(fn_headers); return ret; } /*************** * BAM sorting * ***************/ #include typedef bam1_t *bam1_p; static int change_SO(bam_header_t *h, const char *so) { char *p, *q, *beg = 0, *end = 0, *newtext; if (h->l_text > 3) { if (strncmp(h->text, "@HD", 3) == 0) { if ((p = strchr(h->text, '\n')) == 0) return -1; *p = '\0'; if ((q = strstr(h->text, "\tSO:")) != 0) { *p = '\n'; // change back if (strncmp(q + 4, so, p - q - 4) != 0) { beg = q; for (q += 4; *q != '\n' && *q != '\t'; ++q); end = q; } else return 0; // no need to change } else beg = end = p, *p = '\n'; } } if (beg == 0) { // no @HD h->l_text += strlen(so) + 15; newtext = malloc(h->l_text + 1); sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so); strcat(newtext, h->text); } else { // has @HD but different or no SO h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end); newtext = malloc(h->l_text + 1); strncpy(newtext, h->text, beg - h->text); sprintf(newtext + (beg - h->text), "\tSO:%s", so); strcat(newtext, end); } free(h->text); h->text = newtext; return 0; } static inline int bam1_lt(const bam1_p a, const bam1_p b) { if (g_is_by_qname) { int t = strnum_cmp(bam1_qname(a), bam1_qname(b)); return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0))); } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b))); } KSORT_INIT(sort, bam1_p, bam1_lt) typedef struct { size_t buf_len; const char *prefix; bam1_p *buf; const bam_header_t *h; int index; } worker_t; static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads) { size_t i; bamFile fp; fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode); if (fp == 0) return; bam_header_write(fp, h); if (n_threads > 1) bgzf_mt(fp, n_threads, 256); for (i = 0; i < l; ++i) bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data); bam_close(fp); } static void *worker(void *data) { worker_t *w = (worker_t*)data; char *name; ks_mergesort(sort, w->buf_len, w->buf, 0); name = (char*)calloc(strlen(w->prefix) + 20, 1); sprintf(name, "%s.%.4d.bam", w->prefix, w->index); write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0); free(name); return 0; } static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads) { int i; size_t rest; bam1_p *b; pthread_t *tid; pthread_attr_t attr; worker_t *w; if (n_threads < 1) n_threads = 1; if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records pthread_attr_init(&attr); pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); w = calloc(n_threads, sizeof(worker_t)); tid = calloc(n_threads, sizeof(pthread_t)); b = buf; rest = k; for (i = 0; i < n_threads; ++i) { w[i].buf_len = rest / (n_threads - i); w[i].buf = b; w[i].prefix = prefix; w[i].h = h; w[i].index = n_files + i; b += w[i].buf_len; rest -= w[i].buf_len; pthread_create(&tid[i], &attr, worker, &w[i]); } for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0); free(tid); free(w); return n_files + n_threads; } /*! @abstract Sort an unsorted BAM file based on the chromosome order and the leftmost position of an alignment @param is_by_qname whether to sort by query name @param fn name of the file to be sorted @param prefix prefix of the output and the temporary files; upon sucessess, prefix.bam will be written. @param max_mem approxiate maximum memory (very inaccurate) @param full_path the given output path is the full path and not just the prefix @discussion It may create multiple temporary subalignment files and then merge them by calling bam_merge_core(). This function is NOT thread safe. */ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path) { int ret, i, n_files = 0; size_t mem, max_k, k, max_mem; bam_header_t *header; bamFile fp; bam1_t *b, **buf; char *fnout = 0; char const *suffix = ".bam"; if (full_path) suffix += 4; if (n_threads < 2) n_threads = 1; g_is_by_qname = is_by_qname; max_k = k = 0; mem = 0; max_mem = _max_mem * n_threads; buf = 0; fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r"); if (fp == 0) { fprintf(pysamerr, "[bam_sort_core] fail to open file %s\n", fn); return; } header = bam_header_read(fp); if (is_by_qname) change_SO(header, "queryname"); else change_SO(header, "coordinate"); // write sub files for (;;) { if (k == max_k) { size_t old_max = max_k; max_k = max_k? max_k<<1 : 0x10000; buf = realloc(buf, max_k * sizeof(void*)); memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max)); } if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t)); b = buf[k]; if ((ret = bam_read1(fp, b)) < 0) break; if (b->data_len < b->m_data>>2) { // shrink b->m_data = b->data_len; kroundup32(b->m_data); b->data = realloc(b->data, b->m_data); } mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays ++k; if (mem >= max_mem) { n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads); mem = k = 0; } } if (ret != -1) fprintf(pysamerr, "[bam_sort_core] truncated file. Continue anyway.\n"); // output file name fnout = calloc(strlen(prefix) + 20, 1); if (is_stdout) sprintf(fnout, "-"); else sprintf(fnout, "%s%s", prefix, suffix); // write the final output if (n_files == 0) { // a single block char mode[8]; strcpy(mode, "w"); if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9); ks_mergesort(sort, k, buf, 0); write_buffer(fnout, mode, k, buf, header, n_threads); } else { // then merge char **fns; n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads); fprintf(pysamerr, "[bam_sort_core] merging from %d files...\n", n_files); fns = (char**)calloc(n_files, sizeof(char*)); for (i = 0; i < n_files; ++i) { fns[i] = (char*)calloc(strlen(prefix) + 20, 1); sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix); } bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level); for (i = 0; i < n_files; ++i) { unlink(fns[i]); free(fns[i]); } free(fns); } free(fnout); // free for (k = 0; k < max_k; ++k) { if (!buf[k]) continue; free(buf[k]->data); free(buf[k]); } free(buf); bam_header_destroy(header); bam_close(fp); } void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem) { bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0); } int bam_sort(int argc, char *argv[]) { size_t max_mem = 768<<20; // 512MB int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0; while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) { switch (c) { case 'f': full_path = 1; break; case 'o': is_stdout = 1; break; case 'n': is_by_qname = 1; break; case 'm': { char *q; max_mem = strtol(optarg, &q, 0); if (*q == 'k' || *q == 'K') max_mem <<= 10; else if (*q == 'm' || *q == 'M') max_mem <<= 20; else if (*q == 'g' || *q == 'G') max_mem <<= 30; break; } case '@': n_threads = atoi(optarg); break; case 'l': level = atoi(optarg); break; } } if (optind + 2 > argc) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools sort [options] \n\n"); fprintf(pysamerr, "Options: -n sort by read name\n"); fprintf(pysamerr, " -f use as full file name instead of prefix\n"); fprintf(pysamerr, " -o final output to stdout\n"); fprintf(pysamerr, " -l INT compression level, from 0 to 9 [-1]\n"); fprintf(pysamerr, " -@ INT number of sorting and compression threads [1]\n"); fprintf(pysamerr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n"); fprintf(pysamerr, "\n"); return 1; } bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path); return 0; } pysam-0.7.7/samtools/bam.h0000664000076400007650000006227112162637166015300 0ustar andreasandreas/* The MIT License Copyright (c) 2008-2010 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ #ifndef BAM_BAM_H #define BAM_BAM_H /*! @header BAM library provides I/O and various operations on manipulating files in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. @copyright Genome Research Ltd. */ #define BAM_VERSION "0.1.19-44428cd" #include #include #include #include #ifndef BAM_LITE #define BAM_VIRTUAL_OFFSET16 #include "bgzf.h" /*! @abstract BAM file handler */ typedef BGZF *bamFile; #define bam_open(fn, mode) bgzf_open(fn, mode) #define bam_dopen(fd, mode) bgzf_fdopen(fd, mode) #define bam_close(fp) bgzf_close(fp) #define bam_read(fp, buf, size) bgzf_read(fp, buf, size) #define bam_write(fp, buf, size) bgzf_write(fp, buf, size) #define bam_tell(fp) bgzf_tell(fp) #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) #else #define BAM_TRUE_OFFSET #include typedef gzFile bamFile; #define bam_open(fn, mode) gzopen(fn, mode) #define bam_dopen(fd, mode) gzdopen(fd, mode) #define bam_close(fp) gzclose(fp) #define bam_read(fp, buf, size) gzread(fp, buf, size) /* no bam_write/bam_tell/bam_seek() here */ #endif /*! @typedef @abstract Structure for the alignment header. @field n_targets number of reference sequences @field target_name names of the reference sequences @field target_len lengths of the referene sequences @field dict header dictionary @field hash hash table for fast name lookup @field rg2lib hash table for @RG-ID -> LB lookup @field l_text length of the plain text in the header @field text plain text @discussion Field hash points to null by default. It is a private member. */ typedef struct { int32_t n_targets; char **target_name; uint32_t *target_len; void *dict, *hash, *rg2lib; uint32_t l_text, n_text; char *text; } bam_header_t; /*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */ #define BAM_FPAIRED 1 /*! @abstract the read is mapped in a proper pair */ #define BAM_FPROPER_PAIR 2 /*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */ #define BAM_FUNMAP 4 /*! @abstract the mate is unmapped */ #define BAM_FMUNMAP 8 /*! @abstract the read is mapped to the reverse strand */ #define BAM_FREVERSE 16 /*! @abstract the mate is mapped to the reverse strand */ #define BAM_FMREVERSE 32 /*! @abstract this is read1 */ #define BAM_FREAD1 64 /*! @abstract this is read2 */ #define BAM_FREAD2 128 /*! @abstract not primary alignment */ #define BAM_FSECONDARY 256 /*! @abstract QC failure */ #define BAM_FQCFAIL 512 /*! @abstract optical or PCR duplicate */ #define BAM_FDUP 1024 #define BAM_OFDEC 0 #define BAM_OFHEX 1 #define BAM_OFSTR 2 /*! @abstract defautl mask for pileup */ #define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP) #define BAM_CORE_SIZE sizeof(bam1_core_t) /** * Describing how CIGAR operation/length is packed in a 32-bit integer. */ #define BAM_CIGAR_SHIFT 4 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) /* CIGAR operations. */ /*! @abstract CIGAR: M = match or mismatch*/ #define BAM_CMATCH 0 /*! @abstract CIGAR: I = insertion to the reference */ #define BAM_CINS 1 /*! @abstract CIGAR: D = deletion from the reference */ #define BAM_CDEL 2 /*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */ #define BAM_CREF_SKIP 3 /*! @abstract CIGAR: S = clip on the read with clipped sequence present in qseq */ #define BAM_CSOFT_CLIP 4 /*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */ #define BAM_CHARD_CLIP 5 /*! @abstract CIGAR: P = padding */ #define BAM_CPAD 6 /*! @abstract CIGAR: equals = match */ #define BAM_CEQUAL 7 /*! @abstract CIGAR: X = mismatch */ #define BAM_CDIFF 8 #define BAM_CBACK 9 #define BAM_CIGAR_STR "MIDNSHP=XB" #define BAM_CIGAR_TYPE 0x3C1A7 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK) #define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT) #define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)]) #define bam_cigar_gen(l, o) ((l)<>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference /*! @typedef @abstract Structure for core alignment information. @field tid chromosome ID, defined by bam_header_t @field pos 0-based leftmost coordinate @field bin bin calculated by bam_reg2bin() @field qual mapping quality @field l_qname length of the query name @field flag bitwise flag @field n_cigar number of CIGAR operations @field l_qseq length of the query sequence (read) */ typedef struct { int32_t tid; int32_t pos; uint32_t bin:16, qual:8, l_qname:8; uint32_t flag:16, n_cigar:16; int32_t l_qseq; int32_t mtid; int32_t mpos; int32_t isize; } bam1_core_t; /*! @typedef @abstract Structure for one alignment. @field core core information about the alignment @field l_aux length of auxiliary data @field data_len current length of bam1_t::data @field m_data maximum length of bam1_t::data @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux @discussion Notes: 1. qname is zero tailing and core.l_qname includes the tailing '\0'. 2. l_qseq is calculated from the total length of an alignment block on reading or from CIGAR. 3. cigar data is encoded 4 bytes per CIGAR operation. 4. seq is nybble-encoded according to bam_nt16_table. */ typedef struct { bam1_core_t core; int l_aux, data_len, m_data; uint8_t *data; } bam1_t; typedef struct __bam_iter_t *bam_iter_t; #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0) #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0) /*! @function @abstract Get the CIGAR array @param b pointer to an alignment @return pointer to the CIGAR array @discussion In the CIGAR array, each element is a 32-bit integer. The lower 4 bits gives a CIGAR operation and the higher 28 bits keep the length of a CIGAR. */ #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname)) /*! @function @abstract Get the name of the query @param b pointer to an alignment @return pointer to the name string, null terminated */ #define bam1_qname(b) ((char*)((b)->data)) /*! @function @abstract Get query sequence @param b pointer to an alignment @return pointer to sequence @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G, 8 for T and 15 for N. Two bases are packed in one byte with the base at the higher 4 bits having smaller coordinate on the read. It is recommended to use bam1_seqi() macro to get the base. */ #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname) /*! @function @abstract Get query quality @param b pointer to an alignment @return pointer to quality string */ #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) /*! @function @abstract Get a base on read @param s Query sequence returned by bam1_seq() @param i The i-th position, 0-based @return 4-bit integer representing the base. */ //#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf) #define bam1_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf) #define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) ) /*! @function @abstract Get query sequence and quality @param b pointer to an alignment @return pointer to the concatenated auxiliary data */ #define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2) #ifndef kroundup32 /*! @function @abstract Round an integer to the next closest power-2 integer. @param x integer to be rounded (in place) @discussion x will be modified. */ #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif /*! @abstract Whether the machine is big-endian; modified only in bam_header_init(). */ extern int bam_is_be; /*! @abstract Verbose level between 0 and 3; 0 is supposed to disable all debugging information, though this may not have been implemented. */ extern int bam_verbose; extern int bam_no_B; /*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */ extern unsigned char bam_nt16_table[256]; /*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */ extern char *bam_nt16_rev_table; extern char bam_nt16_nt4_table[]; #ifdef __cplusplus extern "C" { #endif /********************* * Low-level SAM I/O * *********************/ /*! @abstract TAM file handler */ typedef struct __tamFile_t *tamFile; /*! @abstract Open a SAM file for reading, either uncompressed or compressed by gzip/zlib. @param fn SAM file name @return SAM file handler */ tamFile sam_open(const char *fn); /*! @abstract Close a SAM file handler @param fp SAM file handler */ void sam_close(tamFile fp); /*! @abstract Read one alignment from a SAM file handler @param fp SAM file handler @param header header information (ordered names of chromosomes) @param b read alignment; all members in b will be updated @return 0 if successful; otherwise negative */ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b); /*! @abstract Read header information from a TAB-delimited list file. @param fn_list file name for the list @return a pointer to the header structure @discussion Each line in this file consists of chromosome name and the length of chromosome. */ bam_header_t *sam_header_read2(const char *fn_list); /*! @abstract Read header from a SAM file (if present) @param fp SAM file handler @return pointer to header struct; 0 if no @SQ lines available */ bam_header_t *sam_header_read(tamFile fp); /*! @abstract Parse @SQ lines a update a header struct @param h pointer to the header struct to be updated @return number of target sequences @discussion bam_header_t::{n_targets,target_len,target_name} will be destroyed in the first place. */ int sam_header_parse(bam_header_t *h); int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); /*! @abstract Parse @RG lines a update a header struct @param h pointer to the header struct to be updated @return number of @RG lines @discussion bam_header_t::rg2lib will be destroyed in the first place. */ int sam_header_parse_rg(bam_header_t *h); #define sam_write1(header, b) bam_view1(header, b) /******************************** * APIs for string dictionaries * ********************************/ int bam_strmap_put(void *strmap, const char *rg, const char *lib); const char *bam_strmap_get(const void *strmap, const char *rg); void *bam_strmap_dup(const void*); void *bam_strmap_init(); void bam_strmap_destroy(void *strmap); /********************* * Low-level BAM I/O * *********************/ /*! @abstract Initialize a header structure. @return the pointer to the header structure @discussion This function also modifies the global variable bam_is_be. */ bam_header_t *bam_header_init(); /*! @abstract Destroy a header structure. @param header pointer to the header */ void bam_header_destroy(bam_header_t *header); /*! @abstract Read a header structure from BAM. @param fp BAM file handler, opened by bam_open() @return pointer to the header structure @discussion The file position indicator must be placed at the beginning of the file. Upon success, the position indicator will be set at the start of the first alignment. */ bam_header_t *bam_header_read(bamFile fp); /*! @abstract Write a header structure to BAM. @param fp BAM file handler @param header pointer to the header structure @return always 0 currently */ int bam_header_write(bamFile fp, const bam_header_t *header); /*! @abstract Read an alignment from BAM. @param fp BAM file handler @param b read alignment; all members are updated. @return number of bytes read from the file @discussion The file position indicator must be placed right before an alignment. Upon success, this function will set the position indicator to the start of the next alignment. This function is not affected by the machine endianness. */ int bam_read1(bamFile fp, bam1_t *b); int bam_remove_B(bam1_t *b); /*! @abstract Write an alignment to BAM. @param fp BAM file handler @param c pointer to the bam1_core_t structure @param data_len total length of variable size data related to the alignment @param data pointer to the concatenated data @return number of bytes written to the file @discussion This function is not affected by the machine endianness. */ int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data); /*! @abstract Write an alignment to BAM. @param fp BAM file handler @param b alignment to write @return number of bytes written to the file @abstract It is equivalent to: bam_write1_core(fp, &b->core, b->data_len, b->data) */ int bam_write1(bamFile fp, const bam1_t *b); /*! @function @abstract Initiate a pointer to bam1_t struct */ #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t))) /*! @function @abstract Free the memory allocated for an alignment. @param b pointer to an alignment */ #define bam_destroy1(b) do { \ if (b) { free((b)->data); free(b); } \ } while (0) /*! @abstract Format a BAM record in the SAM format @param header pointer to the header structure @param b alignment to print @return a pointer to the SAM string */ char *bam_format1(const bam_header_t *header, const bam1_t *b); char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of); /*! @abstract Check whether a BAM record is plausibly valid @param header associated header structure, or NULL if unavailable @param b alignment to validate @return 0 if the alignment is invalid; non-zero otherwise @discussion Simple consistency check of some of the fields of the alignment record. If the header is provided, several additional checks are made. Not all fields are checked, so a non-zero result is not a guarantee that the record is valid. However it is usually good enough to detect when bam_seek() has been called with a virtual file offset that is not the offset of an alignment record. */ int bam_validate1(const bam_header_t *header, const bam1_t *b); const char *bam_get_library(bam_header_t *header, const bam1_t *b); /*************** * pileup APIs * ***************/ /*! @typedef @abstract Structure for one alignment covering the pileup position. @field b pointer to the alignment @field qpos position of the read base at the pileup site, 0-based @field indel indel length; 0 for no indel, positive for ins and negative for del @field is_del 1 iff the base on the padded read is a deletion @field level the level of the read in the "viewer" mode @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The difference between the two functions is that the former does not set bam_pileup1_t::level, while the later does. Level helps the implementation of alignment viewers, but calculating this has some overhead. */ typedef struct { bam1_t *b; int32_t qpos; int indel, level; uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28; } bam_pileup1_t; typedef int (*bam_plp_auto_f)(void *data, bam1_t *b); struct __bam_plp_t; typedef struct __bam_plp_t *bam_plp_t; bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data); int bam_plp_push(bam_plp_t iter, const bam1_t *b); const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp); void bam_plp_set_mask(bam_plp_t iter, int mask); void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt); void bam_plp_reset(bam_plp_t iter); void bam_plp_destroy(bam_plp_t iter); struct __bam_mplp_t; typedef struct __bam_mplp_t *bam_mplp_t; bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data); void bam_mplp_destroy(bam_mplp_t iter); void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt); int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); /*! @typedef @abstract Type of function to be called by bam_plbuf_push(). @param tid chromosome ID as is defined in the header @param pos start coordinate of the alignment, 0-based @param n number of elements in pl array @param pl array of alignments @param data user provided data @discussion See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t. */ typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); typedef struct { bam_plp_t iter; bam_pileup_f func; void *data; } bam_plbuf_t; void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask); void bam_plbuf_reset(bam_plbuf_t *buf); bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data); void bam_plbuf_destroy(bam_plbuf_t *buf); int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf); int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data); struct __bam_lplbuf_t; typedef struct __bam_lplbuf_t bam_lplbuf_t; void bam_lplbuf_reset(bam_lplbuf_t *buf); /*! @abstract bam_plbuf_init() equivalent with level calculated. */ bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data); /*! @abstract bam_plbuf_destroy() equivalent with level calculated. */ void bam_lplbuf_destroy(bam_lplbuf_t *tv); /*! @abstract bam_plbuf_push() equivalent with level calculated. */ int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf); /********************* * BAM indexing APIs * *********************/ struct __bam_index_t; typedef struct __bam_index_t bam_index_t; /*! @abstract Build index for a BAM file. @discussion Index file "fn.bai" will be created. @param fn name of the BAM file @return always 0 currently */ int bam_index_build(const char *fn); /*! @abstract Load index from file "fn.bai". @param fn name of the BAM file (NOT the index file) @return pointer to the index structure */ bam_index_t *bam_index_load(const char *fn); /*! @abstract Destroy an index structure. @param idx pointer to the index structure */ void bam_index_destroy(bam_index_t *idx); /*! @typedef @abstract Type of function to be called by bam_fetch(). @param b the alignment @param data user provided data */ typedef int (*bam_fetch_f)(const bam1_t *b, void *data); /*! @abstract Retrieve the alignments that are overlapped with the specified region. @discussion A user defined function will be called for each retrieved alignment ordered by its start position. @param fp BAM file handler @param idx pointer to the alignment index @param tid chromosome ID as is defined in the header @param beg start coordinate, 0-based @param end end coordinate, 0-based @param data user provided data (will be transferred to func) @param func user defined function */ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end); int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b); void bam_iter_destroy(bam_iter_t iter); /*! @abstract Parse a region in the format: "chr2:100,000-200,000". @discussion bam_header_t::hash will be initialized if empty. @param header pointer to the header structure @param str string to be parsed @param ref_id the returned chromosome ID @param begin the returned start coordinate @param end the returned end coordinate @return 0 on success; -1 on failure */ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end); /************************** * APIs for optional tags * **************************/ /*! @abstract Retrieve data of a tag @param b pointer to an alignment struct @param tag two-character tag to be retrieved @return pointer to the type and data. The first character is the type that can be 'iIsScCdfAZH'. @discussion Use bam_aux2?() series to convert the returned data to the corresponding type. */ uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]); int32_t bam_aux2i(const uint8_t *s); float bam_aux2f(const uint8_t *s); double bam_aux2d(const uint8_t *s); char bam_aux2A(const uint8_t *s); char *bam_aux2Z(const uint8_t *s); int bam_aux_del(bam1_t *b, uint8_t *s); void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data); uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get() /***************** * Miscellaneous * *****************/ /*! @abstract Calculate the rightmost coordinate of an alignment on the reference genome. @param c pointer to the bam1_core_t structure @param cigar the corresponding CIGAR array (from bam1_t::cigar) @return the rightmost coordinate, 0-based */ uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar); /*! @abstract Calculate the length of the query sequence from CIGAR. @param c pointer to the bam1_core_t structure @param cigar the corresponding CIGAR array (from bam1_t::cigar) @return length of the query sequence */ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar); #ifdef __cplusplus } #endif /*! @abstract Calculate the minimum bin that contains a region [beg,end). @param beg start of the region, 0-based @param end end of the region, 0-based @return bin */ static inline int bam_reg2bin(uint32_t beg, uint32_t end) { --end; if (beg>>14 == end>>14) return 4681 + (beg>>14); if (beg>>17 == end>>17) return 585 + (beg>>17); if (beg>>20 == end>>20) return 73 + (beg>>20); if (beg>>23 == end>>23) return 9 + (beg>>23); if (beg>>26 == end>>26) return 1 + (beg>>26); return 0; } /*! @abstract Copy an alignment @param bdst destination alignment struct @param bsrc source alignment struct @return pointer to the destination alignment struct */ static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc) { uint8_t *data = bdst->data; int m_data = bdst->m_data; // backup data and m_data if (m_data < bsrc->data_len) { // double the capacity m_data = bsrc->data_len; kroundup32(m_data); data = (uint8_t*)realloc(data, m_data); } memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data *bdst = *bsrc; // copy the rest // restore the backup bdst->m_data = m_data; bdst->data = data; return bdst; } /*! @abstract Duplicate an alignment @param src source alignment struct @return pointer to the destination alignment struct */ static inline bam1_t *bam_dup1(const bam1_t *src) { bam1_t *b; b = bam_init1(); *b = *src; b->m_data = b->data_len; b->data = (uint8_t*)calloc(b->data_len, 1); memcpy(b->data, src->data, b->data_len); return b; } static inline int bam_aux_type2size(int x) { if (x == 'C' || x == 'c' || x == 'A') return 1; else if (x == 'S' || x == 's') return 2; else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4; else return 0; } /********************************* *** Compatibility with htslib *** *********************************/ typedef bam_header_t bam_hdr_t; #define bam_get_qname(b) bam1_qname(b) #define bam_get_cigar(b) bam1_cigar(b) #define bam_hdr_read(fp) bam_header_read(fp) #define bam_hdr_write(fp, h) bam_header_write(fp, h) #define bam_hdr_destroy(fp) bam_header_destroy(fp) #endif pysam-0.7.7/samtools/win32/0000775000076400007650000000000012241575073015316 5ustar andreasandreaspysam-0.7.7/samtools/win32/zconf.h0000660000076400007650000002251012162637166016606 0ustar andreasandreas/* zconf.h -- configuration of the zlib compression library * Copyright (C) 1995-2005 Jean-loup Gailly. * For conditions of distribution and use, see copyright notice in zlib.h */ /* @(#) $Id$ */ #ifndef ZCONF_H #define ZCONF_H /* * If you *really* need a unique prefix for all types and library functions, * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it. */ #ifdef Z_PREFIX # define deflateInit_ z_deflateInit_ # define deflate z_deflate # define deflateEnd z_deflateEnd # define inflateInit_ z_inflateInit_ # define inflate z_inflate # define inflateEnd z_inflateEnd # define deflateInit2_ z_deflateInit2_ # define deflateSetDictionary z_deflateSetDictionary # define deflateCopy z_deflateCopy # define deflateReset z_deflateReset # define deflateParams z_deflateParams # define deflateBound z_deflateBound # define deflatePrime z_deflatePrime # define inflateInit2_ z_inflateInit2_ # define inflateSetDictionary z_inflateSetDictionary # define inflateSync z_inflateSync # define inflateSyncPoint z_inflateSyncPoint # define inflateCopy z_inflateCopy # define inflateReset z_inflateReset # define inflateBack z_inflateBack # define inflateBackEnd z_inflateBackEnd # define compress z_compress # define compress2 z_compress2 # define compressBound z_compressBound # define uncompress z_uncompress # define adler32 z_adler32 # define crc32 z_crc32 # define get_crc_table z_get_crc_table # define zError z_zError # define alloc_func z_alloc_func # define free_func z_free_func # define in_func z_in_func # define out_func z_out_func # define Byte z_Byte # define uInt z_uInt # define uLong z_uLong # define Bytef z_Bytef # define charf z_charf # define intf z_intf # define uIntf z_uIntf # define uLongf z_uLongf # define voidpf z_voidpf # define voidp z_voidp #endif #if defined(__MSDOS__) && !defined(MSDOS) # define MSDOS #endif #if (defined(OS_2) || defined(__OS2__)) && !defined(OS2) # define OS2 #endif #if defined(_WINDOWS) && !defined(WINDOWS) # define WINDOWS #endif #if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__) # ifndef WIN32 # define WIN32 # endif #endif #if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32) # if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__) # ifndef SYS16BIT # define SYS16BIT # endif # endif #endif /* * Compile with -DMAXSEG_64K if the alloc function cannot allocate more * than 64k bytes at a time (needed on systems with 16-bit int). */ #ifdef SYS16BIT # define MAXSEG_64K #endif #ifdef MSDOS # define UNALIGNED_OK #endif #ifdef __STDC_VERSION__ # ifndef STDC # define STDC # endif # if __STDC_VERSION__ >= 199901L # ifndef STDC99 # define STDC99 # endif # endif #endif #if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus)) # define STDC #endif #if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__)) # define STDC #endif #if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32)) # define STDC #endif #if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__)) # define STDC #endif #if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */ # define STDC #endif #ifndef STDC # ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */ # define const /* note: need a more gentle solution here */ # endif #endif /* Some Mac compilers merge all .h files incorrectly: */ #if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__) # define NO_DUMMY_DECL #endif /* Maximum value for memLevel in deflateInit2 */ #ifndef MAX_MEM_LEVEL # ifdef MAXSEG_64K # define MAX_MEM_LEVEL 8 # else # define MAX_MEM_LEVEL 9 # endif #endif /* Maximum value for windowBits in deflateInit2 and inflateInit2. * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files * created by gzip. (Files created by minigzip can still be extracted by * gzip.) */ #ifndef MAX_WBITS # define MAX_WBITS 15 /* 32K LZ77 window */ #endif /* The memory requirements for deflate are (in bytes): (1 << (windowBits+2)) + (1 << (memLevel+9)) that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values) plus a few kilobytes for small objects. For example, if you want to reduce the default memory requirements from 256K to 128K, compile with make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7" Of course this will generally degrade compression (there's no free lunch). The memory requirements for inflate are (in bytes) 1 << windowBits that is, 32K for windowBits=15 (default value) plus a few kilobytes for small objects. */ /* Type declarations */ #ifndef OF /* function prototypes */ # ifdef STDC # define OF(args) args # else # define OF(args) () # endif #endif /* The following definitions for FAR are needed only for MSDOS mixed * model programming (small or medium model with some far allocations). * This was tested only with MSC; for other MSDOS compilers you may have * to define NO_MEMCPY in zutil.h. If you don't need the mixed model, * just define FAR to be empty. */ #ifdef SYS16BIT # if defined(M_I86SM) || defined(M_I86MM) /* MSC small or medium model */ # define SMALL_MEDIUM # ifdef _MSC_VER # define FAR _far # else # define FAR far # endif # endif # if (defined(__SMALL__) || defined(__MEDIUM__)) /* Turbo C small or medium model */ # define SMALL_MEDIUM # ifdef __BORLANDC__ # define FAR _far # else # define FAR far # endif # endif #endif #if defined(WINDOWS) || defined(WIN32) /* If building or using zlib as a DLL, define ZLIB_DLL. * This is not mandatory, but it offers a little performance increase. */ # ifdef ZLIB_DLL # if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500)) # ifdef ZLIB_INTERNAL # define ZEXTERN extern __declspec(dllexport) # else # define ZEXTERN extern __declspec(dllimport) # endif # endif # endif /* ZLIB_DLL */ /* If building or using zlib with the WINAPI/WINAPIV calling convention, * define ZLIB_WINAPI. * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI. */ # ifdef ZLIB_WINAPI # ifdef FAR # undef FAR # endif # include /* No need for _export, use ZLIB.DEF instead. */ /* For complete Windows compatibility, use WINAPI, not __stdcall. */ # define ZEXPORT WINAPI # ifdef WIN32 # define ZEXPORTVA WINAPIV # else # define ZEXPORTVA FAR CDECL # endif # endif #endif #if defined (__BEOS__) # ifdef ZLIB_DLL # ifdef ZLIB_INTERNAL # define ZEXPORT __declspec(dllexport) # define ZEXPORTVA __declspec(dllexport) # else # define ZEXPORT __declspec(dllimport) # define ZEXPORTVA __declspec(dllimport) # endif # endif #endif #ifndef ZEXTERN # define ZEXTERN extern #endif #ifndef ZEXPORT # define ZEXPORT #endif #ifndef ZEXPORTVA # define ZEXPORTVA #endif #ifndef FAR # define FAR #endif #if !defined(__MACTYPES__) typedef unsigned char Byte; /* 8 bits */ #endif typedef unsigned int uInt; /* 16 bits or more */ typedef unsigned long uLong; /* 32 bits or more */ #ifdef SMALL_MEDIUM /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */ # define Bytef Byte FAR #else typedef Byte FAR Bytef; #endif typedef char FAR charf; typedef int FAR intf; typedef uInt FAR uIntf; typedef uLong FAR uLongf; #ifdef STDC typedef void const *voidpc; typedef void FAR *voidpf; typedef void *voidp; #else typedef Byte const *voidpc; typedef Byte FAR *voidpf; typedef Byte *voidp; #endif #if 0 /* HAVE_UNISTD_H -- this line is updated by ./configure */ # include /* for off_t */ # include /* for SEEK_* and off_t */ # ifdef VMS # include /* for off_t */ # endif # define z_off_t off_t #endif #ifndef SEEK_SET # define SEEK_SET 0 /* Seek from beginning of file. */ # define SEEK_CUR 1 /* Seek from current position. */ # define SEEK_END 2 /* Set file pointer to EOF plus "offset" */ #endif #ifndef z_off_t # define z_off_t long #endif #if defined(__OS400__) # define NO_vsnprintf #endif #if defined(__MVS__) # define NO_vsnprintf # ifdef FAR # undef FAR # endif #endif /* MVS linker does not support external names larger than 8 bytes */ #if defined(__MVS__) # pragma map(deflateInit_,"DEIN") # pragma map(deflateInit2_,"DEIN2") # pragma map(deflateEnd,"DEEND") # pragma map(deflateBound,"DEBND") # pragma map(inflateInit_,"ININ") # pragma map(inflateInit2_,"ININ2") # pragma map(inflateEnd,"INEND") # pragma map(inflateSync,"INSY") # pragma map(inflateSetDictionary,"INSEDI") # pragma map(compressBound,"CMBND") # pragma map(inflate_table,"INTABL") # pragma map(inflate_fast,"INFA") # pragma map(inflate_copyright,"INCOPY") #endif #endif /* ZCONF_H */ pysam-0.7.7/samtools/win32/zlib.h0000660000076400007650000020121412162637166016427 0ustar andreasandreas/* zlib.h -- interface of the 'zlib' general purpose compression library version 1.2.3, July 18th, 2005 Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu The data format used by the zlib library is described by RFCs (Request for Comments) 1950 to 1952 in the files http://www.ietf.org/rfc/rfc1950.txt (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format). */ #ifndef ZLIB_H #define ZLIB_H #include "zconf.h" #ifdef __cplusplus extern "C" { #endif #define ZLIB_VERSION "1.2.3" #define ZLIB_VERNUM 0x1230 /* The 'zlib' compression library provides in-memory compression and decompression functions, including integrity checks of the uncompressed data. This version of the library supports only one compression method (deflation) but other algorithms will be added later and will have the same stream interface. Compression can be done in a single step if the buffers are large enough (for example if an input file is mmap'ed), or can be done by repeated calls of the compression function. In the latter case, the application must provide more input and/or consume the output (providing more output space) before each call. The compressed data format used by default by the in-memory functions is the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped around a deflate stream, which is itself documented in RFC 1951. The library also supports reading and writing files in gzip (.gz) format with an interface similar to that of stdio using the functions that start with "gz". The gzip format is different from the zlib format. gzip is a gzip wrapper, documented in RFC 1952, wrapped around a deflate stream. This library can optionally read and write gzip streams in memory as well. The zlib format was designed to be compact and fast for use in memory and on communications channels. The gzip format was designed for single- file compression on file systems, has a larger header than zlib to maintain directory information, and uses a different, slower check method than zlib. The library does not install any signal handler. The decoder checks the consistency of the compressed data, so the library should never crash even in case of corrupted input. */ typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size)); typedef void (*free_func) OF((voidpf opaque, voidpf address)); struct internal_state; typedef struct z_stream_s { Bytef *next_in; /* next input byte */ uInt avail_in; /* number of bytes available at next_in */ uLong total_in; /* total nb of input bytes read so far */ Bytef *next_out; /* next output byte should be put there */ uInt avail_out; /* remaining free space at next_out */ uLong total_out; /* total nb of bytes output so far */ char *msg; /* last error message, NULL if no error */ struct internal_state FAR *state; /* not visible by applications */ alloc_func zalloc; /* used to allocate the internal state */ free_func zfree; /* used to free the internal state */ voidpf opaque; /* private data object passed to zalloc and zfree */ int data_type; /* best guess about the data type: binary or text */ uLong adler; /* adler32 value of the uncompressed data */ uLong reserved; /* reserved for future use */ } z_stream; typedef z_stream FAR *z_streamp; /* gzip header information passed to and from zlib routines. See RFC 1952 for more details on the meanings of these fields. */ typedef struct gz_header_s { int text; /* true if compressed data believed to be text */ uLong time; /* modification time */ int xflags; /* extra flags (not used when writing a gzip file) */ int os; /* operating system */ Bytef *extra; /* pointer to extra field or Z_NULL if none */ uInt extra_len; /* extra field length (valid if extra != Z_NULL) */ uInt extra_max; /* space at extra (only when reading header) */ Bytef *name; /* pointer to zero-terminated file name or Z_NULL */ uInt name_max; /* space at name (only when reading header) */ Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */ uInt comm_max; /* space at comment (only when reading header) */ int hcrc; /* true if there was or will be a header crc */ int done; /* true when done reading gzip header (not used when writing a gzip file) */ } gz_header; typedef gz_header FAR *gz_headerp; /* The application must update next_in and avail_in when avail_in has dropped to zero. It must update next_out and avail_out when avail_out has dropped to zero. The application must initialize zalloc, zfree and opaque before calling the init function. All other fields are set by the compression library and must not be updated by the application. The opaque value provided by the application will be passed as the first parameter for calls of zalloc and zfree. This can be useful for custom memory management. The compression library attaches no meaning to the opaque value. zalloc must return Z_NULL if there is not enough memory for the object. If zlib is used in a multi-threaded application, zalloc and zfree must be thread safe. On 16-bit systems, the functions zalloc and zfree must be able to allocate exactly 65536 bytes, but will not be required to allocate more than this if the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers returned by zalloc for objects of exactly 65536 bytes *must* have their offset normalized to zero. The default allocation function provided by this library ensures this (see zutil.c). To reduce memory requirements and avoid any allocation of 64K objects, at the expense of compression ratio, compile the library with -DMAX_WBITS=14 (see zconf.h). The fields total_in and total_out can be used for statistics or progress reports. After compression, total_in holds the total size of the uncompressed data and may be saved for use in the decompressor (particularly if the decompressor wants to decompress everything in a single step). */ /* constants */ #define Z_NO_FLUSH 0 #define Z_PARTIAL_FLUSH 1 /* will be removed, use Z_SYNC_FLUSH instead */ #define Z_SYNC_FLUSH 2 #define Z_FULL_FLUSH 3 #define Z_FINISH 4 #define Z_BLOCK 5 /* Allowed flush values; see deflate() and inflate() below for details */ #define Z_OK 0 #define Z_STREAM_END 1 #define Z_NEED_DICT 2 #define Z_ERRNO (-1) #define Z_STREAM_ERROR (-2) #define Z_DATA_ERROR (-3) #define Z_MEM_ERROR (-4) #define Z_BUF_ERROR (-5) #define Z_VERSION_ERROR (-6) /* Return codes for the compression/decompression functions. Negative * values are errors, positive values are used for special but normal events. */ #define Z_NO_COMPRESSION 0 #define Z_BEST_SPEED 1 #define Z_BEST_COMPRESSION 9 #define Z_DEFAULT_COMPRESSION (-1) /* compression levels */ #define Z_FILTERED 1 #define Z_HUFFMAN_ONLY 2 #define Z_RLE 3 #define Z_FIXED 4 #define Z_DEFAULT_STRATEGY 0 /* compression strategy; see deflateInit2() below for details */ #define Z_BINARY 0 #define Z_TEXT 1 #define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */ #define Z_UNKNOWN 2 /* Possible values of the data_type field (though see inflate()) */ #define Z_DEFLATED 8 /* The deflate compression method (the only one supported in this version) */ #define Z_NULL 0 /* for initializing zalloc, zfree, opaque */ #define zlib_version zlibVersion() /* for compatibility with versions < 1.0.2 */ /* basic functions */ ZEXTERN const char * ZEXPORT zlibVersion OF((void)); /* The application can compare zlibVersion and ZLIB_VERSION for consistency. If the first character differs, the library code actually used is not compatible with the zlib.h header file used by the application. This check is automatically made by deflateInit and inflateInit. */ /* ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level)); Initializes the internal stream state for compression. The fields zalloc, zfree and opaque must be initialized before by the caller. If zalloc and zfree are set to Z_NULL, deflateInit updates them to use default allocation functions. The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9: 1 gives best speed, 9 gives best compression, 0 gives no compression at all (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION requests a default compromise between speed and compression (currently equivalent to level 6). deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if level is not a valid compression level, Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible with the version assumed by the caller (ZLIB_VERSION). msg is set to null if there is no error message. deflateInit does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush)); /* deflate compresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. deflate performs one or both of the following actions: - Compress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in and avail_in are updated and processing will resume at this point for the next call of deflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. This action is forced if the parameter flush is non zero. Forcing flush frequently degrades the compression ratio, so this parameter should be set only when necessary (in interactive applications). Some output may be provided even if flush is not set. Before the call of deflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating avail_in or avail_out accordingly; avail_out should never be zero before the call. The application can consume the compressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of deflate(). If deflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to decide how much data to accumualte before producing output, in order to maximize compression. If the parameter flush is set to Z_SYNC_FLUSH, all pending output is flushed to the output buffer and the output is aligned on a byte boundary, so that the decompressor can get all input data available so far. (In particular avail_in is zero after the call if enough output space has been provided before the call.) Flushing may degrade compression for some compression algorithms and so it should be used only when necessary. If flush is set to Z_FULL_FLUSH, all output is flushed as with Z_SYNC_FLUSH, and the compression state is reset so that decompression can restart from this point if previous compressed data has been damaged or if random access is desired. Using Z_FULL_FLUSH too often can seriously degrade compression. If deflate returns with avail_out == 0, this function must be called again with the same value of the flush parameter and more output space (updated avail_out), until the flush is complete (deflate returns with non-zero avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that avail_out is greater than six to avoid repeated flush markers due to avail_out == 0 on return. If the parameter flush is set to Z_FINISH, pending input is processed, pending output is flushed and deflate returns with Z_STREAM_END if there was enough output space; if deflate returns with Z_OK, this function must be called again with Z_FINISH and more output space (updated avail_out) but no more input data, until it returns with Z_STREAM_END or an error. After deflate has returned Z_STREAM_END, the only possible operations on the stream are deflateReset or deflateEnd. Z_FINISH can be used immediately after deflateInit if all the compression is to be done in a single step. In this case, avail_out must be at least the value returned by deflateBound (see below). If deflate does not return Z_STREAM_END, then it must be called again as described above. deflate() sets strm->adler to the adler32 checksum of all input read so far (that is, total_in bytes). deflate() may update strm->data_type if it can make a good guess about the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered binary. This field is only for information purposes and does not affect the compression algorithm in any manner. deflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if all input has been consumed and all output has been produced (only when flush is set to Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example if next_in or next_out was NULL), Z_BUF_ERROR if no progress is possible (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not fatal, and deflate() can be called again with more input and more output space to continue compressing. */ ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent, Z_DATA_ERROR if the stream was freed prematurely (some input or output was discarded). In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm)); Initializes the internal stream state for decompression. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. If next_in is not Z_NULL and avail_in is large enough (the exact value depends on the compression method), inflateInit determines the compression method from the zlib header and allocates all data structures accordingly; otherwise the allocation will be deferred to the first call of inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to use default allocation functions. inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_VERSION_ERROR if the zlib library version is incompatible with the version assumed by the caller. msg is set to null if there is no error message. inflateInit does not perform any decompression apart from reading the zlib header if present: this will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unchanged.) */ ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush)); /* inflate decompresses as much data as possible, and stops when the input buffer becomes empty or the output buffer becomes full. It may introduce some output latency (reading input without producing any output) except when forced to flush. The detailed semantics are as follows. inflate performs one or both of the following actions: - Decompress more input starting at next_in and update next_in and avail_in accordingly. If not all input can be processed (because there is not enough room in the output buffer), next_in is updated and processing will resume at this point for the next call of inflate(). - Provide more output starting at next_out and update next_out and avail_out accordingly. inflate() provides as much output as possible, until there is no more input data or no more space in the output buffer (see below about the flush parameter). Before the call of inflate(), the application should ensure that at least one of the actions is possible, by providing more input and/or consuming more output, and updating the next_* and avail_* values accordingly. The application can consume the uncompressed output when it wants, for example when the output buffer is full (avail_out == 0), or after each call of inflate(). If inflate returns Z_OK and with zero avail_out, it must be called again after making room in the output buffer because there might be more output pending. The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH, or Z_BLOCK. Z_SYNC_FLUSH requests that inflate() flush as much output as possible to the output buffer. Z_BLOCK requests that inflate() stop if and when it gets to the next deflate block boundary. When decoding the zlib or gzip format, this will cause inflate() to return immediately after the header and before the first block. When doing a raw inflate, inflate() will go ahead and process the first block, and will return when it gets to the end of that block, or when it runs out of data. The Z_BLOCK option assists in appending to or combining deflate streams. Also to assist in this, on return inflate() will set strm->data_type to the number of unused bits in the last byte taken from strm->next_in, plus 64 if inflate() is currently decoding the last block in the deflate stream, plus 128 if inflate() returned immediately after decoding an end-of-block code or decoding the complete header up to just before the first byte of the deflate stream. The end-of-block will not be indicated until all of the uncompressed data from that block has been written to strm->next_out. The number of unused bits may in general be greater than seven, except when bit 7 of data_type is set, in which case the number of unused bits will be less than eight. inflate() should normally be called until it returns Z_STREAM_END or an error. However if all decompression is to be performed in a single step (a single call of inflate), the parameter flush should be set to Z_FINISH. In this case all pending input is processed and all pending output is flushed; avail_out must be large enough to hold all the uncompressed data. (The size of the uncompressed data may have been saved by the compressor for this purpose.) The next operation on this stream must be inflateEnd to deallocate the decompression state. The use of Z_FINISH is never required, but can be used to inform inflate that a faster approach may be used for the single inflate() call. In this implementation, inflate() always flushes as much output as possible to the output buffer, and always uses the faster approach on the first call. So the only effect of the flush parameter in this implementation is on the return value of inflate(), as noted below, or when it returns early because Z_BLOCK is used. If a preset dictionary is needed after this call (see inflateSetDictionary below), inflate sets strm->adler to the adler32 checksum of the dictionary chosen by the compressor and returns Z_NEED_DICT; otherwise it sets strm->adler to the adler32 checksum of all output produced so far (that is, total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described below. At the end of the stream, inflate() checks that its computed adler32 checksum is equal to that saved by the compressor and returns Z_STREAM_END only if the checksum is correct. inflate() will decompress and check either zlib-wrapped or gzip-wrapped deflate data. The header type is detected automatically. Any information contained in the gzip header is not retained, so applications that need that information should instead use raw inflate, see inflateInit2() below, or inflateBack() and perform their own processing of the gzip header and trailer. inflate() returns Z_OK if some progress has been made (more input processed or more output produced), Z_STREAM_END if the end of the compressed data has been reached and all uncompressed output has been produced, Z_NEED_DICT if a preset dictionary is needed at this point, Z_DATA_ERROR if the input data was corrupted (input stream not conforming to the zlib format or incorrect check value), Z_STREAM_ERROR if the stream structure was inconsistent (for example if next_in or next_out was NULL), Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if no progress is possible or if there was not enough room in the output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and inflate() can be called again with more input and more output space to continue decompressing. If Z_DATA_ERROR is returned, the application may then call inflateSync() to look for a good compression block if a partial recovery of the data is desired. */ ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm)); /* All dynamically allocated data structures for this stream are freed. This function discards any unprocessed input and does not flush any pending output. inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state was inconsistent. In the error case, msg may be set but then points to a static string (which must not be deallocated). */ /* Advanced functions */ /* The following functions are needed only in some special applications. */ /* ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy)); This is another version of deflateInit with more compression options. The fields next_in, zalloc, zfree and opaque must be initialized before by the caller. The method parameter is the compression method. It must be Z_DEFLATED in this version of the library. The windowBits parameter is the base two logarithm of the window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. Larger values of this parameter result in better compression at the expense of memory usage. The default value is 15 if deflateInit is used instead. windowBits can also be -8..-15 for raw deflate. In this case, -windowBits determines the window size. deflate() will then generate raw deflate data with no zlib header or trailer, and will not compute an adler32 check value. windowBits can also be greater than 15 for optional gzip encoding. Add 16 to windowBits to write a simple gzip header and trailer around the compressed data instead of a zlib wrapper. The gzip header will have no file name, no extra data, no comment, no modification time (set to zero), no header crc, and the operating system will be set to 255 (unknown). If a gzip stream is being written, strm->adler is a crc32 instead of an adler32. The memLevel parameter specifies how much memory should be allocated for the internal compression state. memLevel=1 uses minimum memory but is slow and reduces compression ratio; memLevel=9 uses maximum memory for optimal speed. The default value is 8. See zconf.h for total memory usage as a function of windowBits and memLevel. The strategy parameter is used to tune the compression algorithm. Use the value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no string match), or Z_RLE to limit match distances to one (run-length encoding). Filtered data consists mostly of small values with a somewhat random distribution. In this case, the compression algorithm is tuned to compress them better. The effect of Z_FILTERED is to force more Huffman coding and less string matching; it is somewhat intermediate between Z_DEFAULT and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The strategy parameter only affects the compression ratio but not the correctness of the compressed output even if it is not set appropriately. Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler decoder for special applications. deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if a parameter is invalid (such as an invalid method). msg is set to null if there is no error message. deflateInit2 does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the compression dictionary from the given byte sequence without producing any compressed output. This function must be called immediately after deflateInit, deflateInit2 or deflateReset, before any call of deflate. The compressor and decompressor must use exactly the same dictionary (see inflateSetDictionary). The dictionary should consist of strings (byte sequences) that are likely to be encountered later in the data to be compressed, with the most commonly used strings preferably put towards the end of the dictionary. Using a dictionary is most useful when the data to be compressed is short and can be predicted with good accuracy; the data can then be compressed better than with the default empty dictionary. Depending on the size of the compression data structures selected by deflateInit or deflateInit2, a part of the dictionary may in effect be discarded, for example if the dictionary is larger than the window size in deflate or deflate2. Thus the strings most likely to be useful should be put at the end of the dictionary, not at the front. In addition, the current implementation of deflate will use at most the window size minus 262 bytes of the provided dictionary. Upon return of this function, strm->adler is set to the adler32 value of the dictionary; the decompressor may later use this value to determine which dictionary has been used by the compressor. (The adler32 value applies to the whole dictionary even if only a subset of the dictionary is actually used by the compressor.) If a raw deflate was requested, then the adler32 value is not computed and strm->adler is not set. deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a parameter is invalid (such as NULL dictionary) or the stream state is inconsistent (for example if deflate has already been called for this stream or if the compression method is bsort). deflateSetDictionary does not perform any compression: this will be done by deflate(). */ ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when several compression strategies will be tried, for example when there are several ways of pre-processing the input data with a filter. The streams that will be discarded should then be freed by calling deflateEnd. Note that deflateCopy duplicates the internal compression state which can be quite large, so this strategy is slow and can consume lots of memory. deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm)); /* This function is equivalent to deflateEnd followed by deflateInit, but does not free and reallocate all the internal compression state. The stream will keep the same compression level and any other attributes that may have been set by deflateInit2. deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being NULL). */ ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm, int level, int strategy)); /* Dynamically update the compression level and compression strategy. The interpretation of level and strategy is as in deflateInit2. This can be used to switch between compression and straight copy of the input data, or to switch to a different kind of input data requiring a different strategy. If the compression level is changed, the input available so far is compressed with the old level (and may be flushed); the new level will take effect only at the next call of deflate(). Before the call of deflateParams, the stream state must be set as for a call of deflate(), since the currently available input may have to be compressed and flushed. In particular, strm->avail_out must be non-zero. deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if strm->avail_out was zero. */ ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm, int good_length, int max_lazy, int nice_length, int max_chain)); /* Fine tune deflate's internal compression parameters. This should only be used by someone who understands the algorithm used by zlib's deflate for searching for the best matching string, and even then only by the most fanatic optimizer trying to squeeze out the last compressed bit for their specific input data. Read the deflate.c source code for the meaning of the max_lazy, good_length, nice_length, and max_chain parameters. deflateTune() can be called after deflateInit() or deflateInit2(), and returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream. */ ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm, uLong sourceLen)); /* deflateBound() returns an upper bound on the compressed size after deflation of sourceLen bytes. It must be called after deflateInit() or deflateInit2(). This would be used to allocate an output buffer for deflation in a single pass, and so would be called before deflate(). */ ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm, int bits, int value)); /* deflatePrime() inserts bits in the deflate output stream. The intent is that this function is used to start off the deflate output with the bits leftover from a previous deflate stream when appending to it. As such, this function can only be used for raw deflate, and must be used before the first deflate() call after a deflateInit2() or deflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the output. deflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm, gz_headerp head)); /* deflateSetHeader() provides gzip header information for when a gzip stream is requested by deflateInit2(). deflateSetHeader() may be called after deflateInit2() or deflateReset() and before the first call of deflate(). The text, time, os, extra field, name, and comment information in the provided gz_header structure are written to the gzip header (xflag is ignored -- the extra flags are set according to the compression level). The caller must assure that, if not Z_NULL, name and comment are terminated with a zero byte, and that if extra is not Z_NULL, that extra_len bytes are available there. If hcrc is true, a gzip header crc is included. Note that the current versions of the command-line version of gzip (up through version 1.3.x) do not support header crc's, and will report that it is a "multi-part gzip file" and give up. If deflateSetHeader is not used, the default gzip header has text false, the time set to zero, and os set to 255, with no extra, name, or comment fields. The gzip header is returned to the default state by deflateReset(). deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm, int windowBits)); This is another version of inflateInit with an extra parameter. The fields next_in, avail_in, zalloc, zfree and opaque must be initialized before by the caller. The windowBits parameter is the base two logarithm of the maximum window size (the size of the history buffer). It should be in the range 8..15 for this version of the library. The default value is 15 if inflateInit is used instead. windowBits must be greater than or equal to the windowBits value provided to deflateInit2() while compressing, or it must be equal to 15 if deflateInit2() was not used. If a compressed stream with a larger window size is given as input, inflate() will return with the error code Z_DATA_ERROR instead of trying to allocate a larger window. windowBits can also be -8..-15 for raw inflate. In this case, -windowBits determines the window size. inflate() will then process raw deflate data, not looking for a zlib or gzip header, not generating a check value, and not looking for any check values for comparison at the end of the stream. This is for use with other formats that use the deflate compressed data format such as zip. Those formats provide their own check values. If a custom format is developed using the raw deflate format for compressed data, it is recommended that a check value such as an adler32 or a crc32 be applied to the uncompressed data as is done in the zlib, gzip, and zip formats. For most applications, the zlib format should be used as is. Note that comments above on the use in deflateInit2() applies to the magnitude of windowBits. windowBits can also be greater than 15 for optional gzip decoding. Add 32 to windowBits to enable zlib and gzip decoding with automatic header detection, or add 16 to decode only the gzip format (the zlib format will return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a crc32 instead of an adler32. inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if a parameter is invalid (such as a null strm). msg is set to null if there is no error message. inflateInit2 does not perform any decompression apart from reading the zlib header if present: this will be done by inflate(). (So next_in and avail_in may be modified, but next_out and avail_out are unchanged.) */ ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm, const Bytef *dictionary, uInt dictLength)); /* Initializes the decompression dictionary from the given uncompressed byte sequence. This function must be called immediately after a call of inflate, if that call returned Z_NEED_DICT. The dictionary chosen by the compressor can be determined from the adler32 value returned by that call of inflate. The compressor and decompressor must use exactly the same dictionary (see deflateSetDictionary). For raw inflate, this function can be called immediately after inflateInit2() or inflateReset() and before any call of inflate() to set the dictionary. The application must insure that the dictionary that was used for compression is provided. inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a parameter is invalid (such as NULL dictionary) or the stream state is inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the expected one (incorrect adler32 value). inflateSetDictionary does not perform any decompression: this will be done by subsequent calls of inflate(). */ ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm)); /* Skips invalid compressed data until a full flush point (see above the description of deflate with Z_FULL_FLUSH) can be found, or until all available input is skipped. No output is provided. inflateSync returns Z_OK if a full flush point has been found, Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point has been found, or Z_STREAM_ERROR if the stream structure was inconsistent. In the success case, the application may save the current current value of total_in which indicates where valid compressed data was found. In the error case, the application may repeatedly call inflateSync, providing more input each time, until success or end of the input data. */ ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest, z_streamp source)); /* Sets the destination stream as a complete copy of the source stream. This function can be useful when randomly accessing a large stream. The first pass through the stream can periodically record the inflate state, allowing restarting inflate at those points when randomly accessing the stream. inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc being NULL). msg is left unchanged in both source and destination. */ ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm)); /* This function is equivalent to inflateEnd followed by inflateInit, but does not free and reallocate all the internal decompression state. The stream will keep attributes that may have been set by inflateInit2. inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent (such as zalloc or state being NULL). */ ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm, int bits, int value)); /* This function inserts bits in the inflate input stream. The intent is that this function is used to start inflating at a bit position in the middle of a byte. The provided bits will be used before any bytes are used from next_in. This function should only be used with raw inflate, and should be used before the first inflate() call after inflateInit2() or inflateReset(). bits must be less than or equal to 16, and that many of the least significant bits of value will be inserted in the input. inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm, gz_headerp head)); /* inflateGetHeader() requests that gzip header information be stored in the provided gz_header structure. inflateGetHeader() may be called after inflateInit2() or inflateReset(), and before the first call of inflate(). As inflate() processes the gzip stream, head->done is zero until the header is completed, at which time head->done is set to one. If a zlib stream is being decoded, then head->done is set to -1 to indicate that there will be no gzip header information forthcoming. Note that Z_BLOCK can be used to force inflate() to return immediately after header processing is complete and before any actual data is decompressed. The text, time, xflags, and os fields are filled in with the gzip header contents. hcrc is set to true if there is a header CRC. (The header CRC was valid if done is set to one.) If extra is not Z_NULL, then extra_max contains the maximum number of bytes to write to extra. Once done is true, extra_len contains the actual extra field length, and extra contains the extra field, or that field truncated if extra_max is less than extra_len. If name is not Z_NULL, then up to name_max characters are written there, terminated with a zero unless the length is greater than name_max. If comment is not Z_NULL, then up to comm_max characters are written there, terminated with a zero unless the length is greater than comm_max. When any of extra, name, or comment are not Z_NULL and the respective field is not present in the header, then that field is set to Z_NULL to signal its absence. This allows the use of deflateSetHeader() with the returned structure to duplicate the header. However if those fields are set to allocated memory, then the application will need to save those pointers elsewhere so that they can be eventually freed. If inflateGetHeader is not used, then the header information is simply discarded. The header is always checked for validity, including the header CRC if present. inflateReset() will reset the process to discard the header information. The application would need to call inflateGetHeader() again to retrieve the header from the next gzip stream. inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source stream state was inconsistent. */ /* ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits, unsigned char FAR *window)); Initialize the internal stream state for decompression using inflateBack() calls. The fields zalloc, zfree and opaque in strm must be initialized before the call. If zalloc and zfree are Z_NULL, then the default library- derived memory allocation routines are used. windowBits is the base two logarithm of the window size, in the range 8..15. window is a caller supplied buffer of that size. Except for special applications where it is assured that deflate was used with small window sizes, windowBits must be 15 and a 32K byte window must be supplied to be able to decompress general deflate streams. See inflateBack() for the usage of these routines. inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of the paramaters are invalid, Z_MEM_ERROR if the internal state could not be allocated, or Z_VERSION_ERROR if the version of the library does not match the version of the header file. */ typedef unsigned (*in_func) OF((void FAR *, unsigned char FAR * FAR *)); typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned)); ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm, in_func in, void FAR *in_desc, out_func out, void FAR *out_desc)); /* inflateBack() does a raw inflate with a single call using a call-back interface for input and output. This is more efficient than inflate() for file i/o applications in that it avoids copying between the output and the sliding window by simply making the window itself the output buffer. This function trusts the application to not change the output buffer passed by the output function, at least until inflateBack() returns. inflateBackInit() must be called first to allocate the internal state and to initialize the state with the user-provided window buffer. inflateBack() may then be used multiple times to inflate a complete, raw deflate stream with each call. inflateBackEnd() is then called to free the allocated state. A raw deflate stream is one with no zlib or gzip header or trailer. This routine would normally be used in a utility that reads zip or gzip files and writes out uncompressed files. The utility would decode the header and process the trailer on its own, hence this routine expects only the raw deflate stream to decompress. This is different from the normal behavior of inflate(), which expects either a zlib or gzip header and trailer around the deflate stream. inflateBack() uses two subroutines supplied by the caller that are then called by inflateBack() for input and output. inflateBack() calls those routines until it reads a complete deflate stream and writes out all of the uncompressed data, or until it encounters an error. The function's parameters and return types are defined above in the in_func and out_func typedefs. inflateBack() will call in(in_desc, &buf) which should return the number of bytes of provided input, and a pointer to that input in buf. If there is no input available, in() must return zero--buf is ignored in that case--and inflateBack() will return a buffer error. inflateBack() will call out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out() should return zero on success, or non-zero on failure. If out() returns non-zero, inflateBack() will return with an error. Neither in() nor out() are permitted to change the contents of the window provided to inflateBackInit(), which is also the buffer that out() uses to write from. The length written by out() will be at most the window size. Any non-zero amount of input may be provided by in(). For convenience, inflateBack() can be provided input on the first call by setting strm->next_in and strm->avail_in. If that input is exhausted, then in() will be called. Therefore strm->next_in must be initialized before calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in must also be initialized, and then if strm->avail_in is not zero, input will initially be taken from strm->next_in[0 .. strm->avail_in - 1]. The in_desc and out_desc parameters of inflateBack() is passed as the first parameter of in() and out() respectively when they are called. These descriptors can be optionally used to pass any information that the caller- supplied in() and out() functions need to do their job. On return, inflateBack() will set strm->next_in and strm->avail_in to pass back any unused input that was provided by the last in() call. The return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR if in() or out() returned an error, Z_DATA_ERROR if there was a format error in the deflate stream (in which case strm->msg is set to indicate the nature of the error), or Z_STREAM_ERROR if the stream was not properly initialized. In the case of Z_BUF_ERROR, an input or output error can be distinguished using strm->next_in which will be Z_NULL only if in() returned an error. If strm->next is not Z_NULL, then the Z_BUF_ERROR was due to out() returning non-zero. (in() will always be called before out(), so strm->next_in is assured to be defined if out() returns non-zero.) Note that inflateBack() cannot return Z_OK. */ ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm)); /* All memory allocated by inflateBackInit() is freed. inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream state was inconsistent. */ ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void)); /* Return flags indicating compile-time options. Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other: 1.0: size of uInt 3.2: size of uLong 5.4: size of voidpf (pointer) 7.6: size of z_off_t Compiler, assembler, and debug options: 8: DEBUG 9: ASMV or ASMINF -- use ASM code 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention 11: 0 (reserved) One-time table building (smaller code, but not thread-safe if true): 12: BUILDFIXED -- build static block decoding tables when needed 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed 14,15: 0 (reserved) Library content (indicates missing functionality): 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking deflate code when not needed) 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect and decode gzip streams (to avoid linking crc code) 18-19: 0 (reserved) Operation variations (changes in library functionality): 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate 21: FASTEST -- deflate algorithm with only one, lowest compression level 22,23: 0 (reserved) The sprintf variant used by gzprintf (zero is best): 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure! 26: 0 = returns value, 1 = void -- 1 means inferred string length returned Remainder: 27-31: 0 (reserved) */ /* utility functions */ /* The following utility functions are implemented on top of the basic stream-oriented functions. To simplify the interface, some default options are assumed (compression level and memory usage, standard memory allocation functions). The source code of these utility functions can easily be modified if you need special options. */ ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Compresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. This function can be used to compress a whole file at once if the input file is mmap'ed. compress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer. */ ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen, int level)); /* Compresses the source buffer into the destination buffer. The level parameter has the same meaning as in deflateInit. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be at least the value returned by compressBound(sourceLen). Upon exit, destLen is the actual size of the compressed buffer. compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, Z_STREAM_ERROR if the level parameter is invalid. */ ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen)); /* compressBound() returns an upper bound on the compressed size after compress() or compress2() on sourceLen bytes. It would be used before a compress() or compress2() call to allocate the destination buffer. */ ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen, const Bytef *source, uLong sourceLen)); /* Decompresses the source buffer into the destination buffer. sourceLen is the byte length of the source buffer. Upon entry, destLen is the total size of the destination buffer, which must be large enough to hold the entire uncompressed data. (The size of the uncompressed data must have been saved previously by the compressor and transmitted to the decompressor by some mechanism outside the scope of this compression library.) Upon exit, destLen is the actual size of the compressed buffer. This function can be used to decompress a whole file at once if the input file is mmap'ed. uncompress returns Z_OK if success, Z_MEM_ERROR if there was not enough memory, Z_BUF_ERROR if there was not enough room in the output buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. */ typedef voidp gzFile; ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode)); /* Opens a gzip (.gz) file for reading or writing. The mode parameter is as in fopen ("rb" or "wb") but can also include a compression level ("wb9") or a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman only compression as in "wb1h", or 'R' for run-length encoding as in "wb1R". (See the description of deflateInit2 for more information about the strategy parameter.) gzopen can be used to read a file which is not in gzip format; in this case gzread will directly read from the file without decompression. gzopen returns NULL if the file could not be opened or if there was insufficient memory to allocate the (de)compression state; errno can be checked to distinguish the two cases (if errno is zero, the zlib error is Z_MEM_ERROR). */ ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode)); /* gzdopen() associates a gzFile with the file descriptor fd. File descriptors are obtained from calls like open, dup, creat, pipe or fileno (in the file has been previously opened with fopen). The mode parameter is as in gzopen. The next call of gzclose on the returned gzFile will also close the file descriptor fd, just like fclose(fdopen(fd), mode) closes the file descriptor fd. If you want to keep fd open, use gzdopen(dup(fd), mode). gzdopen returns NULL if there was insufficient memory to allocate the (de)compression state. */ ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy)); /* Dynamically update the compression level or strategy. See the description of deflateInit2 for the meaning of these parameters. gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not opened for writing. */ ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len)); /* Reads the given number of uncompressed bytes from the compressed file. If the input file was not in gzip format, gzread copies the given number of bytes into the buffer. gzread returns the number of uncompressed bytes actually read (0 for end of file, -1 for error). */ ZEXTERN int ZEXPORT gzwrite OF((gzFile file, voidpc buf, unsigned len)); /* Writes the given number of uncompressed bytes into the compressed file. gzwrite returns the number of uncompressed bytes actually written (0 in case of error). */ ZEXTERN int ZEXPORTVA gzprintf OF((gzFile file, const char *format, ...)); /* Converts, formats, and writes the args to the compressed file under control of the format string, as in fprintf. gzprintf returns the number of uncompressed bytes actually written (0 in case of error). The number of uncompressed bytes written is limited to 4095. The caller should assure that this limit is not exceeded. If it is exceeded, then gzprintf() will return return an error (0) with nothing written. In this case, there may also be a buffer overflow with unpredictable consequences, which is possible only if zlib was compiled with the insecure functions sprintf() or vsprintf() because the secure snprintf() or vsnprintf() functions were not available. */ ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s)); /* Writes the given null-terminated string to the compressed file, excluding the terminating null character. gzputs returns the number of characters written, or -1 in case of error. */ ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len)); /* Reads bytes from the compressed file until len-1 characters are read, or a newline character is read and transferred to buf, or an end-of-file condition is encountered. The string is then terminated with a null character. gzgets returns buf, or Z_NULL in case of error. */ ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c)); /* Writes c, converted to an unsigned char, into the compressed file. gzputc returns the value that was written, or -1 in case of error. */ ZEXTERN int ZEXPORT gzgetc OF((gzFile file)); /* Reads one byte from the compressed file. gzgetc returns this byte or -1 in case of end of file or error. */ ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file)); /* Push one character back onto the stream to be read again later. Only one character of push-back is allowed. gzungetc() returns the character pushed, or -1 on failure. gzungetc() will fail if a character has been pushed but not read yet, or if c is -1. The pushed character will be discarded if the stream is repositioned with gzseek() or gzrewind(). */ ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush)); /* Flushes all pending output into the compressed file. The parameter flush is as in the deflate() function. The return value is the zlib error number (see function gzerror below). gzflush returns Z_OK if the flush parameter is Z_FINISH and all output could be flushed. gzflush should be called only when strictly necessary because it can degrade compression. */ ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file, z_off_t offset, int whence)); /* Sets the starting position for the next gzread or gzwrite on the given compressed file. The offset represents a number of bytes in the uncompressed data stream. The whence parameter is defined as in lseek(2); the value SEEK_END is not supported. If the file is opened for reading, this function is emulated but can be extremely slow. If the file is opened for writing, only forward seeks are supported; gzseek then compresses a sequence of zeroes up to the new starting position. gzseek returns the resulting offset location as measured in bytes from the beginning of the uncompressed stream, or -1 in case of error, in particular if the file is opened for writing and the new starting position would be before the current position. */ ZEXTERN int ZEXPORT gzrewind OF((gzFile file)); /* Rewinds the given file. This function is supported only for reading. gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET) */ ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file)); /* Returns the starting position for the next gzread or gzwrite on the given compressed file. This position represents a number of bytes in the uncompressed data stream. gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR) */ ZEXTERN int ZEXPORT gzeof OF((gzFile file)); /* Returns 1 when EOF has previously been detected reading the given input stream, otherwise zero. */ ZEXTERN int ZEXPORT gzdirect OF((gzFile file)); /* Returns 1 if file is being read directly without decompression, otherwise zero. */ ZEXTERN int ZEXPORT gzclose OF((gzFile file)); /* Flushes all pending output if necessary, closes the compressed file and deallocates all the (de)compression state. The return value is the zlib error number (see function gzerror below). */ ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum)); /* Returns the error message for the last error which occurred on the given compressed file. errnum is set to zlib error number. If an error occurred in the file system and not in the compression library, errnum is set to Z_ERRNO and the application may consult errno to get the exact error code. */ ZEXTERN void ZEXPORT gzclearerr OF((gzFile file)); /* Clears the error and end-of-file flags for file. This is analogous to the clearerr() function in stdio. This is useful for continuing to read a gzip file that is being written concurrently. */ /* checksum functions */ /* These functions are not related to compression but are exported anyway because they might be useful in applications using the compression library. */ ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len)); /* Update a running Adler-32 checksum with the bytes buf[0..len-1] and return the updated checksum. If buf is NULL, this function returns the required initial value for the checksum. An Adler-32 checksum is almost as reliable as a CRC32 but can be computed much faster. Usage example: uLong adler = adler32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { adler = adler32(adler, buffer, length); } if (adler != original_adler) error(); */ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2, z_off_t len2)); /* Combine two Adler-32 checksums into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. */ ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len)); /* Update a running CRC-32 with the bytes buf[0..len-1] and return the updated CRC-32. If buf is NULL, this function returns the required initial value for the for the crc. Pre- and post-conditioning (one's complement) is performed within this function so it shouldn't be done by the application. Usage example: uLong crc = crc32(0L, Z_NULL, 0); while (read_buffer(buffer, length) != EOF) { crc = crc32(crc, buffer, length); } if (crc != original_crc) error(); */ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2)); /* Combine two CRC-32 check values into one. For two sequences of bytes, seq1 and seq2 with lengths len1 and len2, CRC-32 check values were calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32 check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and len2. */ /* various hacks, don't look :) */ /* deflateInit and inflateInit are macros to allow checking the zlib version * and the compiler's view of z_stream: */ ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm, const char *version, int stream_size)); ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method, int windowBits, int memLevel, int strategy, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits, const char *version, int stream_size)); ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits, unsigned char FAR *window, const char *version, int stream_size)); #define deflateInit(strm, level) \ deflateInit_((strm), (level), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit(strm) \ inflateInit_((strm), ZLIB_VERSION, sizeof(z_stream)) #define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \ deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\ (strategy), ZLIB_VERSION, sizeof(z_stream)) #define inflateInit2(strm, windowBits) \ inflateInit2_((strm), (windowBits), ZLIB_VERSION, sizeof(z_stream)) #define inflateBackInit(strm, windowBits, window) \ inflateBackInit_((strm), (windowBits), (window), \ ZLIB_VERSION, sizeof(z_stream)) #if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL) struct internal_state {int dummy;}; /* hack for buggy compilers */ #endif ZEXTERN const char * ZEXPORT zError OF((int)); ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp z)); ZEXTERN const uLongf * ZEXPORT get_crc_table OF((void)); #ifdef __cplusplus } #endif #endif /* ZLIB_H */ pysam-0.7.7/samtools/win32/xcurses.h0000660000076400007650000014137312162637166017174 0ustar andreasandreas/* Public Domain Curses */ /* $Id: curses.h,v 1.295 2008/07/15 17:13:25 wmcbrine Exp $ */ /*----------------------------------------------------------------------* * PDCurses * *----------------------------------------------------------------------*/ #ifndef __PDCURSES__ #define __PDCURSES__ 1 /*man-start************************************************************** PDCurses definitions list: (Only define those needed) XCURSES True if compiling for X11. PDC_RGB True if you want to use RGB color definitions (Red = 1, Green = 2, Blue = 4) instead of BGR. PDC_WIDE True if building wide-character support. PDC_DLL_BUILD True if building a Win32 DLL. NCURSES_MOUSE_VERSION Use the ncurses mouse API instead of PDCurses' traditional mouse API. PDCurses portable platform definitions list: PDC_BUILD Defines API build version. PDCURSES Enables access to PDCurses-only routines. XOPEN Always true. SYSVcurses True if you are compiling for SYSV portability. BSDcurses True if you are compiling for BSD portability. **man-end****************************************************************/ #define PDC_BUILD 3401 #define PDCURSES 1 /* PDCurses-only routines */ #define XOPEN 1 /* X/Open Curses routines */ #define SYSVcurses 1 /* System V Curses routines */ #define BSDcurses 1 /* BSD Curses routines */ #define CHTYPE_LONG 1 /* size of chtype; long */ /*----------------------------------------------------------------------*/ #include #include #include /* Required by X/Open usage below */ #ifdef PDC_WIDE # include #endif #if defined(__cplusplus) || defined(__cplusplus__) || defined(__CPLUSPLUS) extern "C" { # define bool _bool #endif /*---------------------------------------------------------------------- * * PDCurses Manifest Constants * */ #ifndef FALSE # define FALSE 0 #endif #ifndef TRUE # define TRUE 1 #endif #ifndef NULL # define NULL (void *)0 #endif #ifndef ERR # define ERR (-1) #endif #ifndef OK # define OK 0 #endif /*---------------------------------------------------------------------- * * PDCurses Type Declarations * */ typedef unsigned char bool; /* PDCurses Boolean type */ #ifdef CHTYPE_LONG # if _LP64 typedef unsigned int chtype; # else typedef unsigned long chtype; /* 16-bit attr + 16-bit char */ # endif #else typedef unsigned short chtype; /* 8-bit attr + 8-bit char */ #endif #ifdef PDC_WIDE typedef chtype cchar_t; #endif typedef chtype attr_t; /*---------------------------------------------------------------------- * * PDCurses Mouse Interface -- SYSVR4, with extensions * */ typedef struct { int x; /* absolute column, 0 based, measured in characters */ int y; /* absolute row, 0 based, measured in characters */ short button[3]; /* state of each button */ int changes; /* flags indicating what has changed with the mouse */ } MOUSE_STATUS; #define BUTTON_RELEASED 0x0000 #define BUTTON_PRESSED 0x0001 #define BUTTON_CLICKED 0x0002 #define BUTTON_DOUBLE_CLICKED 0x0003 #define BUTTON_TRIPLE_CLICKED 0x0004 #define BUTTON_MOVED 0x0005 /* PDCurses */ #define WHEEL_SCROLLED 0x0006 /* PDCurses */ #define BUTTON_ACTION_MASK 0x0007 /* PDCurses */ #define PDC_BUTTON_SHIFT 0x0008 /* PDCurses */ #define PDC_BUTTON_CONTROL 0x0010 /* PDCurses */ #define PDC_BUTTON_ALT 0x0020 /* PDCurses */ #define BUTTON_MODIFIER_MASK 0x0038 /* PDCurses */ #define MOUSE_X_POS (Mouse_status.x) #define MOUSE_Y_POS (Mouse_status.y) /* * Bits associated with the .changes field: * 3 2 1 0 * 210987654321098765432109876543210 * 1 <- button 1 has changed * 10 <- button 2 has changed * 100 <- button 3 has changed * 1000 <- mouse has moved * 10000 <- mouse position report * 100000 <- mouse wheel up * 1000000 <- mouse wheel down */ #define PDC_MOUSE_MOVED 0x0008 #define PDC_MOUSE_POSITION 0x0010 #define PDC_MOUSE_WHEEL_UP 0x0020 #define PDC_MOUSE_WHEEL_DOWN 0x0040 #define A_BUTTON_CHANGED (Mouse_status.changes & 7) #define MOUSE_MOVED (Mouse_status.changes & PDC_MOUSE_MOVED) #define MOUSE_POS_REPORT (Mouse_status.changes & PDC_MOUSE_POSITION) #define BUTTON_CHANGED(x) (Mouse_status.changes & (1 << ((x) - 1))) #define BUTTON_STATUS(x) (Mouse_status.button[(x) - 1]) #define MOUSE_WHEEL_UP (Mouse_status.changes & PDC_MOUSE_WHEEL_UP) #define MOUSE_WHEEL_DOWN (Mouse_status.changes & PDC_MOUSE_WHEEL_DOWN) /* mouse bit-masks */ #define BUTTON1_RELEASED 0x00000001L #define BUTTON1_PRESSED 0x00000002L #define BUTTON1_CLICKED 0x00000004L #define BUTTON1_DOUBLE_CLICKED 0x00000008L #define BUTTON1_TRIPLE_CLICKED 0x00000010L #define BUTTON1_MOVED 0x00000010L /* PDCurses */ #define BUTTON2_RELEASED 0x00000020L #define BUTTON2_PRESSED 0x00000040L #define BUTTON2_CLICKED 0x00000080L #define BUTTON2_DOUBLE_CLICKED 0x00000100L #define BUTTON2_TRIPLE_CLICKED 0x00000200L #define BUTTON2_MOVED 0x00000200L /* PDCurses */ #define BUTTON3_RELEASED 0x00000400L #define BUTTON3_PRESSED 0x00000800L #define BUTTON3_CLICKED 0x00001000L #define BUTTON3_DOUBLE_CLICKED 0x00002000L #define BUTTON3_TRIPLE_CLICKED 0x00004000L #define BUTTON3_MOVED 0x00004000L /* PDCurses */ /* For the ncurses-compatible functions only, BUTTON4_PRESSED and BUTTON5_PRESSED are returned for mouse scroll wheel up and down; otherwise PDCurses doesn't support buttons 4 and 5 */ #define BUTTON4_RELEASED 0x00008000L #define BUTTON4_PRESSED 0x00010000L #define BUTTON4_CLICKED 0x00020000L #define BUTTON4_DOUBLE_CLICKED 0x00040000L #define BUTTON4_TRIPLE_CLICKED 0x00080000L #define BUTTON5_RELEASED 0x00100000L #define BUTTON5_PRESSED 0x00200000L #define BUTTON5_CLICKED 0x00400000L #define BUTTON5_DOUBLE_CLICKED 0x00800000L #define BUTTON5_TRIPLE_CLICKED 0x01000000L #define MOUSE_WHEEL_SCROLL 0x02000000L /* PDCurses */ #define BUTTON_MODIFIER_SHIFT 0x04000000L /* PDCurses */ #define BUTTON_MODIFIER_CONTROL 0x08000000L /* PDCurses */ #define BUTTON_MODIFIER_ALT 0x10000000L /* PDCurses */ #define ALL_MOUSE_EVENTS 0x1fffffffL #define REPORT_MOUSE_POSITION 0x20000000L /* ncurses mouse interface */ typedef unsigned long mmask_t; typedef struct { short id; /* unused, always 0 */ int x, y, z; /* x, y same as MOUSE_STATUS; z unused */ mmask_t bstate; /* equivalent to changes + button[], but in the same format as used for mousemask() */ } MEVENT; #ifdef NCURSES_MOUSE_VERSION # define BUTTON_SHIFT BUTTON_MODIFIER_SHIFT # define BUTTON_CONTROL BUTTON_MODIFIER_CONTROL # define BUTTON_CTRL BUTTON_MODIFIER_CONTROL # define BUTTON_ALT BUTTON_MODIFIER_ALT #else # define BUTTON_SHIFT PDC_BUTTON_SHIFT # define BUTTON_CONTROL PDC_BUTTON_CONTROL # define BUTTON_ALT PDC_BUTTON_ALT #endif /*---------------------------------------------------------------------- * * PDCurses Structure Definitions * */ typedef struct _win /* definition of a window */ { int _cury; /* current pseudo-cursor */ int _curx; int _maxy; /* max window coordinates */ int _maxx; int _begy; /* origin on screen */ int _begx; int _flags; /* window properties */ chtype _attrs; /* standard attributes and colors */ chtype _bkgd; /* background, normally blank */ bool _clear; /* causes clear at next refresh */ bool _leaveit; /* leaves cursor where it is */ bool _scroll; /* allows window scrolling */ bool _nodelay; /* input character wait flag */ bool _immed; /* immediate update flag */ bool _sync; /* synchronise window ancestors */ bool _use_keypad; /* flags keypad key mode active */ chtype **_y; /* pointer to line pointer array */ int *_firstch; /* first changed character in line */ int *_lastch; /* last changed character in line */ int _tmarg; /* top of scrolling region */ int _bmarg; /* bottom of scrolling region */ int _delayms; /* milliseconds of delay for getch() */ int _parx, _pary; /* coords relative to parent (0,0) */ struct _win *_parent; /* subwin's pointer to parent win */ } WINDOW; /* Avoid using the SCREEN struct directly -- use the corresponding functions if possible. This struct may eventually be made private. */ typedef struct { bool alive; /* if initscr() called, and not endwin() */ bool autocr; /* if cr -> lf */ bool cbreak; /* if terminal unbuffered */ bool echo; /* if terminal echo */ bool raw_inp; /* raw input mode (v. cooked input) */ bool raw_out; /* raw output mode (7 v. 8 bits) */ bool audible; /* FALSE if the bell is visual */ bool mono; /* TRUE if current screen is mono */ bool resized; /* TRUE if TERM has been resized */ bool orig_attr; /* TRUE if we have the original colors */ short orig_fore; /* original screen foreground color */ short orig_back; /* original screen foreground color */ int cursrow; /* position of physical cursor */ int curscol; /* position of physical cursor */ int visibility; /* visibility of cursor */ int orig_cursor; /* original cursor size */ int lines; /* new value for LINES */ int cols; /* new value for COLS */ unsigned long _trap_mbe; /* trap these mouse button events */ unsigned long _map_mbe_to_key; /* map mouse buttons to slk */ int mouse_wait; /* time to wait (in ms) for a button release after a press, in order to count it as a click */ int slklines; /* lines in use by slk_init() */ WINDOW *slk_winptr; /* window for slk */ int linesrippedoff; /* lines ripped off via ripoffline() */ int linesrippedoffontop; /* lines ripped off on top via ripoffline() */ int delaytenths; /* 1/10ths second to wait block getch() for */ bool _preserve; /* TRUE if screen background to be preserved */ int _restore; /* specifies if screen background to be restored, and how */ bool save_key_modifiers; /* TRUE if each key modifiers saved with each key press */ bool return_key_modifiers; /* TRUE if modifier keys are returned as "real" keys */ bool key_code; /* TRUE if last key is a special key; used internally by get_wch() */ #ifdef XCURSES int XcurscrSize; /* size of Xcurscr shared memory block */ bool sb_on; int sb_viewport_y; int sb_viewport_x; int sb_total_y; int sb_total_x; int sb_cur_y; int sb_cur_x; #endif short line_color; /* color of line attributes - default -1 */ } SCREEN; /*---------------------------------------------------------------------- * * PDCurses External Variables * */ #ifdef PDC_DLL_BUILD # ifdef CURSES_LIBRARY # define PDCEX __declspec(dllexport) extern # else # define PDCEX __declspec(dllimport) # endif #else # define PDCEX extern #endif PDCEX int LINES; /* terminal height */ PDCEX int COLS; /* terminal width */ PDCEX WINDOW *stdscr; /* the default screen window */ PDCEX WINDOW *curscr; /* the current screen image */ PDCEX SCREEN *SP; /* curses variables */ PDCEX MOUSE_STATUS Mouse_status; PDCEX int COLORS; PDCEX int COLOR_PAIRS; PDCEX int TABSIZE; PDCEX chtype acs_map[]; /* alternate character set map */ PDCEX char ttytype[]; /* terminal name/description */ /*man-start************************************************************** PDCurses Text Attributes ======================== Originally, PDCurses used a short (16 bits) for its chtype. To include color, a number of things had to be sacrificed from the strict Unix and System V support. The main problem was fitting all character attributes and color into an unsigned char (all 8 bits!). Today, PDCurses by default uses a long (32 bits) for its chtype, as in System V. The short chtype is still available, by undefining CHTYPE_LONG and rebuilding the library. The following is the structure of a win->_attrs chtype: short form: ------------------------------------------------- |15|14|13|12|11|10| 9| 8| 7| 6| 5| 4| 3| 2| 1| 0| ------------------------------------------------- color number | attrs | character eg 'a' The available non-color attributes are bold, reverse and blink. Others have no effect. The high order char is an index into an array of physical colors (defined in color.c) -- 32 foreground/background color pairs (5 bits) plus 3 bits for other attributes. long form: ---------------------------------------------------------------------------- |31|30|29|28|27|26|25|24|23|22|21|20|19|18|17|16|15|14|13|12|..| 3| 2| 1| 0| ---------------------------------------------------------------------------- color number | modifiers | character eg 'a' The available non-color attributes are bold, underline, invisible, right-line, left-line, protect, reverse and blink. 256 color pairs (8 bits), 8 bits for other attributes, and 16 bits for character data. **man-end****************************************************************/ /*** Video attribute macros ***/ #define A_NORMAL (chtype)0 #ifdef CHTYPE_LONG # define A_ALTCHARSET (chtype)0x00010000 # define A_RIGHTLINE (chtype)0x00020000 # define A_LEFTLINE (chtype)0x00040000 # define A_INVIS (chtype)0x00080000 # define A_UNDERLINE (chtype)0x00100000 # define A_REVERSE (chtype)0x00200000 # define A_BLINK (chtype)0x00400000 # define A_BOLD (chtype)0x00800000 # define A_ATTRIBUTES (chtype)0xffff0000 # define A_CHARTEXT (chtype)0x0000ffff # define A_COLOR (chtype)0xff000000 # define A_ITALIC A_INVIS # define A_PROTECT (A_UNDERLINE | A_LEFTLINE | A_RIGHTLINE) # define PDC_ATTR_SHIFT 19 # define PDC_COLOR_SHIFT 24 #else # define A_BOLD (chtype)0x0100 /* X/Open */ # define A_REVERSE (chtype)0x0200 /* X/Open */ # define A_BLINK (chtype)0x0400 /* X/Open */ # define A_ATTRIBUTES (chtype)0xff00 /* X/Open */ # define A_CHARTEXT (chtype)0x00ff /* X/Open */ # define A_COLOR (chtype)0xf800 /* System V */ # define A_ALTCHARSET A_NORMAL /* X/Open */ # define A_PROTECT A_NORMAL /* X/Open */ # define A_UNDERLINE A_NORMAL /* X/Open */ # define A_LEFTLINE A_NORMAL # define A_RIGHTLINE A_NORMAL # define A_ITALIC A_NORMAL # define A_INVIS A_NORMAL # define PDC_ATTR_SHIFT 8 # define PDC_COLOR_SHIFT 11 #endif #define A_STANDOUT (A_REVERSE | A_BOLD) /* X/Open */ #define A_DIM A_NORMAL #define CHR_MSK A_CHARTEXT /* Obsolete */ #define ATR_MSK A_ATTRIBUTES /* Obsolete */ #define ATR_NRM A_NORMAL /* Obsolete */ /* For use with attr_t -- X/Open says, "these shall be distinct", so this is a non-conforming implementation. */ #define WA_ALTCHARSET A_ALTCHARSET #define WA_BLINK A_BLINK #define WA_BOLD A_BOLD #define WA_DIM A_DIM #define WA_INVIS A_INVIS #define WA_LEFT A_LEFTLINE #define WA_PROTECT A_PROTECT #define WA_REVERSE A_REVERSE #define WA_RIGHT A_RIGHTLINE #define WA_STANDOUT A_STANDOUT #define WA_UNDERLINE A_UNDERLINE #define WA_HORIZONTAL A_NORMAL #define WA_LOW A_NORMAL #define WA_TOP A_NORMAL #define WA_VERTICAL A_NORMAL /*** Alternate character set macros ***/ /* 'w' = 32-bit chtype; acs_map[] index | A_ALTCHARSET 'n' = 16-bit chtype; it gets the fallback set because no bit is available for A_ALTCHARSET */ #ifdef CHTYPE_LONG # define ACS_PICK(w, n) ((chtype)w | A_ALTCHARSET) #else # define ACS_PICK(w, n) ((chtype)n) #endif /* VT100-compatible symbols -- box chars */ #define ACS_ULCORNER ACS_PICK('l', '+') #define ACS_LLCORNER ACS_PICK('m', '+') #define ACS_URCORNER ACS_PICK('k', '+') #define ACS_LRCORNER ACS_PICK('j', '+') #define ACS_RTEE ACS_PICK('u', '+') #define ACS_LTEE ACS_PICK('t', '+') #define ACS_BTEE ACS_PICK('v', '+') #define ACS_TTEE ACS_PICK('w', '+') #define ACS_HLINE ACS_PICK('q', '-') #define ACS_VLINE ACS_PICK('x', '|') #define ACS_PLUS ACS_PICK('n', '+') /* VT100-compatible symbols -- other */ #define ACS_S1 ACS_PICK('o', '-') #define ACS_S9 ACS_PICK('s', '_') #define ACS_DIAMOND ACS_PICK('`', '+') #define ACS_CKBOARD ACS_PICK('a', ':') #define ACS_DEGREE ACS_PICK('f', '\'') #define ACS_PLMINUS ACS_PICK('g', '#') #define ACS_BULLET ACS_PICK('~', 'o') /* Teletype 5410v1 symbols -- these are defined in SysV curses, but are not well-supported by most terminals. Stick to VT100 characters for optimum portability. */ #define ACS_LARROW ACS_PICK(',', '<') #define ACS_RARROW ACS_PICK('+', '>') #define ACS_DARROW ACS_PICK('.', 'v') #define ACS_UARROW ACS_PICK('-', '^') #define ACS_BOARD ACS_PICK('h', '#') #define ACS_LANTERN ACS_PICK('i', '*') #define ACS_BLOCK ACS_PICK('0', '#') /* That goes double for these -- undocumented SysV symbols. Don't use them. */ #define ACS_S3 ACS_PICK('p', '-') #define ACS_S7 ACS_PICK('r', '-') #define ACS_LEQUAL ACS_PICK('y', '<') #define ACS_GEQUAL ACS_PICK('z', '>') #define ACS_PI ACS_PICK('{', 'n') #define ACS_NEQUAL ACS_PICK('|', '+') #define ACS_STERLING ACS_PICK('}', 'L') /* Box char aliases */ #define ACS_BSSB ACS_ULCORNER #define ACS_SSBB ACS_LLCORNER #define ACS_BBSS ACS_URCORNER #define ACS_SBBS ACS_LRCORNER #define ACS_SBSS ACS_RTEE #define ACS_SSSB ACS_LTEE #define ACS_SSBS ACS_BTEE #define ACS_BSSS ACS_TTEE #define ACS_BSBS ACS_HLINE #define ACS_SBSB ACS_VLINE #define ACS_SSSS ACS_PLUS /* cchar_t aliases */ #ifdef PDC_WIDE # define WACS_ULCORNER (&(acs_map['l'])) # define WACS_LLCORNER (&(acs_map['m'])) # define WACS_URCORNER (&(acs_map['k'])) # define WACS_LRCORNER (&(acs_map['j'])) # define WACS_RTEE (&(acs_map['u'])) # define WACS_LTEE (&(acs_map['t'])) # define WACS_BTEE (&(acs_map['v'])) # define WACS_TTEE (&(acs_map['w'])) # define WACS_HLINE (&(acs_map['q'])) # define WACS_VLINE (&(acs_map['x'])) # define WACS_PLUS (&(acs_map['n'])) # define WACS_S1 (&(acs_map['o'])) # define WACS_S9 (&(acs_map['s'])) # define WACS_DIAMOND (&(acs_map['`'])) # define WACS_CKBOARD (&(acs_map['a'])) # define WACS_DEGREE (&(acs_map['f'])) # define WACS_PLMINUS (&(acs_map['g'])) # define WACS_BULLET (&(acs_map['~'])) # define WACS_LARROW (&(acs_map[','])) # define WACS_RARROW (&(acs_map['+'])) # define WACS_DARROW (&(acs_map['.'])) # define WACS_UARROW (&(acs_map['-'])) # define WACS_BOARD (&(acs_map['h'])) # define WACS_LANTERN (&(acs_map['i'])) # define WACS_BLOCK (&(acs_map['0'])) # define WACS_S3 (&(acs_map['p'])) # define WACS_S7 (&(acs_map['r'])) # define WACS_LEQUAL (&(acs_map['y'])) # define WACS_GEQUAL (&(acs_map['z'])) # define WACS_PI (&(acs_map['{'])) # define WACS_NEQUAL (&(acs_map['|'])) # define WACS_STERLING (&(acs_map['}'])) # define WACS_BSSB WACS_ULCORNER # define WACS_SSBB WACS_LLCORNER # define WACS_BBSS WACS_URCORNER # define WACS_SBBS WACS_LRCORNER # define WACS_SBSS WACS_RTEE # define WACS_SSSB WACS_LTEE # define WACS_SSBS WACS_BTEE # define WACS_BSSS WACS_TTEE # define WACS_BSBS WACS_HLINE # define WACS_SBSB WACS_VLINE # define WACS_SSSS WACS_PLUS #endif /*** Color macros ***/ #define COLOR_BLACK 0 #ifdef PDC_RGB /* RGB */ # define COLOR_RED 1 # define COLOR_GREEN 2 # define COLOR_BLUE 4 #else /* BGR */ # define COLOR_BLUE 1 # define COLOR_GREEN 2 # define COLOR_RED 4 #endif #define COLOR_CYAN (COLOR_BLUE | COLOR_GREEN) #define COLOR_MAGENTA (COLOR_RED | COLOR_BLUE) #define COLOR_YELLOW (COLOR_RED | COLOR_GREEN) #define COLOR_WHITE 7 /*---------------------------------------------------------------------- * * Function and Keypad Key Definitions. * Many are just for compatibility. * */ #define KEY_CODE_YES 0x100 /* If get_wch() gives a key code */ #define KEY_BREAK 0x101 /* Not on PC KBD */ #define KEY_DOWN 0x102 /* Down arrow key */ #define KEY_UP 0x103 /* Up arrow key */ #define KEY_LEFT 0x104 /* Left arrow key */ #define KEY_RIGHT 0x105 /* Right arrow key */ #define KEY_HOME 0x106 /* home key */ #define KEY_BACKSPACE 0x107 /* not on pc */ #define KEY_F0 0x108 /* function keys; 64 reserved */ #define KEY_DL 0x148 /* delete line */ #define KEY_IL 0x149 /* insert line */ #define KEY_DC 0x14a /* delete character */ #define KEY_IC 0x14b /* insert char or enter ins mode */ #define KEY_EIC 0x14c /* exit insert char mode */ #define KEY_CLEAR 0x14d /* clear screen */ #define KEY_EOS 0x14e /* clear to end of screen */ #define KEY_EOL 0x14f /* clear to end of line */ #define KEY_SF 0x150 /* scroll 1 line forward */ #define KEY_SR 0x151 /* scroll 1 line back (reverse) */ #define KEY_NPAGE 0x152 /* next page */ #define KEY_PPAGE 0x153 /* previous page */ #define KEY_STAB 0x154 /* set tab */ #define KEY_CTAB 0x155 /* clear tab */ #define KEY_CATAB 0x156 /* clear all tabs */ #define KEY_ENTER 0x157 /* enter or send (unreliable) */ #define KEY_SRESET 0x158 /* soft/reset (partial/unreliable) */ #define KEY_RESET 0x159 /* reset/hard reset (unreliable) */ #define KEY_PRINT 0x15a /* print/copy */ #define KEY_LL 0x15b /* home down/bottom (lower left) */ #define KEY_ABORT 0x15c /* abort/terminate key (any) */ #define KEY_SHELP 0x15d /* short help */ #define KEY_LHELP 0x15e /* long help */ #define KEY_BTAB 0x15f /* Back tab key */ #define KEY_BEG 0x160 /* beg(inning) key */ #define KEY_CANCEL 0x161 /* cancel key */ #define KEY_CLOSE 0x162 /* close key */ #define KEY_COMMAND 0x163 /* cmd (command) key */ #define KEY_COPY 0x164 /* copy key */ #define KEY_CREATE 0x165 /* create key */ #define KEY_END 0x166 /* end key */ #define KEY_EXIT 0x167 /* exit key */ #define KEY_FIND 0x168 /* find key */ #define KEY_HELP 0x169 /* help key */ #define KEY_MARK 0x16a /* mark key */ #define KEY_MESSAGE 0x16b /* message key */ #define KEY_MOVE 0x16c /* move key */ #define KEY_NEXT 0x16d /* next object key */ #define KEY_OPEN 0x16e /* open key */ #define KEY_OPTIONS 0x16f /* options key */ #define KEY_PREVIOUS 0x170 /* previous object key */ #define KEY_REDO 0x171 /* redo key */ #define KEY_REFERENCE 0x172 /* ref(erence) key */ #define KEY_REFRESH 0x173 /* refresh key */ #define KEY_REPLACE 0x174 /* replace key */ #define KEY_RESTART 0x175 /* restart key */ #define KEY_RESUME 0x176 /* resume key */ #define KEY_SAVE 0x177 /* save key */ #define KEY_SBEG 0x178 /* shifted beginning key */ #define KEY_SCANCEL 0x179 /* shifted cancel key */ #define KEY_SCOMMAND 0x17a /* shifted command key */ #define KEY_SCOPY 0x17b /* shifted copy key */ #define KEY_SCREATE 0x17c /* shifted create key */ #define KEY_SDC 0x17d /* shifted delete char key */ #define KEY_SDL 0x17e /* shifted delete line key */ #define KEY_SELECT 0x17f /* select key */ #define KEY_SEND 0x180 /* shifted end key */ #define KEY_SEOL 0x181 /* shifted clear line key */ #define KEY_SEXIT 0x182 /* shifted exit key */ #define KEY_SFIND 0x183 /* shifted find key */ #define KEY_SHOME 0x184 /* shifted home key */ #define KEY_SIC 0x185 /* shifted input key */ #define KEY_SLEFT 0x187 /* shifted left arrow key */ #define KEY_SMESSAGE 0x188 /* shifted message key */ #define KEY_SMOVE 0x189 /* shifted move key */ #define KEY_SNEXT 0x18a /* shifted next key */ #define KEY_SOPTIONS 0x18b /* shifted options key */ #define KEY_SPREVIOUS 0x18c /* shifted prev key */ #define KEY_SPRINT 0x18d /* shifted print key */ #define KEY_SREDO 0x18e /* shifted redo key */ #define KEY_SREPLACE 0x18f /* shifted replace key */ #define KEY_SRIGHT 0x190 /* shifted right arrow */ #define KEY_SRSUME 0x191 /* shifted resume key */ #define KEY_SSAVE 0x192 /* shifted save key */ #define KEY_SSUSPEND 0x193 /* shifted suspend key */ #define KEY_SUNDO 0x194 /* shifted undo key */ #define KEY_SUSPEND 0x195 /* suspend key */ #define KEY_UNDO 0x196 /* undo key */ /* PDCurses-specific key definitions -- PC only */ #define ALT_0 0x197 #define ALT_1 0x198 #define ALT_2 0x199 #define ALT_3 0x19a #define ALT_4 0x19b #define ALT_5 0x19c #define ALT_6 0x19d #define ALT_7 0x19e #define ALT_8 0x19f #define ALT_9 0x1a0 #define ALT_A 0x1a1 #define ALT_B 0x1a2 #define ALT_C 0x1a3 #define ALT_D 0x1a4 #define ALT_E 0x1a5 #define ALT_F 0x1a6 #define ALT_G 0x1a7 #define ALT_H 0x1a8 #define ALT_I 0x1a9 #define ALT_J 0x1aa #define ALT_K 0x1ab #define ALT_L 0x1ac #define ALT_M 0x1ad #define ALT_N 0x1ae #define ALT_O 0x1af #define ALT_P 0x1b0 #define ALT_Q 0x1b1 #define ALT_R 0x1b2 #define ALT_S 0x1b3 #define ALT_T 0x1b4 #define ALT_U 0x1b5 #define ALT_V 0x1b6 #define ALT_W 0x1b7 #define ALT_X 0x1b8 #define ALT_Y 0x1b9 #define ALT_Z 0x1ba #define CTL_LEFT 0x1bb /* Control-Left-Arrow */ #define CTL_RIGHT 0x1bc #define CTL_PGUP 0x1bd #define CTL_PGDN 0x1be #define CTL_HOME 0x1bf #define CTL_END 0x1c0 #define KEY_A1 0x1c1 /* upper left on Virtual keypad */ #define KEY_A2 0x1c2 /* upper middle on Virt. keypad */ #define KEY_A3 0x1c3 /* upper right on Vir. keypad */ #define KEY_B1 0x1c4 /* middle left on Virt. keypad */ #define KEY_B2 0x1c5 /* center on Virt. keypad */ #define KEY_B3 0x1c6 /* middle right on Vir. keypad */ #define KEY_C1 0x1c7 /* lower left on Virt. keypad */ #define KEY_C2 0x1c8 /* lower middle on Virt. keypad */ #define KEY_C3 0x1c9 /* lower right on Vir. keypad */ #define PADSLASH 0x1ca /* slash on keypad */ #define PADENTER 0x1cb /* enter on keypad */ #define CTL_PADENTER 0x1cc /* ctl-enter on keypad */ #define ALT_PADENTER 0x1cd /* alt-enter on keypad */ #define PADSTOP 0x1ce /* stop on keypad */ #define PADSTAR 0x1cf /* star on keypad */ #define PADMINUS 0x1d0 /* minus on keypad */ #define PADPLUS 0x1d1 /* plus on keypad */ #define CTL_PADSTOP 0x1d2 /* ctl-stop on keypad */ #define CTL_PADCENTER 0x1d3 /* ctl-enter on keypad */ #define CTL_PADPLUS 0x1d4 /* ctl-plus on keypad */ #define CTL_PADMINUS 0x1d5 /* ctl-minus on keypad */ #define CTL_PADSLASH 0x1d6 /* ctl-slash on keypad */ #define CTL_PADSTAR 0x1d7 /* ctl-star on keypad */ #define ALT_PADPLUS 0x1d8 /* alt-plus on keypad */ #define ALT_PADMINUS 0x1d9 /* alt-minus on keypad */ #define ALT_PADSLASH 0x1da /* alt-slash on keypad */ #define ALT_PADSTAR 0x1db /* alt-star on keypad */ #define ALT_PADSTOP 0x1dc /* alt-stop on keypad */ #define CTL_INS 0x1dd /* ctl-insert */ #define ALT_DEL 0x1de /* alt-delete */ #define ALT_INS 0x1df /* alt-insert */ #define CTL_UP 0x1e0 /* ctl-up arrow */ #define CTL_DOWN 0x1e1 /* ctl-down arrow */ #define CTL_TAB 0x1e2 /* ctl-tab */ #define ALT_TAB 0x1e3 #define ALT_MINUS 0x1e4 #define ALT_EQUAL 0x1e5 #define ALT_HOME 0x1e6 #define ALT_PGUP 0x1e7 #define ALT_PGDN 0x1e8 #define ALT_END 0x1e9 #define ALT_UP 0x1ea /* alt-up arrow */ #define ALT_DOWN 0x1eb /* alt-down arrow */ #define ALT_RIGHT 0x1ec /* alt-right arrow */ #define ALT_LEFT 0x1ed /* alt-left arrow */ #define ALT_ENTER 0x1ee /* alt-enter */ #define ALT_ESC 0x1ef /* alt-escape */ #define ALT_BQUOTE 0x1f0 /* alt-back quote */ #define ALT_LBRACKET 0x1f1 /* alt-left bracket */ #define ALT_RBRACKET 0x1f2 /* alt-right bracket */ #define ALT_SEMICOLON 0x1f3 /* alt-semi-colon */ #define ALT_FQUOTE 0x1f4 /* alt-forward quote */ #define ALT_COMMA 0x1f5 /* alt-comma */ #define ALT_STOP 0x1f6 /* alt-stop */ #define ALT_FSLASH 0x1f7 /* alt-forward slash */ #define ALT_BKSP 0x1f8 /* alt-backspace */ #define CTL_BKSP 0x1f9 /* ctl-backspace */ #define PAD0 0x1fa /* keypad 0 */ #define CTL_PAD0 0x1fb /* ctl-keypad 0 */ #define CTL_PAD1 0x1fc #define CTL_PAD2 0x1fd #define CTL_PAD3 0x1fe #define CTL_PAD4 0x1ff #define CTL_PAD5 0x200 #define CTL_PAD6 0x201 #define CTL_PAD7 0x202 #define CTL_PAD8 0x203 #define CTL_PAD9 0x204 #define ALT_PAD0 0x205 /* alt-keypad 0 */ #define ALT_PAD1 0x206 #define ALT_PAD2 0x207 #define ALT_PAD3 0x208 #define ALT_PAD4 0x209 #define ALT_PAD5 0x20a #define ALT_PAD6 0x20b #define ALT_PAD7 0x20c #define ALT_PAD8 0x20d #define ALT_PAD9 0x20e #define CTL_DEL 0x20f /* clt-delete */ #define ALT_BSLASH 0x210 /* alt-back slash */ #define CTL_ENTER 0x211 /* ctl-enter */ #define SHF_PADENTER 0x212 /* shift-enter on keypad */ #define SHF_PADSLASH 0x213 /* shift-slash on keypad */ #define SHF_PADSTAR 0x214 /* shift-star on keypad */ #define SHF_PADPLUS 0x215 /* shift-plus on keypad */ #define SHF_PADMINUS 0x216 /* shift-minus on keypad */ #define SHF_UP 0x217 /* shift-up on keypad */ #define SHF_DOWN 0x218 /* shift-down on keypad */ #define SHF_IC 0x219 /* shift-insert on keypad */ #define SHF_DC 0x21a /* shift-delete on keypad */ #define KEY_MOUSE 0x21b /* "mouse" key */ #define KEY_SHIFT_L 0x21c /* Left-shift */ #define KEY_SHIFT_R 0x21d /* Right-shift */ #define KEY_CONTROL_L 0x21e /* Left-control */ #define KEY_CONTROL_R 0x21f /* Right-control */ #define KEY_ALT_L 0x220 /* Left-alt */ #define KEY_ALT_R 0x221 /* Right-alt */ #define KEY_RESIZE 0x222 /* Window resize */ #define KEY_SUP 0x223 /* Shifted up arrow */ #define KEY_SDOWN 0x224 /* Shifted down arrow */ #define KEY_MIN KEY_BREAK /* Minimum curses key value */ #define KEY_MAX KEY_SDOWN /* Maximum curses key */ #define KEY_F(n) (KEY_F0 + (n)) /*---------------------------------------------------------------------- * * PDCurses Function Declarations * */ /* Standard */ int addch(const chtype); int addchnstr(const chtype *, int); int addchstr(const chtype *); int addnstr(const char *, int); int addstr(const char *); int attroff(chtype); int attron(chtype); int attrset(chtype); int attr_get(attr_t *, short *, void *); int attr_off(attr_t, void *); int attr_on(attr_t, void *); int attr_set(attr_t, short, void *); int baudrate(void); int beep(void); int bkgd(chtype); void bkgdset(chtype); int border(chtype, chtype, chtype, chtype, chtype, chtype, chtype, chtype); int box(WINDOW *, chtype, chtype); bool can_change_color(void); int cbreak(void); int chgat(int, attr_t, short, const void *); int clearok(WINDOW *, bool); int clear(void); int clrtobot(void); int clrtoeol(void); int color_content(short, short *, short *, short *); int color_set(short, void *); int copywin(const WINDOW *, WINDOW *, int, int, int, int, int, int, int); int curs_set(int); int def_prog_mode(void); int def_shell_mode(void); int delay_output(int); int delch(void); int deleteln(void); void delscreen(SCREEN *); int delwin(WINDOW *); WINDOW *derwin(WINDOW *, int, int, int, int); int doupdate(void); WINDOW *dupwin(WINDOW *); int echochar(const chtype); int echo(void); int endwin(void); char erasechar(void); int erase(void); void filter(void); int flash(void); int flushinp(void); chtype getbkgd(WINDOW *); int getnstr(char *, int); int getstr(char *); WINDOW *getwin(FILE *); int halfdelay(int); bool has_colors(void); bool has_ic(void); bool has_il(void); int hline(chtype, int); void idcok(WINDOW *, bool); int idlok(WINDOW *, bool); void immedok(WINDOW *, bool); int inchnstr(chtype *, int); int inchstr(chtype *); chtype inch(void); int init_color(short, short, short, short); int init_pair(short, short, short); WINDOW *initscr(void); int innstr(char *, int); int insch(chtype); int insdelln(int); int insertln(void); int insnstr(const char *, int); int insstr(const char *); int instr(char *); int intrflush(WINDOW *, bool); bool isendwin(void); bool is_linetouched(WINDOW *, int); bool is_wintouched(WINDOW *); char *keyname(int); int keypad(WINDOW *, bool); char killchar(void); int leaveok(WINDOW *, bool); char *longname(void); int meta(WINDOW *, bool); int move(int, int); int mvaddch(int, int, const chtype); int mvaddchnstr(int, int, const chtype *, int); int mvaddchstr(int, int, const chtype *); int mvaddnstr(int, int, const char *, int); int mvaddstr(int, int, const char *); int mvchgat(int, int, int, attr_t, short, const void *); int mvcur(int, int, int, int); int mvdelch(int, int); int mvderwin(WINDOW *, int, int); int mvgetch(int, int); int mvgetnstr(int, int, char *, int); int mvgetstr(int, int, char *); int mvhline(int, int, chtype, int); chtype mvinch(int, int); int mvinchnstr(int, int, chtype *, int); int mvinchstr(int, int, chtype *); int mvinnstr(int, int, char *, int); int mvinsch(int, int, chtype); int mvinsnstr(int, int, const char *, int); int mvinsstr(int, int, const char *); int mvinstr(int, int, char *); int mvprintw(int, int, const char *, ...); int mvscanw(int, int, const char *, ...); int mvvline(int, int, chtype, int); int mvwaddchnstr(WINDOW *, int, int, const chtype *, int); int mvwaddchstr(WINDOW *, int, int, const chtype *); int mvwaddch(WINDOW *, int, int, const chtype); int mvwaddnstr(WINDOW *, int, int, const char *, int); int mvwaddstr(WINDOW *, int, int, const char *); int mvwchgat(WINDOW *, int, int, int, attr_t, short, const void *); int mvwdelch(WINDOW *, int, int); int mvwgetch(WINDOW *, int, int); int mvwgetnstr(WINDOW *, int, int, char *, int); int mvwgetstr(WINDOW *, int, int, char *); int mvwhline(WINDOW *, int, int, chtype, int); int mvwinchnstr(WINDOW *, int, int, chtype *, int); int mvwinchstr(WINDOW *, int, int, chtype *); chtype mvwinch(WINDOW *, int, int); int mvwinnstr(WINDOW *, int, int, char *, int); int mvwinsch(WINDOW *, int, int, chtype); int mvwinsnstr(WINDOW *, int, int, const char *, int); int mvwinsstr(WINDOW *, int, int, const char *); int mvwinstr(WINDOW *, int, int, char *); int mvwin(WINDOW *, int, int); int mvwprintw(WINDOW *, int, int, const char *, ...); int mvwscanw(WINDOW *, int, int, const char *, ...); int mvwvline(WINDOW *, int, int, chtype, int); int napms(int); WINDOW *newpad(int, int); SCREEN *newterm(const char *, FILE *, FILE *); WINDOW *newwin(int, int, int, int); int nl(void); int nocbreak(void); int nodelay(WINDOW *, bool); int noecho(void); int nonl(void); void noqiflush(void); int noraw(void); int notimeout(WINDOW *, bool); int overlay(const WINDOW *, WINDOW *); int overwrite(const WINDOW *, WINDOW *); int pair_content(short, short *, short *); int pechochar(WINDOW *, chtype); int pnoutrefresh(WINDOW *, int, int, int, int, int, int); int prefresh(WINDOW *, int, int, int, int, int, int); int printw(const char *, ...); int putwin(WINDOW *, FILE *); void qiflush(void); int raw(void); int redrawwin(WINDOW *); int refresh(void); int reset_prog_mode(void); int reset_shell_mode(void); int resetty(void); int ripoffline(int, int (*)(WINDOW *, int)); int savetty(void); int scanw(const char *, ...); int scr_dump(const char *); int scr_init(const char *); int scr_restore(const char *); int scr_set(const char *); int scrl(int); int scroll(WINDOW *); int scrollok(WINDOW *, bool); SCREEN *set_term(SCREEN *); int setscrreg(int, int); int slk_attroff(const chtype); int slk_attr_off(const attr_t, void *); int slk_attron(const chtype); int slk_attr_on(const attr_t, void *); int slk_attrset(const chtype); int slk_attr_set(const attr_t, short, void *); int slk_clear(void); int slk_color(short); int slk_init(int); char *slk_label(int); int slk_noutrefresh(void); int slk_refresh(void); int slk_restore(void); int slk_set(int, const char *, int); int slk_touch(void); int standend(void); int standout(void); int start_color(void); WINDOW *subpad(WINDOW *, int, int, int, int); WINDOW *subwin(WINDOW *, int, int, int, int); int syncok(WINDOW *, bool); chtype termattrs(void); attr_t term_attrs(void); char *termname(void); void timeout(int); int touchline(WINDOW *, int, int); int touchwin(WINDOW *); int typeahead(int); int untouchwin(WINDOW *); void use_env(bool); int vidattr(chtype); int vid_attr(attr_t, short, void *); int vidputs(chtype, int (*)(int)); int vid_puts(attr_t, short, void *, int (*)(int)); int vline(chtype, int); int vw_printw(WINDOW *, const char *, va_list); int vwprintw(WINDOW *, const char *, va_list); int vw_scanw(WINDOW *, const char *, va_list); int vwscanw(WINDOW *, const char *, va_list); int waddchnstr(WINDOW *, const chtype *, int); int waddchstr(WINDOW *, const chtype *); int waddch(WINDOW *, const chtype); int waddnstr(WINDOW *, const char *, int); int waddstr(WINDOW *, const char *); int wattroff(WINDOW *, chtype); int wattron(WINDOW *, chtype); int wattrset(WINDOW *, chtype); int wattr_get(WINDOW *, attr_t *, short *, void *); int wattr_off(WINDOW *, attr_t, void *); int wattr_on(WINDOW *, attr_t, void *); int wattr_set(WINDOW *, attr_t, short, void *); void wbkgdset(WINDOW *, chtype); int wbkgd(WINDOW *, chtype); int wborder(WINDOW *, chtype, chtype, chtype, chtype, chtype, chtype, chtype, chtype); int wchgat(WINDOW *, int, attr_t, short, const void *); int wclear(WINDOW *); int wclrtobot(WINDOW *); int wclrtoeol(WINDOW *); int wcolor_set(WINDOW *, short, void *); void wcursyncup(WINDOW *); int wdelch(WINDOW *); int wdeleteln(WINDOW *); int wechochar(WINDOW *, const chtype); int werase(WINDOW *); int wgetch(WINDOW *); int wgetnstr(WINDOW *, char *, int); int wgetstr(WINDOW *, char *); int whline(WINDOW *, chtype, int); int winchnstr(WINDOW *, chtype *, int); int winchstr(WINDOW *, chtype *); chtype winch(WINDOW *); int winnstr(WINDOW *, char *, int); int winsch(WINDOW *, chtype); int winsdelln(WINDOW *, int); int winsertln(WINDOW *); int winsnstr(WINDOW *, const char *, int); int winsstr(WINDOW *, const char *); int winstr(WINDOW *, char *); int wmove(WINDOW *, int, int); int wnoutrefresh(WINDOW *); int wprintw(WINDOW *, const char *, ...); int wredrawln(WINDOW *, int, int); int wrefresh(WINDOW *); int wscanw(WINDOW *, const char *, ...); int wscrl(WINDOW *, int); int wsetscrreg(WINDOW *, int, int); int wstandend(WINDOW *); int wstandout(WINDOW *); void wsyncdown(WINDOW *); void wsyncup(WINDOW *); void wtimeout(WINDOW *, int); int wtouchln(WINDOW *, int, int, int); int wvline(WINDOW *, chtype, int); /* Wide-character functions */ #ifdef PDC_WIDE int addnwstr(const wchar_t *, int); int addwstr(const wchar_t *); int add_wch(const cchar_t *); int add_wchnstr(const cchar_t *, int); int add_wchstr(const cchar_t *); int border_set(const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *); int box_set(WINDOW *, const cchar_t *, const cchar_t *); int echo_wchar(const cchar_t *); int erasewchar(wchar_t *); int getbkgrnd(cchar_t *); int getcchar(const cchar_t *, wchar_t *, attr_t *, short *, void *); int getn_wstr(wint_t *, int); int get_wch(wint_t *); int get_wstr(wint_t *); int hline_set(const cchar_t *, int); int innwstr(wchar_t *, int); int ins_nwstr(const wchar_t *, int); int ins_wch(const cchar_t *); int ins_wstr(const wchar_t *); int inwstr(wchar_t *); int in_wch(cchar_t *); int in_wchnstr(cchar_t *, int); int in_wchstr(cchar_t *); char *key_name(wchar_t); int killwchar(wchar_t *); int mvaddnwstr(int, int, const wchar_t *, int); int mvaddwstr(int, int, const wchar_t *); int mvadd_wch(int, int, const cchar_t *); int mvadd_wchnstr(int, int, const cchar_t *, int); int mvadd_wchstr(int, int, const cchar_t *); int mvgetn_wstr(int, int, wint_t *, int); int mvget_wch(int, int, wint_t *); int mvget_wstr(int, int, wint_t *); int mvhline_set(int, int, const cchar_t *, int); int mvinnwstr(int, int, wchar_t *, int); int mvins_nwstr(int, int, const wchar_t *, int); int mvins_wch(int, int, const cchar_t *); int mvins_wstr(int, int, const wchar_t *); int mvinwstr(int, int, wchar_t *); int mvin_wch(int, int, cchar_t *); int mvin_wchnstr(int, int, cchar_t *, int); int mvin_wchstr(int, int, cchar_t *); int mvvline_set(int, int, const cchar_t *, int); int mvwaddnwstr(WINDOW *, int, int, const wchar_t *, int); int mvwaddwstr(WINDOW *, int, int, const wchar_t *); int mvwadd_wch(WINDOW *, int, int, const cchar_t *); int mvwadd_wchnstr(WINDOW *, int, int, const cchar_t *, int); int mvwadd_wchstr(WINDOW *, int, int, const cchar_t *); int mvwgetn_wstr(WINDOW *, int, int, wint_t *, int); int mvwget_wch(WINDOW *, int, int, wint_t *); int mvwget_wstr(WINDOW *, int, int, wint_t *); int mvwhline_set(WINDOW *, int, int, const cchar_t *, int); int mvwinnwstr(WINDOW *, int, int, wchar_t *, int); int mvwins_nwstr(WINDOW *, int, int, const wchar_t *, int); int mvwins_wch(WINDOW *, int, int, const cchar_t *); int mvwins_wstr(WINDOW *, int, int, const wchar_t *); int mvwin_wch(WINDOW *, int, int, cchar_t *); int mvwin_wchnstr(WINDOW *, int, int, cchar_t *, int); int mvwin_wchstr(WINDOW *, int, int, cchar_t *); int mvwinwstr(WINDOW *, int, int, wchar_t *); int mvwvline_set(WINDOW *, int, int, const cchar_t *, int); int pecho_wchar(WINDOW *, const cchar_t*); int setcchar(cchar_t*, const wchar_t*, const attr_t, short, const void*); int slk_wset(int, const wchar_t *, int); int unget_wch(const wchar_t); int vline_set(const cchar_t *, int); int waddnwstr(WINDOW *, const wchar_t *, int); int waddwstr(WINDOW *, const wchar_t *); int wadd_wch(WINDOW *, const cchar_t *); int wadd_wchnstr(WINDOW *, const cchar_t *, int); int wadd_wchstr(WINDOW *, const cchar_t *); int wbkgrnd(WINDOW *, const cchar_t *); void wbkgrndset(WINDOW *, const cchar_t *); int wborder_set(WINDOW *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *, const cchar_t *); int wecho_wchar(WINDOW *, const cchar_t *); int wgetbkgrnd(WINDOW *, cchar_t *); int wgetn_wstr(WINDOW *, wint_t *, int); int wget_wch(WINDOW *, wint_t *); int wget_wstr(WINDOW *, wint_t *); int whline_set(WINDOW *, const cchar_t *, int); int winnwstr(WINDOW *, wchar_t *, int); int wins_nwstr(WINDOW *, const wchar_t *, int); int wins_wch(WINDOW *, const cchar_t *); int wins_wstr(WINDOW *, const wchar_t *); int winwstr(WINDOW *, wchar_t *); int win_wch(WINDOW *, cchar_t *); int win_wchnstr(WINDOW *, cchar_t *, int); int win_wchstr(WINDOW *, cchar_t *); wchar_t *wunctrl(cchar_t *); int wvline_set(WINDOW *, const cchar_t *, int); #endif /* Quasi-standard */ chtype getattrs(WINDOW *); int getbegx(WINDOW *); int getbegy(WINDOW *); int getmaxx(WINDOW *); int getmaxy(WINDOW *); int getparx(WINDOW *); int getpary(WINDOW *); int getcurx(WINDOW *); int getcury(WINDOW *); void traceoff(void); void traceon(void); char *unctrl(chtype); int crmode(void); int nocrmode(void); int draino(int); int resetterm(void); int fixterm(void); int saveterm(void); int setsyx(int, int); int mouse_set(unsigned long); int mouse_on(unsigned long); int mouse_off(unsigned long); int request_mouse_pos(void); int map_button(unsigned long); void wmouse_position(WINDOW *, int *, int *); unsigned long getmouse(void); unsigned long getbmap(void); /* ncurses */ int assume_default_colors(int, int); const char *curses_version(void); bool has_key(int); int use_default_colors(void); int wresize(WINDOW *, int, int); int mouseinterval(int); mmask_t mousemask(mmask_t, mmask_t *); bool mouse_trafo(int *, int *, bool); int nc_getmouse(MEVENT *); int ungetmouse(MEVENT *); bool wenclose(const WINDOW *, int, int); bool wmouse_trafo(const WINDOW *, int *, int *, bool); /* PDCurses */ int addrawch(chtype); int insrawch(chtype); bool is_termresized(void); int mvaddrawch(int, int, chtype); int mvdeleteln(int, int); int mvinsertln(int, int); int mvinsrawch(int, int, chtype); int mvwaddrawch(WINDOW *, int, int, chtype); int mvwdeleteln(WINDOW *, int, int); int mvwinsertln(WINDOW *, int, int); int mvwinsrawch(WINDOW *, int, int, chtype); int raw_output(bool); int resize_term(int, int); WINDOW *resize_window(WINDOW *, int, int); int waddrawch(WINDOW *, chtype); int winsrawch(WINDOW *, chtype); char wordchar(void); #ifdef PDC_WIDE wchar_t *slk_wlabel(int); #endif void PDC_debug(const char *, ...); int PDC_ungetch(int); int PDC_set_blink(bool); int PDC_set_line_color(short); void PDC_set_title(const char *); int PDC_clearclipboard(void); int PDC_freeclipboard(char *); int PDC_getclipboard(char **, long *); int PDC_setclipboard(const char *, long); unsigned long PDC_get_input_fd(void); unsigned long PDC_get_key_modifiers(void); int PDC_return_key_modifiers(bool); int PDC_save_key_modifiers(bool); #ifdef XCURSES WINDOW *Xinitscr(int, char **); void XCursesExit(void); int sb_init(void); int sb_set_horz(int, int, int); int sb_set_vert(int, int, int); int sb_get_horz(int *, int *, int *); int sb_get_vert(int *, int *, int *); int sb_refresh(void); #endif /*** Functions defined as macros ***/ /* getch() and ungetch() conflict with some DOS libraries */ #define getch() wgetch(stdscr) #define ungetch(ch) PDC_ungetch(ch) #define COLOR_PAIR(n) (((chtype)(n) << PDC_COLOR_SHIFT) & A_COLOR) #define PAIR_NUMBER(n) (((n) & A_COLOR) >> PDC_COLOR_SHIFT) /* These will _only_ work as macros */ #define getbegyx(w, y, x) (y = getbegy(w), x = getbegx(w)) #define getmaxyx(w, y, x) (y = getmaxy(w), x = getmaxx(w)) #define getparyx(w, y, x) (y = getpary(w), x = getparx(w)) #define getyx(w, y, x) (y = getcury(w), x = getcurx(w)) #define getsyx(y, x) { if (curscr->_leaveit) (y)=(x)=-1; \ else getyx(curscr,(y),(x)); } #ifdef NCURSES_MOUSE_VERSION # define getmouse(x) nc_getmouse(x) #endif /* return codes from PDC_getclipboard() and PDC_setclipboard() calls */ #define PDC_CLIP_SUCCESS 0 #define PDC_CLIP_ACCESS_ERROR 1 #define PDC_CLIP_EMPTY 2 #define PDC_CLIP_MEMORY_ERROR 3 /* PDCurses key modifier masks */ #define PDC_KEY_MODIFIER_SHIFT 1 #define PDC_KEY_MODIFIER_CONTROL 2 #define PDC_KEY_MODIFIER_ALT 4 #define PDC_KEY_MODIFIER_NUMLOCK 8 #if defined(__cplusplus) || defined(__cplusplus__) || defined(__CPLUSPLUS) # undef bool } #endif #endif /* __PDCURSES__ */ pysam-0.7.7/samtools/win32/__init__.py0000664000076400007650000000000012162643106017410 0ustar andreasandreaspysam-0.7.7/samtools/misc/0000775000076400007650000000000012241575073015307 5ustar andreasandreaspysam-0.7.7/samtools/misc/md5.h0000660000076400007650000000324512162637166016151 0ustar andreasandreas/* This file is adapted from a program in this page: http://www.fourmilab.ch/md5/ The original source code does not work on 64-bit machines due to the wrong typedef "uint32". I also added prototypes. -lh3 */ #ifndef MD5_H #define MD5_H /* The following tests optimise behaviour on little-endian machines, where there is no need to reverse the byte order of 32 bit words in the MD5 computation. By default, HIGHFIRST is defined, which indicates we're running on a big-endian (most significant byte first) machine, on which the byteReverse function in md5.c must be invoked. However, byteReverse is coded in such a way that it is an identity function when run on a little-endian machine, so calling it on such a platform causes no harm apart from wasting time. If the platform is known to be little-endian, we speed things up by undefining HIGHFIRST, which defines byteReverse as a null macro. Doing things in this manner insures we work on new platforms regardless of their byte order. */ #define HIGHFIRST #if __LITTLE_ENDIAN__ != 0 #undef HIGHFIRST #endif #include struct MD5Context { uint32_t buf[4]; uint32_t bits[2]; unsigned char in[64]; }; void MD5Init(struct MD5Context *ctx); void MD5Update(struct MD5Context *ctx, unsigned char *buf, unsigned len); void MD5Final(unsigned char digest[16], struct MD5Context *ctx); /* * This is needed to make RSAREF happy on some MS-DOS compilers. */ typedef struct MD5Context MD5_CTX; /* Define CHECK_HARDWARE_PROPERTIES to have main,c verify byte order and uint32_t settings. */ #define CHECK_HARDWARE_PROPERTIES #endif /* !MD5_H */ pysam-0.7.7/samtools/misc/ace2sam.c.pysam.c0000664000076400007650000002342312162637166020347 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2011 Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "kstring.h" #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define N_TMPSTR 5 #define LINE_LEN 60 // append a CIGAR operation plus length #define write_cigar(_c, _n, _m, _v) do { \ if (_n == _m) { \ _m = _m? _m<<1 : 4; \ _c = realloc(_c, _m * sizeof(unsigned)); \ } \ _c[_n++] = (_v); \ } while (0) // a fatal error static void fatal(const char *msg) { fprintf(pysamerr, "E %s\n", msg); exit(1); } // remove pads static void remove_pads(const kstring_t *src, kstring_t *dst) { int i, j; dst->l = 0; kputsn(src->s, src->l, dst); for (i = j = 0; i < dst->l; ++i) if (dst->s[i] != '*') dst->s[j++] = dst->s[i]; dst->s[j] = 0; dst->l = j; } int main(int argc, char *argv[]) { gzFile fp; kstream_t *ks; kstring_t s, t[N_TMPSTR]; int dret, i, k, af_n, af_max, af_i, c, is_padded = 0, write_cns = 0, *p2u = 0; long m_cigar = 0, n_cigar = 0; unsigned *af, *cigar = 0; while ((c = getopt(argc, argv, "pc")) >= 0) { switch (c) { case 'p': is_padded = 1; break; case 'c': write_cns = 1; break; } } if (argc == optind) { fprintf(pysamerr, "\nUsage: ace2sam [-pc] \n\n"); fprintf(pysamerr, "Options: -p output padded SAM\n"); fprintf(pysamerr, " -c write the contig sequence in SAM\n\n"); fprintf(pysamerr, "Notes: 1. Fields must appear in the following order: (CO->[BQ]->(AF)->(RD->QA))\n"); fprintf(pysamerr, " 2. The order of reads in AF and in RD must be identical\n"); fprintf(pysamerr, " 3. Except in BQ, words and numbers must be separated by a single SPACE or TAB\n"); fprintf(pysamerr, " 4. This program writes the headerless SAM to stdout and header to pysamerr\n\n"); return 1; } s.l = s.m = 0; s.s = 0; af_n = af_max = af_i = 0; af = 0; for (i = 0; i < N_TMPSTR; ++i) t[i].l = t[i].m = 0, t[i].s = 0; fp = strcmp(argv[1], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r"); ks = ks_init(fp); while (ks_getuntil(ks, 0, &s, &dret) >= 0) { if (strcmp(s.s, "CO") == 0) { // contig sequence kstring_t *cns; t[0].l = t[1].l = t[2].l = t[3].l = t[4].l = 0; // 0: name; 1: padded ctg; 2: unpadded ctg/padded read; 3: unpadded read; 4: SAM line af_n = af_i = 0; // reset the af array ks_getuntil(ks, 0, &s, &dret); kputs(s.s, &t[0]); // contig name ks_getuntil(ks, '\n', &s, &dret); // read the whole line while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputsn(s.s, s.l, &t[1]); // read the padded consensus sequence remove_pads(&t[1], &t[2]); // construct the unpadded sequence // compute the array for mapping padded positions to unpadded positions p2u = realloc(p2u, t[1].m * sizeof(int)); for (i = k = 0; i < t[1].l; ++i) { p2u[i] = k; if (t[1].s[i] != '*') ++k; } // write out the SAM header and contig sequences fprintf(pysamerr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line cns = &t[is_padded?1:2]; fprintf(pysamerr, "S >%s\n", t[0].s); for (i = 0; i < cns->l; i += LINE_LEN) { fputs("S ", pysamerr); for (k = 0; k < LINE_LEN && i + k < cns->l; ++k) fputc(cns->s[i + k], pysamerr); fputc('\n', pysamerr); } #define __padded2cigar(sp) do { \ int i, l_M = 0, l_D = 0; \ for (i = 0; i < sp.l; ++i) { \ if (sp.s[i] == '*') { \ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \ ++l_D; l_M = 0; \ } else { \ if (l_D) write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \ ++l_M; l_D = 0; \ } \ } \ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \ else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \ } while (0) if (write_cns) { // write the consensus SAM line (dummy read) n_cigar = 0; if (is_padded) __padded2cigar(t[1]); else write_cigar(cigar, n_cigar, m_cigar, t[2].l<<4); kputsn(t[0].s, t[0].l, &t[4]); kputs("\t516\t", &t[4]); kputsn(t[0].s, t[0].l, &t[4]); kputs("\t1\t60\t", &t[4]); for (i = 0; i < n_cigar; ++i) { kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]); } kputs("\t*\t0\t0\t", &t[4]); kputsn(t[2].s, t[2].l, &t[4]); kputs("\t*", &t[4]); } } else if (strcmp(s.s, "BQ") == 0) { // contig quality if (t[0].l == 0) fatal("come to 'BQ' before reading 'CO'"); if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire "BQ" line if (write_cns) t[4].s[--t[4].l] = 0; // remove the trailing "*" for (i = 0; i < t[2].l; ++i) { // read the consensus quality int q; if (ks_getuntil(ks, 0, &s, &dret) < 0) fprintf(pysamerr, "E truncated contig quality\n"); if (s.l) { q = atoi(s.s) + 33; if (q > 126) q = 126; if (write_cns) kputc(q, &t[4]); } else --i; } if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); ks_getuntil(ks, '\n', &s, &dret); // skip the empty line if (write_cns) puts(t[4].s); t[4].l = 0; } else if (strcmp(s.s, "AF") == 0) { // padded read position int reversed, neg, pos; if (t[0].l == 0) fatal("come to 'AF' before reading 'CO'"); if (write_cns) { if (t[4].l) puts(t[4].s); t[4].l = 0; } ks_getuntil(ks, 0, &s, &dret); // read name ks_getuntil(ks, 0, &s, &dret); reversed = s.s[0] == 'C'? 1 : 0; // strand ks_getuntil(ks, 0, &s, &dret); pos = atoi(s.s); neg = pos < 0? 1 : 0; pos = pos < 0? -pos : pos; // position if (af_n == af_max) { // double the af array af_max = af_max? af_max<<1 : 4; af = realloc(af, af_max * sizeof(unsigned)); } af[af_n++] = pos << 2 | neg << 1 | reversed; // keep the placement information } else if (strcmp(s.s, "RD") == 0) { // read sequence if (af_i >= af_n) fatal("more 'RD' records than 'AF'"); t[2].l = t[3].l = t[4].l = 0; ks_getuntil(ks, 0, &t[4], &dret); // QNAME if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire RD line while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputs(s.s, &t[2]); // read the read sequence } else if (strcmp(s.s, "QA") == 0) { // clipping if (af_i >= af_n) fatal("more 'QA' records than 'AF'"); int beg, end, pos, op; ks_getuntil(ks, 0, &s, &dret); ks_getuntil(ks, 0, &s, &dret); // skip quality clipping ks_getuntil(ks, 0, &s, &dret); beg = atoi(s.s) - 1; // align clipping start ks_getuntil(ks, 0, &s, &dret); end = atoi(s.s); // clipping end if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // compute 1-based POS pos = af[af_i]>>2; // retrieve the position information if (af[af_i]>>1&1) pos = -pos; pos += beg; // now pos is the true padded position // generate CIGAR remove_pads(&t[2], &t[3]); // backup the unpadded read sequence n_cigar = 0; if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4); if (is_padded) { __padded2cigar(t[2]); if (beg && n_cigar > 1) cigar[1] -= beg<<4; // fix the left-hand CIGAR if (end < t[2].l && n_cigar) cigar[n_cigar-1] -= (t[2].l - end)<<4; // fix the right-hand CIGAR } else { // generate flattened CIGAR string for (i = beg, k = pos - 1; i < end; ++i, ++k) t[2].s[i] = t[2].s[i] != '*'? (t[1].s[k] != '*'? 0 : 1) : (t[1].s[k] != '*'? 2 : 6); // generate the proper CIGAR for (i = beg + 1, k = 1, op = t[2].s[beg]; i < end; ++i) { if (op != t[2].s[i]) { write_cigar(cigar, n_cigar, m_cigar, k<<4|op); op = t[2].s[i]; k = 1; } else ++k; } write_cigar(cigar, n_cigar, m_cigar, k<<4|op); // remove unnecessary "P" and possibly merge adjacent operations for (i = 2; i < n_cigar; ++i) { if ((cigar[i]&0xf) != 1 && (cigar[i-1]&0xf) == 6 && (cigar[i-2]&0xf) != 1) { cigar[i-1] = 0; if ((cigar[i]&0xf) == (cigar[i-2]&0xf)) // merge operations cigar[i] += cigar[i-2], cigar[i-2] = 0; } } for (i = k = 0; i < n_cigar; ++i) // squeeze out dumb operations if (cigar[i]) cigar[k++] = cigar[i]; n_cigar = k; } if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l - end)<<4|4); // write the SAM line for the read kputc('\t', &t[4]); // QNAME has already been written kputw((af[af_i]&1)? 16 : 0, &t[4]); kputc('\t', &t[4]); // FLAG kputsn(t[0].s, t[0].l, &t[4]); kputc('\t', &t[4]); // RNAME kputw(is_padded? pos : p2u[pos-1]+1, &t[4]); // POS kputs("\t60\t", &t[4]); // MAPQ for (i = 0; i < n_cigar; ++i) { // CIGAR kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]); } kputs("\t*\t0\t0\t", &t[4]); // empty MRNM, MPOS and TLEN kputsn(t[3].s, t[3].l, &t[4]); // unpadded SEQ kputs("\t*", &t[4]); // QUAL puts(t[4].s); // print to stdout ++af_i; } else if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); } ks_destroy(ks); gzclose(fp); free(af); free(s.s); free(cigar); free(p2u); for (i = 0; i < N_TMPSTR; ++i) free(t[i].s); return 0; } pysam-0.7.7/samtools/misc/md5.c.pysam.c0000664000076400007650000002161112162637166017516 0ustar andreasandreas#include "pysam.h" /* * This code implements the MD5 message-digest algorithm. * The algorithm is due to Ron Rivest. This code was * written by Colin Plumb in 1993, no copyright is claimed. * This code is in the public domain; do with it what you wish. * * Equivalent code is available from RSA Data Security, Inc. * This code has been tested against that, and is equivalent, * except that you don't need to include two pages of legalese * with every copy. * * To compute the message digest of a chunk of bytes, declare an * MD5Context structure, pass it to MD5Init, call MD5Update as * needed on buffers full of bytes, and then call MD5Final, which * will fill a supplied 16-byte array with the digest. */ /* Brutally hacked by John Walker back from ANSI C to K&R (no prototypes) to maintain the tradition that Netfone will compile with Sun's original "cc". */ #include #include "md5.h" #ifndef HIGHFIRST #define byteReverse(buf, len) /* Nothing */ #else /* * Note: this code is harmless on little-endian machines. */ void byteReverse(buf, longs) unsigned char *buf; unsigned longs; { uint32_t t; do { t = (uint32_t) ((unsigned) buf[3] << 8 | buf[2]) << 16 | ((unsigned) buf[1] << 8 | buf[0]); *(uint32_t *) buf = t; buf += 4; } while (--longs); } #endif void MD5Transform(uint32_t buf[4], uint32_t in[16]); /* * Start MD5 accumulation. Set bit count to 0 and buffer to mysterious * initialization constants. */ void MD5Init(ctx) struct MD5Context *ctx; { ctx->buf[0] = 0x67452301; ctx->buf[1] = 0xefcdab89; ctx->buf[2] = 0x98badcfe; ctx->buf[3] = 0x10325476; ctx->bits[0] = 0; ctx->bits[1] = 0; } /* * Update context to reflect the concatenation of another buffer full * of bytes. */ void MD5Update(ctx, buf, len) struct MD5Context *ctx; unsigned char *buf; unsigned len; { uint32_t t; /* Update bitcount */ t = ctx->bits[0]; if ((ctx->bits[0] = t + ((uint32_t) len << 3)) < t) ctx->bits[1]++; /* Carry from low to high */ ctx->bits[1] += len >> 29; t = (t >> 3) & 0x3f; /* Bytes already in shsInfo->data */ /* Handle any leading odd-sized chunks */ if (t) { unsigned char *p = (unsigned char *) ctx->in + t; t = 64 - t; if (len < t) { memcpy(p, buf, len); return; } memcpy(p, buf, t); byteReverse(ctx->in, 16); MD5Transform(ctx->buf, (uint32_t *) ctx->in); buf += t; len -= t; } /* Process data in 64-byte chunks */ while (len >= 64) { memcpy(ctx->in, buf, 64); byteReverse(ctx->in, 16); MD5Transform(ctx->buf, (uint32_t *) ctx->in); buf += 64; len -= 64; } /* Handle any remaining bytes of data. */ memcpy(ctx->in, buf, len); } /* * Final wrapup - pad to 64-byte boundary with the bit pattern * 1 0* (64-bit count of bits processed, MSB-first) */ void MD5Final(digest, ctx) unsigned char digest[16]; struct MD5Context *ctx; { unsigned count; unsigned char *p; /* Compute number of bytes mod 64 */ count = (ctx->bits[0] >> 3) & 0x3F; /* Set the first char of padding to 0x80. This is safe since there is always at least one byte free */ p = ctx->in + count; *p++ = 0x80; /* Bytes of padding needed to make 64 bytes */ count = 64 - 1 - count; /* Pad out to 56 mod 64 */ if (count < 8) { /* Two lots of padding: Pad the first block to 64 bytes */ memset(p, 0, count); byteReverse(ctx->in, 16); MD5Transform(ctx->buf, (uint32_t *) ctx->in); /* Now fill the next block with 56 bytes */ memset(ctx->in, 0, 56); } else { /* Pad block to 56 bytes */ memset(p, 0, count - 8); } byteReverse(ctx->in, 14); /* Append length in bits and transform */ ((uint32_t *) ctx->in)[14] = ctx->bits[0]; ((uint32_t *) ctx->in)[15] = ctx->bits[1]; MD5Transform(ctx->buf, (uint32_t *) ctx->in); byteReverse((unsigned char *) ctx->buf, 4); memcpy(digest, ctx->buf, 16); memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ } /* The four core functions - F1 is optimized somewhat */ /* #define F1(x, y, z) (x & y | ~x & z) */ #define F1(x, y, z) (z ^ (x & (y ^ z))) #define F2(x, y, z) F1(z, x, y) #define F3(x, y, z) (x ^ y ^ z) #define F4(x, y, z) (y ^ (x | ~z)) /* This is the central step in the MD5 algorithm. */ #define MD5STEP(f, w, x, y, z, data, s) \ ( w += f(x, y, z) + data, w = w<>(32-s), w += x ) /* * The core of the MD5 algorithm, this alters an existing MD5 hash to * reflect the addition of 16 longwords of new data. MD5Update blocks * the data and converts bytes into longwords for this routine. */ void MD5Transform(buf, in) uint32_t buf[4]; uint32_t in[16]; { register uint32_t a, b, c, d; a = buf[0]; b = buf[1]; c = buf[2]; d = buf[3]; MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478, 7); MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756, 12); MD5STEP(F1, c, d, a, b, in[2] + 0x242070db, 17); MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceee, 22); MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0faf, 7); MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62a, 12); MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613, 17); MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501, 22); MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8, 7); MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7af, 12); MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1, 17); MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7be, 22); MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122, 7); MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193, 12); MD5STEP(F1, c, d, a, b, in[14] + 0xa679438e, 17); MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821, 22); MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562, 5); MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340, 9); MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51, 14); MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aa, 20); MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105d, 5); MD5STEP(F2, d, a, b, c, in[10] + 0x02441453, 9); MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681, 14); MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8, 20); MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6, 5); MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6, 9); MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87, 14); MD5STEP(F2, b, c, d, a, in[8] + 0x455a14ed, 20); MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905, 5); MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8, 9); MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9, 14); MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8a, 20); MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942, 4); MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681, 11); MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122, 16); MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380c, 23); MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44, 4); MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9, 11); MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60, 16); MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70, 23); MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6, 4); MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127fa, 11); MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085, 16); MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05, 23); MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039, 4); MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5, 11); MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8, 16); MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665, 23); MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244, 6); MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97, 10); MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7, 15); MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039, 21); MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3, 6); MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92, 10); MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47d, 15); MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1, 21); MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4f, 6); MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0, 10); MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314, 15); MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1, 21); MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82, 6); MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235, 10); MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bb, 15); MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391, 21); buf[0] += a; buf[1] += b; buf[2] += c; buf[3] += d; } /* lh3: the following code is added by me */ #ifdef MD5SUM_MAIN #include #include #include #define HEX_STR "0123456789abcdef" static void md5_one(const char *fn) { unsigned char buf[4096], digest[16]; MD5_CTX md5; int l; FILE *fp; fp = strcmp(fn, "-")? fopen(fn, "r") : stdin; if (fp == 0) { fprintf(pysamerr, "md5sum: %s: No such file or directory\n", fn); exit(1); } MD5Init(&md5); while ((l = fread(buf, 1, 4096, fp)) > 0) MD5Update(&md5, buf, l); MD5Final(digest, &md5); if (fp != stdin) fclose(fp); for (l = 0; l < 16; ++l) printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]); printf(" %s\n", fn); } int main(int argc, char *argv[]) { int i; if (argc == 1) md5_one("-"); else for (i = 1; i < argc; ++i) md5_one(argv[i]); return 0; } #endif pysam-0.7.7/samtools/bam_color.c.pysam.c0000664000076400007650000000643112162637166020036 0ustar andreasandreas#include "pysam.h" #include #include "bam.h" /*! @abstract Get the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color @discussion Returns 0 no color information is found. */ char bam_aux_getCSi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam1_strand(b)) { i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam1_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= cigar >> BAM_CIGAR_SHIFT; } } else { i++; } return cs[i]; } /*! @abstract Get the color quality of the color encoding the previous and current base @param b pointer to an alignment @param i The i-th position, 0-based @return color quality @discussion Returns 0 no color information is found. */ char bam_aux_getCQi(bam1_t *b, int i) { uint8_t *c = bam_aux_get(b, "CQ"); char *cq = NULL; // return the base if the tag was not found if(0 == c) return 0; cq = bam_aux2Z(c); // adjust for strandedness if(bam1_strand(b)) { i = strlen(cq) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam1_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { i -= (cigar >> BAM_CIGAR_SHIFT); } } return cq[i]; } char bam_aux_nt2int(char a) { switch(toupper(a)) { case 'A': return 0; break; case 'C': return 1; break; case 'G': return 2; break; case 'T': return 3; break; default: return 4; break; } } char bam_aux_ntnt2cs(char a, char b) { a = bam_aux_nt2int(a); b = bam_aux_nt2int(b); if(4 == a || 4 == b) return '4'; return "0123"[(int)(a ^ b)]; } /*! @abstract Get the color error profile at the give position @param b pointer to an alignment @return the original color if the color was an error, '-' (dash) otherwise @discussion Returns 0 no color information is found. */ char bam_aux_getCEi(bam1_t *b, int i) { int cs_i; uint8_t *c = bam_aux_get(b, "CS"); char *cs = NULL; char prev_b, cur_b; char cur_color, cor_color; // return the base if the tag was not found if(0 == c) return 0; cs = bam_aux2Z(c); // adjust for strandedness and leading adaptor if(bam1_strand(b)) { //reverse strand cs_i = strlen(cs) - 1 - i; // adjust for leading hard clip uint32_t cigar = bam1_cigar(b)[0]; if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) { cs_i -= cigar >> BAM_CIGAR_SHIFT; } // get current color cur_color = cs[cs_i]; // get previous base. Note: must rc adaptor prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)]; // get current base cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; } else { cs_i=i+1; // get current color cur_color = cs[cs_i]; // get previous base prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)]; // get current base cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; } // corrected color cor_color = bam_aux_ntnt2cs(prev_b, cur_b); if(cur_color == cor_color) { return '-'; } else { return cur_color; } } pysam-0.7.7/samtools/bam_pileup.c.pysam.c0000664000076400007650000003127012162637166020215 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include "sam.h" typedef struct { int k, x, y, end; } cstate_t; static cstate_t g_cstate_null = { -1, 0, 0, 0 }; typedef struct __linkbuf_t { bam1_t b; uint32_t beg, end; cstate_t s; struct __linkbuf_t *next; } lbnode_t; /* --- BEGIN: Memory pool */ typedef struct { int cnt, n, max; lbnode_t **buf; } mempool_t; static mempool_t *mp_init() { mempool_t *mp; mp = (mempool_t*)calloc(1, sizeof(mempool_t)); return mp; } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) { free(mp->buf[k]->b.data); free(mp->buf[k]); } free(mp->buf); free(mp); } static inline lbnode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, lbnode_t *p) { --mp->cnt; p->next = 0; // clear lbnode_t::next here if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max); } mp->buf[mp->n++] = p; } /* --- END: Memory pool */ /* --- BEGIN: Auxiliary functions */ /* s->k: the index of the CIGAR operator that has just been processed. s->x: the reference coordinate of the start of s->k s->y: the query coordiante of the start of s->k */ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s) { #define _cop(c) ((c)&BAM_CIGAR_MASK) #define _cln(c) ((c)>>BAM_CIGAR_SHIFT) bam1_t *b = p->b; bam1_core_t *c = &b->core; uint32_t *cigar = bam1_cigar(b); int k, is_head = 0; // determine the current CIGAR operation // fprintf(pysamerr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y); if (s->k == -1) { // never processed is_head = 1; if (c->n_cigar == 1) { // just one operation, save a loop if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0; } else { // find the first match or deletion for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { int op = _cop(cigar[k]); int l = _cln(cigar[k]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break; else if (op == BAM_CREF_SKIP) s->x += l; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; } assert(k < c->n_cigar); s->k = k; } } else { // the read has been processed before int op, l = _cln(cigar[s->k]); if (pos - s->x >= l) { // jump to the next operation assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case op = _cop(cigar[s->k+1]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; s->x += l; ++s->k; } else { // find the next M/D/N/=/X if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l; s->x += l; for (k = s->k + 1; k < c->n_cigar; ++k) { op = _cop(cigar[k]), l = _cln(cigar[k]); if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l; } s->k = k; } assert(s->k < c->n_cigar); // otherwise a bug } // else, do nothing } { // collect pileup information int op, l; op = _cop(cigar[s->k]); l = _cln(cigar[s->k]); p->is_del = p->indel = p->is_refskip = 0; if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation int op2 = _cop(cigar[s->k+1]); int l2 = _cln(cigar[s->k+1]); if (op2 == BAM_CDEL) p->indel = -(int)l2; else if (op2 == BAM_CINS) p->indel = l2; else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding int l3 = 0; for (k = s->k + 2; k < c->n_cigar; ++k) { op2 = _cop(cigar[k]); l2 = _cln(cigar[k]); if (op2 == BAM_CINS) l3 += l2; else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break; } if (l3 > 0) p->indel = l3; } } if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { p->qpos = s->y + (pos - s->x); } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!! p->is_refskip = (op == BAM_CREF_SKIP); } // cannot be other operations; otherwise a bug p->is_head = (pos == c->pos); p->is_tail = (pos == s->end); } return 1; } /* --- END: Auxiliary functions */ /******************* * pileup iterator * *******************/ struct __bam_plp_t { mempool_t *mp; lbnode_t *head, *tail, *dummy; int32_t tid, pos, max_tid, max_pos; int is_eof, flag_mask, max_plp, error, maxcnt; bam_pileup1_t *plp; // for the "auto" interface only bam1_t *b; bam_plp_auto_f func; void *data; }; bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data) { bam_plp_t iter; iter = calloc(1, sizeof(struct __bam_plp_t)); iter->mp = mp_init(); iter->head = iter->tail = mp_alloc(iter->mp); iter->dummy = mp_alloc(iter->mp); iter->max_tid = iter->max_pos = -1; iter->flag_mask = BAM_DEF_MASK; iter->maxcnt = 8000; if (func) { iter->func = func; iter->data = data; iter->b = bam_init1(); } return iter; } void bam_plp_destroy(bam_plp_t iter) { mp_free(iter->mp, iter->dummy); mp_free(iter->mp, iter->head); if (iter->mp->cnt != 0) fprintf(pysamerr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt); mp_destroy(iter->mp); if (iter->b) bam_destroy1(iter->b); free(iter->plp); free(iter); } const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) { if (iter->error) { *_n_plp = -1; return 0; } *_n_plp = 0; if (iter->is_eof && iter->head->next == 0) return 0; while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) { int n_plp = 0; lbnode_t *p, *q; // write iter->plp at iter->pos iter->dummy->next = iter->head; for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) { if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove q->next = p->next; mp_free(iter->mp, p); p = q; } else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup if (n_plp == iter->max_plp) { // then double the capacity iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256; iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp); } iter->plp[n_plp].b = &p->b; if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true... } } iter->head = iter->dummy->next; // dummy->next may be changed *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos; // update iter->tid and iter->pos if (iter->head->next) { if (iter->tid > iter->head->b.core.tid) { fprintf(pysamerr, "[%s] unsorted input. Pileup aborts.\n", __func__); iter->error = 1; *_n_plp = -1; return 0; } } if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid iter->pos = iter->head->beg; // jump to the next position } else ++iter->pos; // scan contiguously // return if (n_plp) return iter->plp; if (iter->is_eof && iter->head->next == 0) break; } return 0; } int bam_plp_push(bam_plp_t iter, const bam1_t *b) { if (iter->error) return -1; if (b) { if (b->core.tid < 0) return 0; if (b->core.flag & iter->flag_mask) return 0; if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0; bam_copy1(&iter->tail->b, b); iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b)); iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t if (b->core.tid < iter->max_tid) { fprintf(pysamerr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n"); iter->error = 1; return -1; } if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) { fprintf(pysamerr, "[bam_pileup_core] the input is not sorted (reads out of order)\n"); iter->error = 1; return -1; } iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg; if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) { iter->tail->next = mp_alloc(iter->mp); iter->tail = iter->tail->next; } } else iter->is_eof = 1; return 0; } const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp) { const bam_pileup1_t *plp; if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; } if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; else { // no pileup line can be obtained; read alignments *_n_plp = 0; if (iter->is_eof) return 0; while (iter->func(iter->data, iter->b) >= 0) { if (bam_plp_push(iter, iter->b) < 0) { *_n_plp = -1; return 0; } if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; // otherwise no pileup line can be returned; read the next alignment. } bam_plp_push(iter, 0); if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp; return 0; } } void bam_plp_reset(bam_plp_t iter) { lbnode_t *p, *q; iter->max_tid = iter->max_pos = -1; iter->tid = iter->pos = 0; iter->is_eof = 0; for (p = iter->head; p->next;) { q = p->next; mp_free(iter->mp, p); p = q; } iter->head = iter->tail; } void bam_plp_set_mask(bam_plp_t iter, int mask) { iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask); } void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt) { iter->maxcnt = maxcnt; } /***************** * callback APIs * *****************/ int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data) { bam_plbuf_t *buf; int ret; bam1_t *b; b = bam_init1(); buf = bam_plbuf_init(func, func_data); bam_plbuf_set_mask(buf, mask); while ((ret = bam_read1(fp, b)) >= 0) bam_plbuf_push(b, buf); bam_plbuf_push(0, buf); bam_plbuf_destroy(buf); bam_destroy1(b); return 0; } void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask) { bam_plp_set_mask(buf->iter, mask); } void bam_plbuf_reset(bam_plbuf_t *buf) { bam_plp_reset(buf->iter); } bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data) { bam_plbuf_t *buf; buf = calloc(1, sizeof(bam_plbuf_t)); buf->iter = bam_plp_init(0, 0); buf->func = func; buf->data = data; return buf; } void bam_plbuf_destroy(bam_plbuf_t *buf) { bam_plp_destroy(buf->iter); free(buf); } int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf) { int ret, n_plp, tid, pos; const bam_pileup1_t *plp; ret = bam_plp_push(buf->iter, b); if (ret < 0) return ret; while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0) buf->func(tid, pos, n_plp, plp, buf->data); return 0; } /*********** * mpileup * ***********/ struct __bam_mplp_t { int n; uint64_t min, *pos; bam_plp_t *iter; int *n_plp; const bam_pileup1_t **plp; }; bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data) { int i; bam_mplp_t iter; iter = calloc(1, sizeof(struct __bam_mplp_t)); iter->pos = calloc(n, 8); iter->n_plp = calloc(n, sizeof(int)); iter->plp = calloc(n, sizeof(void*)); iter->iter = calloc(n, sizeof(void*)); iter->n = n; iter->min = (uint64_t)-1; for (i = 0; i < n; ++i) { iter->iter[i] = bam_plp_init(func, data[i]); iter->pos[i] = iter->min; } return iter; } void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt) { int i; for (i = 0; i < iter->n; ++i) iter->iter[i]->maxcnt = maxcnt; } void bam_mplp_destroy(bam_mplp_t iter) { int i; for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]); free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp); free(iter); } int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp) { int i, ret = 0; uint64_t new_min = (uint64_t)-1; for (i = 0; i < iter->n; ++i) { if (iter->pos[i] == iter->min) { int tid, pos; iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]); iter->pos[i] = (uint64_t)tid<<32 | pos; } if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i]; } iter->min = new_min; if (new_min == (uint64_t)-1) return 0; *_tid = new_min>>32; *_pos = (uint32_t)new_min; for (i = 0; i < iter->n; ++i) { if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line" n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i]; ++ret; } else n_plp[i] = 0, plp[i] = 0; } return ret; } pysam-0.7.7/samtools/kaln.c.pysam.c0000664000076400007650000003562212162637166017032 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2003-2006, 2008, 2009, by Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "kaln.h" #define FROM_M 0 #define FROM_I 1 #define FROM_D 2 typedef struct { int i, j; unsigned char ctype; } path_t; int aln_sm_blosum62[] = { /* A R N D C Q E G H I L K M F P S T W Y V * X */ 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0, -1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1, -2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1, -2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1, 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2, -1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1, -1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1, 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1, -2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1, -1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1, -1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1, -1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1, -1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1, -2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1, -1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2, 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0, 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0, -3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2, -2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1, 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1, -4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4, 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1 }; int aln_sm_blast[] = { 1, -3, -3, -3, -2, -3, 1, -3, -3, -2, -3, -3, 1, -3, -2, -3, -3, -3, 1, -2, -2, -2, -2, -2, -2 }; int aln_sm_qual[] = { 0, -23, -23, -23, 0, -23, 0, -23, -23, 0, -23, -23, 0, -23, 0, -23, -23, -23, 0, 0, 0, 0, 0, 0, 0 }; ka_param_t ka_param_blast = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; ka_param_t ka_param_aa2aa = { 10, 2, 10, 2, aln_sm_blosum62, 22, 50 }; ka_param2_t ka_param2_qual = { 37, 11, 37, 11, 37, 11, 0, 0, aln_sm_qual, 5, 50 }; static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar) { int i, n; uint32_t *cigar; unsigned char last_type; if (path_len == 0 || path == 0) { *n_cigar = 0; return 0; } last_type = path->ctype; for (i = n = 1; i < path_len; ++i) { if (last_type != path[i].ctype) ++n; last_type = path[i].ctype; } *n_cigar = n; cigar = (uint32_t*)calloc(*n_cigar, 4); cigar[0] = 1u << 4 | path[path_len-1].ctype; last_type = path[path_len-1].ctype; for (i = path_len - 2, n = 0; i >= 0; --i) { if (path[i].ctype == last_type) cigar[n] += 1u << 4; else { cigar[++n] = 1u << 4 | path[i].ctype; last_type = path[i].ctype; } } return cigar; } /***************************/ /* START OF common_align.c */ /***************************/ #define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF; #define set_M(MM, cur, p, sc) \ { \ if ((p)->M >= (p)->I) { \ if ((p)->M >= (p)->D) { \ (MM) = (p)->M + (sc); (cur)->Mt = FROM_M; \ } else { \ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \ } \ } else { \ if ((p)->I > (p)->D) { \ (MM) = (p)->I + (sc); (cur)->Mt = FROM_I; \ } else { \ (MM) = (p)->D + (sc); (cur)->Mt = FROM_D; \ } \ } \ } #define set_I(II, cur, p) \ { \ if ((p)->M - gap_open > (p)->I) { \ (cur)->It = FROM_M; \ (II) = (p)->M - gap_open - gap_ext; \ } else { \ (cur)->It = FROM_I; \ (II) = (p)->I - gap_ext; \ } \ } #define set_end_I(II, cur, p) \ { \ if (gap_end_ext >= 0) { \ if ((p)->M - gap_end_open > (p)->I) { \ (cur)->It = FROM_M; \ (II) = (p)->M - gap_end_open - gap_end_ext; \ } else { \ (cur)->It = FROM_I; \ (II) = (p)->I - gap_end_ext; \ } \ } else set_I(II, cur, p); \ } #define set_D(DD, cur, p) \ { \ if ((p)->M - gap_open > (p)->D) { \ (cur)->Dt = FROM_M; \ (DD) = (p)->M - gap_open - gap_ext; \ } else { \ (cur)->Dt = FROM_D; \ (DD) = (p)->D - gap_ext; \ } \ } #define set_end_D(DD, cur, p) \ { \ if (gap_end_ext >= 0) { \ if ((p)->M - gap_end_open > (p)->D) { \ (cur)->Dt = FROM_M; \ (DD) = (p)->M - gap_end_open - gap_end_ext; \ } else { \ (cur)->Dt = FROM_D; \ (DD) = (p)->D - gap_end_ext; \ } \ } else set_D(DD, cur, p); \ } typedef struct { uint8_t Mt:3, It:2, Dt:3; } dpcell_t; typedef struct { int M, I, D; } dpscore_t; /*************************** * banded global alignment * ***************************/ uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar) { int i, j; dpcell_t **dpcell, *q; dpscore_t *curr, *last, *s; int b1, b2, tmp_end; int *mat, end, max = 0; uint8_t type, ctype; uint32_t *cigar = 0; int gap_open, gap_ext, gap_end_open, gap_end_ext, b; int *score_matrix, N_MATRIX_ROW; /* initialize some align-related parameters. just for compatibility */ gap_open = ap->gap_open; gap_ext = ap->gap_ext; gap_end_open = ap->gap_end_open; gap_end_ext = ap->gap_end_ext; b = ap->band_width; score_matrix = ap->matrix; N_MATRIX_ROW = ap->row; if (n_cigar) *n_cigar = 0; if (len1 == 0 || len2 == 0) return 0; /* calculate b1 and b2 */ if (len1 > len2) { b1 = len1 - len2 + b; b2 = b; } else { b1 = b; b2 = len2 - len1 + b; } if (b1 > len1) b1 = len1; if (b2 > len2) b2 = len2; --seq1; --seq2; /* allocate memory */ end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1); dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1)); for (j = 0; j <= len2; ++j) dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end); for (j = b2 + 1; j <= len2; ++j) dpcell[j] -= j - b2; curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1)); last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1)); /* set first row */ SET_INF(*curr); curr->M = 0; for (i = 1, s = curr + 1; i < b1; ++i, ++s) { SET_INF(*s); set_end_D(s->D, dpcell[0] + i, s - 1); } s = curr; curr = last; last = s; /* core dynamic programming, part 1 */ tmp_end = (b2 < len2)? b2 : len2 - 1; for (j = 1; j <= tmp_end; ++j) { q = dpcell[j]; s = curr; SET_INF(*s); set_end_I(s->I, q, last); end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1; mat = score_matrix + seq2[j] * N_MATRIX_ROW; ++s; ++q; for (i = 1; i != end; ++i, ++s, ++q) { set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */ set_I(s->I, q, last + i); set_D(s->D, q, s - 1); } set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_D(s->D, q, s - 1); if (j + b1 - 1 > len1) { /* bug fixed, 040227 */ set_end_I(s->I, q, last + i); } else s->I = MINOR_INF; s = curr; curr = last; last = s; } /* last row for part 1, use set_end_D() instead of set_D() */ if (j == len2 && b2 != len2 - 1) { q = dpcell[j]; s = curr; SET_INF(*s); set_end_I(s->I, q, last); end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1; mat = score_matrix + seq2[j] * N_MATRIX_ROW; ++s; ++q; for (i = 1; i != end; ++i, ++s, ++q) { set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */ set_I(s->I, q, last + i); set_end_D(s->D, q, s - 1); } set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_end_D(s->D, q, s - 1); if (j + b1 - 1 > len1) { /* bug fixed, 040227 */ set_end_I(s->I, q, last + i); } else s->I = MINOR_INF; s = curr; curr = last; last = s; ++j; } /* core dynamic programming, part 2 */ for (; j <= len2 - b2 + 1; ++j) { SET_INF(curr[j - b2]); mat = score_matrix + seq2[j] * N_MATRIX_ROW; end = j + b1 - 1; for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) { set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_I(s->I, q, last + i); set_D(s->D, q, s - 1); } set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_D(s->D, q, s - 1); s->I = MINOR_INF; s = curr; curr = last; last = s; } /* core dynamic programming, part 3 */ for (; j < len2; ++j) { SET_INF(curr[j - b2]); mat = score_matrix + seq2[j] * N_MATRIX_ROW; for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) { set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_I(s->I, q, last + i); set_D(s->D, q, s - 1); } set_M(s->M, q, last + len1 - 1, mat[seq1[i]]); set_end_I(s->I, q, last + i); set_D(s->D, q, s - 1); s = curr; curr = last; last = s; } /* last row */ if (j == len2) { SET_INF(curr[j - b2]); mat = score_matrix + seq2[j] * N_MATRIX_ROW; for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) { set_M(s->M, q, last + i - 1, mat[seq1[i]]); set_I(s->I, q, last + i); set_end_D(s->D, q, s - 1); } set_M(s->M, q, last + len1 - 1, mat[seq1[i]]); set_end_I(s->I, q, last + i); set_end_D(s->D, q, s - 1); s = curr; curr = last; last = s; } *_score = last[len1].M; if (n_cigar) { /* backtrace */ path_t *p, *path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 2)); i = len1; j = len2; q = dpcell[j] + i; s = last + len1; max = s->M; type = q->Mt; ctype = FROM_M; if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; } if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; } p = path; p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */ ++p; do { switch (ctype) { case FROM_M: --i; --j; break; case FROM_I: --j; break; case FROM_D: --i; break; } q = dpcell[j] + i; ctype = type; switch (type) { case FROM_M: type = q->Mt; break; case FROM_I: type = q->It; break; case FROM_D: type = q->Dt; break; } p->ctype = ctype; p->i = i; p->j = j; ++p; } while (i || j); cigar = ka_path2cigar32(path, p - path - 1, n_cigar); free(path); } /* free memory */ for (j = b2 + 1; j <= len2; ++j) dpcell[j] += j - b2; for (j = 0; j <= len2; ++j) free(dpcell[j]); free(dpcell); free(curr); free(last); return cigar; } typedef struct { int M, I, D; } score_aux_t; #define MINUS_INF -0x40000000 // matrix: len2 rows and len1 columns int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap) { #define __score_aux(_p, _q0, _sc, _io, _ie, _do, _de) { \ int t1, t2; \ score_aux_t *_q; \ _q = _q0; \ _p->M = _q->M >= _q->I? _q->M : _q->I; \ _p->M = _p->M >= _q->D? _p->M : _q->D; \ _p->M += (_sc); \ ++_q; t1 = _q->M - _io - _ie; t2 = _q->I - _ie; _p->I = t1 >= t2? t1 : t2; \ _q = _p-1; t1 = _q->M - _do - _de; t2 = _q->D - _de; _p->D = t1 >= t2? t1 : t2; \ } int i, j, bw, scmat_size = ap->row, *scmat = ap->matrix, ret; const uint8_t *seq1, *seq2; score_aux_t *curr, *last, *swap; bw = abs(len1 - len2) + ap->band_width; i = len1 > len2? len1 : len2; if (bw > i + 1) bw = i + 1; seq1 = _seq1 - 1; seq2 = _seq2 - 1; curr = calloc(len1 + 2, sizeof(score_aux_t)); last = calloc(len1 + 2, sizeof(score_aux_t)); { // the zero-th row int x, end = len1; score_aux_t *p; j = 0; x = j + bw; end = len1 < x? len1 : x; // band end p = curr; p->M = 0; p->I = p->D = MINUS_INF; for (i = 1, p = &curr[1]; i <= end; ++i, ++p) p->M = p->I = MINUS_INF, p->D = -(ap->edo + ap->ede * i); p->M = p->I = p->D = MINUS_INF; swap = curr; curr = last; last = swap; } for (j = 1; j < len2; ++j) { int x, beg = 0, end = len1, *scrow, col_end; score_aux_t *p; x = j - bw; beg = 0 > x? 0 : x; // band start x = j + bw; end = len1 < x? len1 : x; // band end if (beg == 0) { // from zero-th column p = curr; p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j); ++beg; // then beg = 1 } scrow = scmat + seq2[j] * scmat_size; if (end == len1) col_end = 1, --end; else col_end = 0; for (i = beg, p = &curr[beg]; i <= end; ++i, ++p) __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->ido, ap->ide); if (col_end) { __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->ido, ap->ide); ++p; } p->M = p->I = p->D = MINUS_INF; // for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n'); swap = curr; curr = last; last = swap; } { // the last row int x, beg = 0, *scrow; score_aux_t *p; j = len2; x = j - bw; beg = 0 > x? 0 : x; // band start if (beg == 0) { // from zero-th column p = curr; p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j); ++beg; // then beg = 1 } scrow = scmat + seq2[j] * scmat_size; for (i = beg, p = &curr[beg]; i < len1; ++i, ++p) __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->edo, ap->ede); __score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->edo, ap->ede); // for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n'); } ret = curr[len1].M >= curr[len1].I? curr[len1].M : curr[len1].I; ret = ret >= curr[len1].D? ret : curr[len1].D; free(curr); free(last); return ret; } #ifdef _MAIN int main(int argc, char *argv[]) { // int len1 = 35, len2 = 35; // uint8_t *seq1 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\0\1"; // uint8_t *seq2 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\1\0"; int len1 = 4, len2 = 4; uint8_t *seq1 = (uint8_t*)"\1\0\0\1"; uint8_t *seq2 = (uint8_t*)"\1\0\1\0"; int sc; // ka_global_core(seq1, 2, seq2, 1, &ka_param_qual, &sc, 0); sc = ka_global_score(seq1, len1, seq2, len2, &ka_param2_qual); printf("%d\n", sc); return 0; } #endif pysam-0.7.7/samtools/bamshuf.c.pysam.c0000664000076400007650000000734212163150647017523 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "sam.h" #include "ksort.h" #define DEF_CLEVEL 1 static inline unsigned hash_Wang(unsigned key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } static inline unsigned hash_X31_Wang(const char *s) { unsigned h = *s; if (h) { for (++s ; *s; ++s) h = (h << 5) - h + *s; return hash_Wang(h); } else return 0; } typedef struct { unsigned key; bam1_t *b; } elem_t; static inline int elem_lt(elem_t x, elem_t y) { if (x.key < y.key) return 1; if (x.key == y.key) { int t; t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b)); if (t < 0) return 1; return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3))); } else return 0; } KSORT_INIT(bamshuf, elem_t, elem_lt) static void bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout) { BGZF *fp, *fpw, **fpt; char **fnt, modew[8]; bam1_t *b; int i, l; bam_hdr_t *h; int64_t *cnt; // split fp = strcmp(fn, "-")? bgzf_open(fn, "r") : bgzf_dopen(fileno(stdin), "r"); assert(fp); h = bam_hdr_read(fp); fnt = (char**)calloc(n_files, sizeof(void*)); fpt = (BGZF**)calloc(n_files, sizeof(void*)); cnt = (int64_t*)calloc(n_files, 8); l = strlen(pre); for (i = 0; i < n_files; ++i) { fnt[i] = (char*)calloc(l + 10, 1); sprintf(fnt[i], "%s.%.4d.bam", pre, i); fpt[i] = bgzf_open(fnt[i], "w1"); bam_hdr_write(fpt[i], h); } b = bam_init1(); while (bam_read1(fp, b) >= 0) { uint32_t x; x = hash_X31_Wang(bam_get_qname(b)) % n_files; bam_write1(fpt[x], b); ++cnt[x]; } bam_destroy1(b); for (i = 0; i < n_files; ++i) bgzf_close(fpt[i]); free(fpt); bgzf_close(fp); // merge sprintf(modew, "w%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL); if (!is_stdout) { // output to a file char *fnw = (char*)calloc(l + 5, 1); sprintf(fnw, "%s.bam", pre); fpw = bgzf_open(fnw, modew); free(fnw); } else fpw = bgzf_dopen(fileno(stdout), modew); // output to stdout bam_hdr_write(fpw, h); bam_hdr_destroy(h); for (i = 0; i < n_files; ++i) { int64_t j, c = cnt[i]; elem_t *a; fp = bgzf_open(fnt[i], "r"); bam_hdr_destroy(bam_hdr_read(fp)); a = (elem_t*)calloc(c, sizeof(elem_t)); for (j = 0; j < c; ++j) { a[j].b = bam_init1(); // added by pysam to prevent seg-fault // was: assert( bam_read1(fp, a[j].b ); // Assume that assertion was optimized out // and a[j].b not set. int _l = bam_read1(fp, a[j].b); assert( _l >= 0 ); a[j].key = hash_X31_Wang(bam_get_qname(a[j].b)); } bgzf_close(fp); unlink(fnt[i]); free(fnt[i]); ks_introsort(bamshuf, c, a); for (j = 0; j < c; ++j) { bam_write1(fpw, a[j].b); bam_destroy1(a[j].b); } free(a); } bgzf_close(fpw); free(fnt); free(cnt); } int main_bamshuf(int argc, char *argv[]) { int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0; while ((c = getopt(argc, argv, "n:l:uO")) >= 0) { switch (c) { case 'n': n_files = atoi(optarg); break; case 'l': clevel = atoi(optarg); break; case 'u': is_un = 1; break; case 'O': is_stdout = 1; break; } } if (is_un) clevel = 0; if (optind + 2 > argc) { fprintf(pysamerr, "\nUsage: bamshuf [-Ou] [-n nFiles] [-c cLevel] \n\n"); fprintf(pysamerr, "Options: -O output to stdout\n"); fprintf(pysamerr, " -u uncompressed BAM output\n"); fprintf(pysamerr, " -l INT compression level [%d]\n", DEF_CLEVEL); fprintf(pysamerr, " -n INT number of temporary files [%d]\n", n_files); fprintf(pysamerr, "\n"); return 1; } bamshuf(argv[optind], n_files, argv[optind+1], clevel, is_stdout); return 0; } pysam-0.7.7/samtools/kprobaln.c.pysam.c0000664000076400007650000002472112162637166017713 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2003-2006, 2008-2010, by Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include "kprobaln.h" /***************************************** * Probabilistic banded glocal alignment * *****************************************/ #define EI .25 #define EM .33333333333 static float g_qual2prob[256]; #define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; } kpa_par_t kpa_par_def = { 0.001, 0.1, 10 }; kpa_par_t kpa_par_alt = { 0.0001, 0.01, 10 }; /* The topology of the profile HMM: /\ /\ /\ /\ I[1] I[k-1] I[k] I[L] ^ \ \ ^ \ ^ \ \ ^ | \ \ | \ | \ \ | M[0] M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1] \ \/ \/ \/ / \ /\ /\ /\ / -> D[k-1] -> D[k] -> M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1]. On input, _ref is the reference sequence and _query is the query sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an ambiguous residue. iqual is the base quality. c sets the gap open probability, gap extension probability and band width. On output, state and q are arrays of length l_query. The higher 30 bits give the reference position the query base is matched to and the lower two bits can be 0 (an alignment match) or 1 (an insertion). q[i] gives the phred scaled posterior probability of state[i] being wrong. */ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual, const kpa_par_t *c, int *state, uint8_t *q) { double **f, **b = 0, *s, m[9], sI, sM, bI, bM, pb; float *qual, *_qual; const uint8_t *ref, *query; int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; if ( l_ref<=0 || l_query<=0 ) return 0; // FIXME: this may not be an ideal fix, just prevents sefgault /*** initialization ***/ is_backward = state && q? 1 : 0; ref = _ref - 1; query = _query - 1; // change to 1-based coordinate bw = l_ref > l_query? l_ref : l_query; if (bw > c->bw) bw = c->bw; if (bw < abs(l_ref - l_query)) bw = abs(l_ref - l_query); bw2 = bw * 2 + 1; // allocate the forward and backward matrices f[][] and b[][] and the scaling array s[] f = calloc(l_query+1, sizeof(void*)); if (is_backward) b = calloc(l_query+1, sizeof(void*)); for (i = 0; i <= l_query; ++i) { // FIXME: this will lead in segfault for l_query==0 f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double)); } s = calloc(l_query+2, sizeof(double)); // s[] is the scaling factor to avoid underflow // initialize qual _qual = calloc(l_query, sizeof(float)); if (g_qual2prob[0] == 0) for (i = 0; i < 256; ++i) g_qual2prob[i] = pow(10, -i/10.); for (i = 0; i < l_query; ++i) _qual[i] = g_qual2prob[iqual? iqual[i] : 30]; qual = _qual - 1; // initialize transition probability sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof m[0*3+0] = (1 - c->d - c->d) * (1 - sM); m[0*3+1] = m[0*3+2] = c->d * (1 - sM); m[1*3+0] = (1 - c->e) * (1 - sI); m[1*3+1] = c->e * (1 - sI); m[1*3+2] = 0.; m[2*3+0] = 1 - c->e; m[2*3+1] = 0.; m[2*3+2] = c->e; bM = (1 - c->d) / l_ref; bI = c->d / l_ref; // (bM+bI)*l_ref==1 /*** forward ***/ // f[0] set_u(k, bw, 0, 0); f[0][k] = s[0] = 1.; { // f[1] double *fi = f[1], sum; int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end; for (k = beg, sum = 0.; k <= end; ++k) { int u; double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM; set_u(u, bw, 1, k); fi[u+0] = e * bM; fi[u+1] = EI * bI; sum += fi[u] + fi[u+1]; } // rescale s[1] = sum; set_u(_beg, bw, 1, beg); set_u(_end, bw, 1, end); _end += 2; for (k = _beg; k <= _end; ++k) fi[k] /= sum; } // f[2..l_query] for (i = 2; i <= l_query; ++i) { double *fi = f[i], *fi1 = f[i-1], sum, qli = qual[i]; int beg = 1, end = l_ref, x, _beg, _end; uint8_t qyi = query[i]; x = i - bw; beg = beg > x? beg : x; // band start x = i + bw; end = end < x? end : x; // band end for (k = beg, sum = 0.; k <= end; ++k) { int u, v11, v01, v10; double e; e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli * EM; set_u(u, bw, i, k); set_u(v11, bw, i-1, k-1); set_u(v10, bw, i-1, k); set_u(v01, bw, i, k-1); fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]); fi[u+1] = EI * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]); fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2]; sum += fi[u] + fi[u+1] + fi[u+2]; // fprintf(pysamerr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG } // rescale s[i] = sum; set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2; for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum; } { // f[l_query+1] double sum; for (k = 1, sum = 0.; k <= l_ref; ++k) { int u; set_u(u, bw, l_query, k); if (u < 3 || u >= bw2*3+3) continue; sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI; } s[l_query+1] = sum; // the last scaling factor } { // compute likelihood double p = 1., Pr1 = 0.; for (i = 0; i <= l_query + 1; ++i) { p *= s[i]; if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.; } Pr1 += -4.343 * log(p * l_ref * l_query); Pr = (int)(Pr1 + .499); if (!is_backward) { // skip backward and MAP for (i = 0; i <= l_query; ++i) free(f[i]); free(f); free(s); free(_qual); return Pr; } } /*** backward ***/ // b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from) for (k = 1; k <= l_ref; ++k) { int u; double *bi = b[l_query]; set_u(u, bw, l_query, k); if (u < 3 || u >= bw2*3+3) continue; bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1]; } // b[l_query-1..1] for (i = l_query - 1; i >= 1; --i) { int beg = 1, end = l_ref, x, _beg, _end; double *bi = b[i], *bi1 = b[i+1], y = (i > 1), qli1 = qual[i+1]; uint8_t qyi1 = query[i+1]; x = i - bw; beg = beg > x? beg : x; x = i + bw; end = end < x? end : x; for (k = end; k >= beg; --k) { int u, v11, v01, v10; double e; set_u(u, bw, i, k); set_u(v11, bw, i+1, k+1); set_u(v10, bw, i+1, k); set_u(v01, bw, i, k+1); e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 * EM) * bi1[v11]; bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e. bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1]; bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y; // fprintf(pysamerr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG } // rescale set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2; for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y; } { // b[0] int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1; double sum = 0.; for (k = end; k >= beg; --k) { int u; double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM; set_u(u, bw, 1, k); if (u < 3 || u >= bw2*3+3) continue; sum += e * b[1][u+0] * bM + EI * b[1][u+1] * bI; } set_u(k, bw, 0, 0); pb = b[0][k] = sum / s[0]; // if everything works as is expected, pb == 1.0 } is_diff = fabs(pb - 1.) > 1e-7? 1 : 0; /*** MAP ***/ for (i = 1; i <= l_query; ++i) { double sum = 0., *fi = f[i], *bi = b[i], max = 0.; int beg = 1, end = l_ref, x, max_k = -1; x = i - bw; beg = beg > x? beg : x; x = i + bw; end = end < x? end : x; for (k = beg; k <= end; ++k) { int u; double z; set_u(u, bw, i, k); z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z; z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z; } max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0 if (state) state[i-1] = max_k; if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k; #ifdef _MAIN fprintf(pysamerr, "(%.10lg,%.10lg) (%d,%d:%c,%c:%d) %lg\n", pb, sum, i-1, max_k>>2, "ACGT"[query[i]], "ACGT"[ref[(max_k>>2)+1]], max_k&3, max); // DEBUG #endif } /*** free ***/ for (i = 0; i <= l_query; ++i) { free(f[i]); free(b[i]); } free(f); free(b); free(s); free(_qual); return Pr; } #ifdef _MAIN #include int main(int argc, char *argv[]) { uint8_t conv[256], *iqual, *ref, *query; int c, l_ref, l_query, i, q = 30, b = 10, P; while ((c = getopt(argc, argv, "b:q:")) >= 0) { switch (c) { case 'b': b = atoi(optarg); break; case 'q': q = atoi(optarg); break; } } if (optind + 2 > argc) { fprintf(pysamerr, "Usage: %s [-q %d] [-b %d] \n", argv[0], q, b); // example: acttc attc return 1; } memset(conv, 4, 256); conv['a'] = conv['A'] = 0; conv['c'] = conv['C'] = 1; conv['g'] = conv['G'] = 2; conv['t'] = conv['T'] = 3; ref = (uint8_t*)argv[optind]; query = (uint8_t*)argv[optind+1]; l_ref = strlen((char*)ref); l_query = strlen((char*)query); for (i = 0; i < l_ref; ++i) ref[i] = conv[ref[i]]; for (i = 0; i < l_query; ++i) query[i] = conv[query[i]]; iqual = malloc(l_query); memset(iqual, q, l_query); kpa_par_def.bw = b; P = kpa_glocal(ref, l_ref, query, l_query, iqual, &kpa_par_alt, 0, 0); fprintf(pysamerr, "%d\n", P); free(iqual); return 0; } #endif pysam-0.7.7/samtools/faidx.c.pysam.c0000664000076400007650000002534412162637166017200 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "faidx.h" #include "khash.h" typedef struct { int32_t line_len, line_blen; int64_t len; uint64_t offset; } faidx1_t; KHASH_MAP_INIT_STR(s, faidx1_t) #ifndef _NO_RAZF #include "razf.h" #else #ifdef _WIN32 #define ftello(fp) ftell(fp) #define fseeko(fp, offset, whence) fseek(fp, offset, whence) #else extern off_t ftello(FILE *stream); extern int fseeko(FILE *stream, off_t offset, int whence); #endif #define RAZF FILE #define razf_read(fp, buf, size) fread(buf, 1, size, fp) #define razf_open(fn, mode) fopen(fn, mode) #define razf_close(fp) fclose(fp) #define razf_seek(fp, offset, whence) fseeko(fp, offset, whence) #define razf_tell(fp) ftello(fp) #endif #ifdef _USE_KNETFILE #include "knetfile.h" #endif struct __faidx_t { RAZF *rz; int n, m; char **name; khash_t(s) *hash; }; #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset) { khint_t k; int ret; faidx1_t t; if (idx->n == idx->m) { idx->m = idx->m? idx->m<<1 : 16; idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m); } idx->name[idx->n] = strdup(name); k = kh_put(s, idx->hash, idx->name[idx->n], &ret); t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset; kh_value(idx->hash, k) = t; ++idx->n; } faidx_t *fai_build_core(RAZF *rz) { char c, *name; int l_name, m_name, ret; int line_len, line_blen, state; int l1, l2; faidx_t *idx; uint64_t offset; int64_t len; idx = (faidx_t*)calloc(1, sizeof(faidx_t)); idx->hash = kh_init(s); name = 0; l_name = m_name = 0; len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0; while (razf_read(rz, &c, 1)) { if (c == '\n') { // an empty line if (state == 1) { offset = razf_tell(rz); continue; } else if ((state == 0 && len < 0) || state == 2) continue; } if (c == '>') { // fasta header if (len >= 0) fai_insert_index(idx, name, len, line_len, line_blen, offset); l_name = 0; while ((ret = razf_read(rz, &c, 1)) != 0 && !isspace(c)) { if (m_name < l_name + 2) { m_name = l_name + 2; kroundup32(m_name); name = (char*)realloc(name, m_name); } name[l_name++] = c; } name[l_name] = '\0'; if (ret == 0) { fprintf(pysamerr, "[fai_build_core] the last entry has no sequence\n"); free(name); fai_destroy(idx); return 0; } if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n'); state = 1; len = 0; offset = razf_tell(rz); } else { if (state == 3) { fprintf(pysamerr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name); free(name); fai_destroy(idx); return 0; } if (state == 2) state = 3; l1 = l2 = 0; do { ++l1; if (isgraph(c)) ++l2; } while ((ret = razf_read(rz, &c, 1)) && c != '\n'); if (state == 3 && l2) { fprintf(pysamerr, "[fai_build_core] different line length in sequence '%s'.\n", name); free(name); fai_destroy(idx); return 0; } ++l1; len += l2; if (state == 1) line_len = l1, line_blen = l2, state = 0; else if (state == 0) { if (l1 != line_len || l2 != line_blen) state = 2; } } } fai_insert_index(idx, name, len, line_len, line_blen, offset); free(name); return idx; } void fai_save(const faidx_t *fai, FILE *fp) { khint_t k; int i; for (i = 0; i < fai->n; ++i) { faidx1_t x; k = kh_get(s, fai->hash, fai->name[i]); x = kh_value(fai->hash, k); #ifdef _WIN32 fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len); #else fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len); #endif } } faidx_t *fai_read(FILE *fp) { faidx_t *fai; char *buf, *p; int len, line_len, line_blen; #ifdef _WIN32 long offset; #else long long offset; #endif fai = (faidx_t*)calloc(1, sizeof(faidx_t)); fai->hash = kh_init(s); buf = (char*)calloc(0x10000, 1); while (!feof(fp) && fgets(buf, 0x10000, fp)) { for (p = buf; *p && isgraph(*p); ++p); *p = 0; ++p; #ifdef _WIN32 sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len); #else sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len); #endif fai_insert_index(fai, buf, len, line_len, line_blen, offset); } free(buf); return fai; } void fai_destroy(faidx_t *fai) { int i; for (i = 0; i < fai->n; ++i) free(fai->name[i]); free(fai->name); kh_destroy(s, fai->hash); if (fai->rz) razf_close(fai->rz); free(fai); } int fai_build(const char *fn) { char *str; RAZF *rz; FILE *fp; faidx_t *fai; str = (char*)calloc(strlen(fn) + 5, 1); sprintf(str, "%s.fai", fn); rz = razf_open(fn, "r"); if (rz == 0) { fprintf(pysamerr, "[fai_build] fail to open the FASTA file %s\n",fn); free(str); return -1; } fai = fai_build_core(rz); razf_close(rz); fp = fopen(str, "wb"); if (fp == 0) { fprintf(pysamerr, "[fai_build] fail to write FASTA index %s\n",str); fai_destroy(fai); free(str); return -1; } fai_save(fai, fp); fclose(fp); free(str); fai_destroy(fai); return 0; } #ifdef _USE_KNETFILE FILE *download_and_open(const char *fn) { const int buf_size = 1 * 1024 * 1024; uint8_t *buf; FILE *fp; knetFile *fp_remote; const char *url = fn; const char *p; int l = strlen(fn); for (p = fn + l - 1; p >= fn; --p) if (*p == '/') break; fn = p + 1; // First try to open a local copy fp = fopen(fn, "r"); if (fp) return fp; // If failed, download from remote and open fp_remote = knet_open(url, "rb"); if (fp_remote == 0) { fprintf(pysamerr, "[download_from_remote] fail to open remote file %s\n",url); return NULL; } if ((fp = fopen(fn, "wb")) == 0) { fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory %s\n",fn); knet_close(fp_remote); return NULL; } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) fwrite(buf, 1, l, fp); free(buf); fclose(fp); knet_close(fp_remote); return fopen(fn, "r"); } #endif faidx_t *fai_load(const char *fn) { char *str; FILE *fp; faidx_t *fai; str = (char*)calloc(strlen(fn) + 5, 1); sprintf(str, "%s.fai", fn); #ifdef _USE_KNETFILE if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn) { fp = download_and_open(str); if ( !fp ) { fprintf(pysamerr, "[fai_load] failed to open remote FASTA index %s\n", str); free(str); return 0; } } else #endif fp = fopen(str, "rb"); if (fp == 0) { fprintf(pysamerr, "[fai_load] build FASTA index.\n"); fai_build(fn); fp = fopen(str, "rb"); if (fp == 0) { fprintf(pysamerr, "[fai_load] fail to open FASTA index.\n"); free(str); return 0; } } fai = fai_read(fp); fclose(fp); fai->rz = razf_open(fn, "rb"); free(str); if (fai->rz == 0) { fprintf(pysamerr, "[fai_load] fail to open FASTA file.\n"); return 0; } return fai; } char *fai_fetch(const faidx_t *fai, const char *str, int *len) { char *s, c; int i, l, k, name_end; khiter_t iter; faidx1_t val; khash_t(s) *h; int beg, end; beg = end = -1; h = fai->hash; name_end = l = strlen(str); s = (char*)malloc(l+1); // remove space for (i = k = 0; i < l; ++i) if (!isspace(str[i])) s[k++] = str[i]; s[k] = 0; l = k; // determine the sequence name for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end if (i >= 0) name_end = i; if (name_end < l) { // check if this is really the end int n_hyphen = 0; for (i = name_end + 1; i < l; ++i) { if (s[i] == '-') ++n_hyphen; else if (!isdigit(s[i]) && s[i] != ',') break; } if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name s[name_end] = 0; iter = kh_get(s, h, s); if (iter == kh_end(h)) { // cannot find the sequence name iter = kh_get(s, h, str); // try str as the name if (iter == kh_end(h)) { *len = 0; free(s); return 0; } else s[name_end] = ':', name_end = l; } } else iter = kh_get(s, h, str); if(iter == kh_end(h)) { fprintf(pysamerr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str); free(s); return 0; }; val = kh_value(h, iter); // parse the interval if (name_end < l) { for (i = k = name_end + 1; i < l; ++i) if (s[i] != ',') s[k++] = s[i]; s[k] = 0; beg = atoi(s + name_end + 1); for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break; end = i < k? atoi(s + i + 1) : val.len; if (beg > 0) --beg; } else beg = 0, end = val.len; if (beg >= val.len) beg = val.len; if (end >= val.len) end = val.len; if (beg > end) beg = end; free(s); // now retrieve the sequence l = 0; s = (char*)malloc(end - beg + 2); razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET); while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err) if (isgraph(c)) s[l++] = c; s[l] = '\0'; *len = l; return s; } int faidx_main(int argc, char *argv[]) { if (argc == 1) { fprintf(pysamerr, "Usage: faidx [ [...]]\n"); return 1; } else { if (argc == 2) fai_build(argv[1]); else { int i, j, k, l; char *s; faidx_t *fai; fai = fai_load(argv[1]); if (fai == 0) return 1; for (i = 2; i != argc; ++i) { printf(">%s\n", argv[i]); s = fai_fetch(fai, argv[i], &l); for (j = 0; j < l; j += 60) { for (k = 0; k < 60 && k < l - j; ++k) putchar(s[j + k]); putchar('\n'); } free(s); } fai_destroy(fai); } } return 0; } int faidx_fetch_nseq(const faidx_t *fai) { return fai->n; } char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len) { int l; char c; khiter_t iter; faidx1_t val; char *seq=NULL; // Adjust position iter = kh_get(s, fai->hash, c_name); if(iter == kh_end(fai->hash)) return 0; val = kh_value(fai->hash, iter); if(p_end_i < p_beg_i) p_beg_i = p_end_i; if(p_beg_i < 0) p_beg_i = 0; else if(val.len <= p_beg_i) p_beg_i = val.len - 1; if(p_end_i < 0) p_end_i = 0; else if(val.len <= p_end_i) p_end_i = val.len - 1; // Now retrieve the sequence l = 0; seq = (char*)malloc(p_end_i - p_beg_i + 2); razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET); while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1) if (isgraph(c)) seq[l++] = c; seq[l] = '\0'; *len = l; return seq; } #ifdef FAIDX_MAIN int main(int argc, char *argv[]) { return faidx_main(argc, argv); } #endif pysam-0.7.7/samtools/bam_reheader.c.pysam.c0000664000076400007650000000277412162637166020505 0ustar andreasandreas#include "pysam.h" #include #include #include "knetfile.h" #include "bgzf.h" #include "bam.h" #define BUF_SIZE 0x10000 int bam_reheader(BGZF *in, const bam_header_t *h, int fd) { BGZF *fp; bam_header_t *old; int len; uint8_t *buf; if (in->is_write) return -1; buf = malloc(BUF_SIZE); old = bam_header_read(in); fp = bgzf_fdopen(fd, "w"); bam_header_write(fp, h); if (in->block_offset < in->block_length) { bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset); bgzf_flush(fp); } #ifdef _USE_KNETFILE while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) fwrite(buf, 1, len, fp->fp); #else while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) fwrite(buf, 1, len, fp->file); #endif free(buf); fp->block_offset = in->block_offset = 0; bgzf_close(fp); return 0; } int main_reheader(int argc, char *argv[]) { bam_header_t *h; BGZF *in; if (argc != 3) { fprintf(pysamerr, "Usage: samtools reheader \n"); return 1; } { // read the header tamFile fph = sam_open(argv[1]); if (fph == 0) { fprintf(pysamerr, "[%s] fail to read the header from %s.\n", __func__, argv[1]); return 1; } h = sam_header_read(fph); sam_close(fph); } in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r"); if (in == 0) { fprintf(pysamerr, "[%s] fail to open file %s.\n", __func__, argv[2]); return 1; } bam_reheader(in, h, fileno(stdout)); bgzf_close(in); return 0; } pysam-0.7.7/samtools/bam_rmdup.c.pysam.c0000664000076400007650000001304512162637166020046 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "sam.h" typedef bam1_t *bam1_p; #include "khash.h" KHASH_SET_INIT_STR(name) KHASH_MAP_INIT_INT64(pos, bam1_p) #define BUFFER_SIZE 0x40000 typedef struct { uint64_t n_checked, n_removed; khash_t(pos) *best_hash; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) typedef struct { int n, max; bam1_t **a; } tmp_stack_t; static inline void stack_insert(tmp_stack_t *stack, bam1_t *b) { if (stack->n == stack->max) { stack->max = stack->max? stack->max<<1 : 0x10000; stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max); } stack->a[stack->n++] = b; } static inline void dump_best(tmp_stack_t *stack, samfile_t *out) { int i; for (i = 0; i != stack->n; ++i) { samwrite(out, stack->a[i]); bam_destroy1(stack->a[i]); } stack->n = 0; } static void clear_del_set(khash_t(name) *del_set) { khint_t k; for (k = kh_begin(del_set); k < kh_end(del_set); ++k) if (kh_exist(del_set, k)) free((char*)kh_key(del_set, k)); kh_clear(name, del_set); } static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->n_checked = q->n_removed = 0; q->best_hash = kh_init(pos); return q; } else return &kh_val(aux, k); } static void clear_best(khash_t(lib) *aux, int max) { khint_t k; for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); if (kh_size(q->best_hash) >= max) kh_clear(pos, q->best_hash); } } } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam1_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } void bam_rmdup_core(samfile_t *in, samfile_t *out) { bam1_t *b; int last_tid = -1, last_pos = -1; tmp_stack_t stack; khint_t k; khash_t(lib) *aux; khash_t(name) *del_set; aux = kh_init(lib); del_set = kh_init(name); b = bam_init1(); memset(&stack, 0, sizeof(tmp_stack_t)); kh_resize(name, del_set, 4 * BUFFER_SIZE); while (samread(in, b) >= 0) { bam1_core_t *c = &b->core; if (c->tid != last_tid || last_pos != c->pos) { dump_best(&stack, out); // write the result clear_best(aux, BUFFER_SIZE); if (c->tid != last_tid) { clear_best(aux, 0); if (kh_size(del_set)) { // check fprintf(pysamerr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set)); clear_del_set(del_set); } if ((int)c->tid == -1) { // append unmapped reads samwrite(out, b); while (samread(in, b) >= 0) samwrite(out, b); break; } last_tid = c->tid; fprintf(pysamerr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]); } } if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) { samwrite(out, b); } else if (c->isize > 0) { // paired, head uint64_t key = (uint64_t)c->pos<<32 | c->isize; const char *lib; lib_aux_t *q; int ret; lib = bam_get_library(in->header, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; k = kh_put(pos, q->best_hash, key, &ret); if (ret == 0) { // found in best_hash bam1_t *p = kh_val(q->best_hash, k); ++q->n_removed; if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed bam_copy1(p, b); // replaced as b } else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed if (ret == 0) fprintf(pysamerr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b)); } else { // not found in best_hash kh_val(q->best_hash, k) = bam_dup1(b); stack_insert(&stack, kh_val(q->best_hash, k)); } } else { // paired, tail k = kh_get(name, del_set, bam1_qname(b)); if (k != kh_end(del_set)) { free((char*)kh_key(del_set, k)); kh_del(name, del_set, k); } else samwrite(out, b); } last_pos = c->pos; } for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); dump_best(&stack, out); fprintf(pysamerr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(pos, q->best_hash); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); clear_del_set(del_set); kh_destroy(name, del_set); free(stack.a); bam_destroy1(b); } void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se); int bam_rmdup(int argc, char *argv[]) { int c, is_se = 0, force_se = 0; samfile_t *in, *out; while ((c = getopt(argc, argv, "sS")) >= 0) { switch (c) { case 's': is_se = 1; break; case 'S': force_se = is_se = 1; break; } } if (optind + 2 > argc) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools rmdup [-sS] \n\n"); fprintf(pysamerr, "Option: -s rmdup for SE reads\n"); fprintf(pysamerr, " -S treat PE reads as SE in rmdup (force -s)\n\n"); return 1; } in = samopen(argv[optind], "rb", 0); out = samopen(argv[optind+1], "wb", in->header); if (in == 0 || out == 0) { fprintf(pysamerr, "[bam_rmdup] fail to read/write input files\n"); return 1; } if (is_se) bam_rmdupse_core(in, out, force_se); else bam_rmdup_core(in, out); samclose(in); samclose(out); return 0; } pysam-0.7.7/samtools/cut_target.c.pysam.c0000664000076400007650000001307312162637166020242 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bam.h" #include "errmod.h" #include "faidx.h" #define ERR_DEP 0.83f typedef struct { int e[2][3], p[2][2]; } score_param_t; /* Note that although the two matrics have 10 parameters in total, only 4 * (probably 3) are free. Changing the scoring matrices in a sort of symmetric * way will not change the result. */ static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} }; typedef struct { int min_baseQ, tid, max_bases; uint16_t *bases; bamFile fp; bam_header_t *h; char *ref; faidx_t *fai; errmod_t *em; } ct_t; static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp) { int i, j, ret, tmp, k, sum[4], qual; float q[16]; if (n > g->max_bases) { // enlarge g->bases g->max_bases = n; kroundup32(g->max_bases); g->bases = realloc(g->bases, g->max_bases * 2); } for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_refskip || p->is_del) continue; baseQ = bam1_qual(p->b)[p->qpos]; if (baseQ < g->min_baseQ) continue; seq = bam1_seq(p->b); b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b; } if (k == 0) return 0; errmod_cal(g->em, k, 4, g->bases, q); for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i; for (i = 1; i < 4; ++i) // insertion sort for (j = i; j > 0 && sum[j] < sum[j-1]; --j) tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp; qual = (sum[1]>>2) - (sum[0]>>2); k = k < 256? k : 255; ret = (qual < 63? qual : 63) << 2 | (sum[0]&3); return ret<<8|k; } static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns) { int i, f[2][2], *prev, *curr, *swap_tmp, s; uint8_t *b; // backtrack array b = calloc(l, 1); f[0][0] = f[0][1] = 0; prev = f[0]; curr = f[1]; // fill the backtrack matrix for (i = 0; i < l; ++i) { int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2; int tmp0, tmp1; // compute f[0] tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0) tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1) if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0; else curr[0] = tmp1, b[i] = 1; // compute f[1] tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0) tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1) if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1; else curr[1] = tmp1, b[i] |= 1<<1; // swap swap_tmp = prev; prev = curr; curr = swap_tmp; } // backtrack s = prev[0] > prev[1]? 0 : 1; for (i = l - 1; i > 0; --i) { b[i] |= s<<2; s = b[i]>>s&1; } // print for (i = 0, s = -1; i <= l; ++i) { if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) { if (s >= 0) { int j; printf("%s:%d-%d\t0\t%s\t%d\t60\t%dM\t*\t0\t0\t", h->target_name[tid], s+1, i, h->target_name[tid], s+1, i-s); for (j = s; j < i; ++j) { int c = cns[j]>>8; if (c == 0) putchar('N'); else putchar("ACGT"[c&3]); } putchar('\t'); for (j = s; j < i; ++j) putchar(33 + (cns[j]>>8>>2)); putchar('\n'); } //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s); s = -1; } else if ((b[i]>>2&3) && s < 0) s = i; } free(b); } static int read_aln(void *data, bam1_t *b) { extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag); ct_t *g = (ct_t*)data; int ret, len; ret = bam_read1(g->fp, b); if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) { if (b->core.tid != g->tid) { // then load the sequence free(g->ref); g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len); g->tid = b->core.tid; } bam_prob_realn_core(b, g->ref, 1<<1|1); } return ret; } int main_cut_target(int argc, char *argv[]) { int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; const bam_pileup1_t *p; bam_plp_t plp; uint16_t *cns; ct_t g; memset(&g, 0, sizeof(ct_t)); g.min_baseQ = 13; g.tid = -1; while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) { switch (c) { case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE case '1': g_param.e[1][1] = atoi(optarg); break; case '2': g_param.e[1][2] = atoi(optarg); break; case 'f': g.fai = fai_load(optarg); if (g.fai == 0) fprintf(pysamerr, "[%s] fail to load the fasta index.\n", __func__); break; } } if (argc == optind) { fprintf(pysamerr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] \n"); return 1; } l = max_l = 0; cns = 0; g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r"); g.h = bam_header_read(g.fp); g.em = errmod_init(1 - ERR_DEP); plp = bam_plp_init(read_aln, &g); while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) { if (tid < 0) break; if (tid != lasttid) { // change of chromosome if (cns) process_cns(g.h, lasttid, l, cns); if (max_l < g.h->target_len[tid]) { max_l = g.h->target_len[tid]; kroundup32(max_l); cns = realloc(cns, max_l * 2); } l = g.h->target_len[tid]; memset(cns, 0, max_l * 2); lasttid = tid; } cns[pos] = gencns(&g, n, p); lastpos = pos; } process_cns(g.h, lasttid, l, cns); free(cns); bam_header_destroy(g.h); bam_plp_destroy(plp); bam_close(g.fp); if (g.fai) { fai_destroy(g.fai); free(g.ref); } errmod_destroy(g.em); free(g.bases); return 0; } pysam-0.7.7/samtools/bam_import.c.pysam.c0000664000076400007650000004016712162637166020236 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include #ifdef _WIN32 #include #endif #include "kstring.h" #include "bam.h" #include "sam_header.h" #include "kseq.h" #include "khash.h" KSTREAM_INIT(gzFile, gzread, 16384) KHASH_MAP_INIT_STR(ref, uint64_t) void bam_init_header_hash(bam_header_t *header); void bam_destroy_header_hash(bam_header_t *header); int32_t bam_get_tid(const bam_header_t *header, const char *seq_name); unsigned char bam_nt16_table[256] = { 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15, 15,15, 5, 6, 8,15, 7, 9, 15,10,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15 }; unsigned short bam_char2flag_table[256] = { 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0, BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0 }; char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN"; struct __tamFile_t { gzFile fp; kstream_t *ks; kstring_t *str; uint64_t n_lines; int is_first; }; char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only { char **list = 0, *s; int n = 0, dret, m = 0; gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r"); kstream_t *ks; kstring_t *str; str = (kstring_t*)calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, '\n', str, &dret) > 0) { if (n == m) { m = m? m << 1 : 16; list = (char**)realloc(list, m * sizeof(char*)); } if (str->s[str->l-1] == '\r') str->s[--str->l] = '\0'; s = list[n++] = (char*)calloc(str->l + 1, 1); strcpy(s, str->s); } ks_destroy(ks); gzclose(fp); free(str->s); free(str); *_n = n; return list; } static bam_header_t *hash2header(const kh_ref_t *hash) { bam_header_t *header; khiter_t k; header = bam_header_init(); header->n_targets = kh_size(hash); header->target_name = (char**)calloc(kh_size(hash), sizeof(char*)); header->target_len = (uint32_t*)calloc(kh_size(hash), 4); for (k = kh_begin(hash); k != kh_end(hash); ++k) { if (kh_exist(hash, k)) { int i = (int)kh_value(hash, k); header->target_name[i] = (char*)kh_key(hash, k); header->target_len[i] = kh_value(hash, k)>>32; } } bam_init_header_hash(header); return header; } bam_header_t *sam_header_read2(const char *fn) { bam_header_t *header; int c, dret, ret, error = 0; gzFile fp; kstream_t *ks; kstring_t *str; kh_ref_t *hash; khiter_t k; if (fn == 0) return 0; fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r"); if (fp == 0) return 0; hash = kh_init(ref); ks = ks_init(fp); str = (kstring_t*)calloc(1, sizeof(kstring_t)); while (ks_getuntil(ks, 0, str, &dret) > 0) { char *s = strdup(str->s); int len, i; i = kh_size(hash); ks_getuntil(ks, 0, str, &dret); len = atoi(str->s); k = kh_put(ref, hash, s, &ret); if (ret == 0) { fprintf(pysamerr, "[sam_header_read2] duplicated sequence name: %s\n", s); error = 1; } kh_value(hash, k) = (uint64_t)len<<32 | i; if (dret != '\n') while ((c = ks_getc(ks)) != '\n' && c != -1); } ks_destroy(ks); gzclose(fp); free(str->s); free(str); fprintf(pysamerr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash)); if (error) return 0; header = hash2header(hash); kh_destroy(ref, hash); return header; } static inline uint8_t *alloc_data(bam1_t *b, int size) { if (b->m_data < size) { b->m_data = size; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } return b->data; } static inline void parse_error(int64_t n_lines, const char * __restrict msg) { fprintf(pysamerr, "Parse error at line %lld: %s\n", (long long)n_lines, msg); abort(); } static inline void append_text(bam_header_t *header, kstring_t *str) { size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null kroundup32(x); kroundup32(y); if (x < y) { header->n_text = y; header->text = (char*)realloc(header->text, y); if ( !header->text ) { fprintf(pysamerr,"realloc failed to alloc %ld bytes\n", y); abort(); } } // Sanity check if ( header->l_text+str->l+1 >= header->n_text ) { fprintf(pysamerr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y); abort(); } strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here. header->l_text += str->l + 1; header->text[header->l_text] = 0; } int sam_header_parse(bam_header_t *h) { char **tmp; int i; free(h->target_len); free(h->target_name); h->n_targets = 0; h->target_len = 0; h->target_name = 0; if (h->l_text < 3) return 0; if (h->dict == 0) h->dict = sam_header_parse2(h->text); tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets); if (h->n_targets == 0) return 0; h->target_name = calloc(h->n_targets, sizeof(void*)); for (i = 0; i < h->n_targets; ++i) h->target_name[i] = strdup(tmp[i]); free(tmp); tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets); h->target_len = calloc(h->n_targets, 4); for (i = 0; i < h->n_targets; ++i) h->target_len[i] = atoi(tmp[i]); free(tmp); return h->n_targets; } bam_header_t *sam_header_read(tamFile fp) { int ret, dret; bam_header_t *header = bam_header_init(); kstring_t *str = fp->str; while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header str->s[str->l] = dret; // note that str->s is NOT null terminated!! append_text(header, str); if (dret != '\n') { ret = ks_getuntil(fp->ks, '\n', str, &dret); str->s[str->l] = '\n'; // NOT null terminated!! append_text(header, str); } ++fp->n_lines; } sam_header_parse(header); bam_init_header_hash(header); fp->is_first = 1; return header; } int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b) { int ret, doff, doff0, dret, z = 0; bam1_core_t *c = &b->core; kstring_t *str = fp->str; kstream_t *ks = fp->ks; if (fp->is_first) { fp->is_first = 0; ret = str->l; } else { do { // special consideration for empty lines ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret); if (ret >= 0) z += str->l + 1; } while (ret == 0); } if (ret < 0) return -1; ++fp->n_lines; doff = 0; { // name c->l_qname = strlen(str->s) + 1; memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname); doff += c->l_qname; } { // flag long flag; char *s; ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; flag = strtol((char*)str->s, &s, 0); if (*s) { // not the end of the string flag = 0; for (s = str->s; *s; ++s) flag |= bam_char2flag_table[(int)*s]; } c->flag = flag; } { // tid, pos, qual ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s); if (c->tid < 0 && strcmp(str->s, "*")) { if (header->n_targets == 0) { fprintf(pysamerr, "[sam_read1] missing header? Abort!\n"); exit(1); } else fprintf(pysamerr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s); } ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1; ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0; if (ret < 0) return -2; } { // cigar char *s, *t; int i, op; long x; c->n_cigar = 0; if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3; z += str->l + 1; if (str->s[0] != '*') { uint32_t *cigar; for (s = str->s; *s; ++s) { if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar; else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character"); } b->data = alloc_data(b, doff + c->n_cigar * 4); cigar = bam1_cigar(b); for (i = 0, s = str->s; i != c->n_cigar; ++i) { x = strtol(s, &t, 10); op = toupper(*t); if (op == 'M') op = BAM_CMATCH; else if (op == 'I') op = BAM_CINS; else if (op == 'D') op = BAM_CDEL; else if (op == 'N') op = BAM_CREF_SKIP; else if (op == 'S') op = BAM_CSOFT_CLIP; else if (op == 'H') op = BAM_CHARD_CLIP; else if (op == 'P') op = BAM_CPAD; else if (op == '=') op = BAM_CEQUAL; else if (op == 'X') op = BAM_CDIFF; else if (op == 'B') op = BAM_CBACK; else parse_error(fp->n_lines, "invalid CIGAR operation"); s = t + 1; cigar[i] = bam_cigar_gen(x, op); } if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation"); c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar)); doff += c->n_cigar * 4; } else { if (!(c->flag&BAM_FUNMAP)) { fprintf(pysamerr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines); c->flag |= BAM_FUNMAP; } c->bin = bam_reg2bin(c->pos, c->pos + 1); } } { // mtid, mpos, isize ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid; ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1; ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0; if (ret < 0) return -4; } { // seq and qual int i; uint8_t *p = 0; if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq z += str->l + 1; if (strcmp(str->s, "*")) { c->l_qseq = strlen(str->s); if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) { fprintf(pysamerr, "Line %ld, sequence length %i vs %i from CIGAR\n", (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b))); parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent"); } p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff; memset(p, 0, (c->l_qseq+1)/2); for (i = 0; i < c->l_qseq; ++i) p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2); } else c->l_qseq = 0; if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual z += str->l + 1; if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s)) parse_error(fp->n_lines, "sequence and quality are inconsistent"); p += (c->l_qseq+1)/2; if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff; else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33; doff += c->l_qseq + (c->l_qseq+1)/2; } doff0 = doff; if (dret != '\n' && dret != '\r') { // aux while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) { uint8_t *s, type, key[2]; z += str->l + 1; if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':') parse_error(fp->n_lines, "missing colon in auxiliary data"); key[0] = str->s[0]; key[1] = str->s[1]; type = str->s[3]; s = alloc_data(b, doff + 3) + doff; s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2; if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility s = alloc_data(b, doff + 2) + doff; *s++ = 'A'; *s = str->s[5]; doff += 2; } else if (type == 'I' || type == 'i') { long long x; s = alloc_data(b, doff + 5) + doff; x = (long long)atoll(str->s + 5); if (x < 0) { if (x >= -127) { *s++ = 'c'; *(int8_t*)s = (int8_t)x; s += 1; doff += 2; } else if (x >= -32767) { *s++ = 's'; *(int16_t*)s = (int16_t)x; s += 2; doff += 3; } else { *s++ = 'i'; *(int32_t*)s = (int32_t)x; s += 4; doff += 5; if (x < -2147483648ll) fprintf(pysamerr, "Parse warning at line %lld: integer %lld is out of range.", (long long)fp->n_lines, x); } } else { if (x <= 255) { *s++ = 'C'; *s++ = (uint8_t)x; doff += 2; } else if (x <= 65535) { *s++ = 'S'; *(uint16_t*)s = (uint16_t)x; s += 2; doff += 3; } else { *s++ = 'I'; *(uint32_t*)s = (uint32_t)x; s += 4; doff += 5; if (x > 4294967295ll) fprintf(pysamerr, "Parse warning at line %lld: integer %lld is out of range.", (long long)fp->n_lines, x); } } } else if (type == 'f') { s = alloc_data(b, doff + 5) + doff; *s++ = 'f'; *(float*)s = (float)atof(str->s + 5); s += 4; doff += 5; } else if (type == 'd') { s = alloc_data(b, doff + 9) + doff; *s++ = 'd'; *(float*)s = (float)atof(str->s + 9); s += 8; doff += 9; } else if (type == 'Z' || type == 'H') { int size = 1 + (str->l - 5) + 1; if (type == 'H') { // check whether the hex string is valid int i; if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even"); for (i = 0; i < str->l - 5; ++i) { int c = toupper(str->s[5 + i]); if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F'))) parse_error(fp->n_lines, "invalid hex character"); } } s = alloc_data(b, doff + size) + doff; *s++ = type; memcpy(s, str->s + 5, str->l - 5); s[str->l - 5] = 0; doff += size; } else if (type == 'B') { int32_t n = 0, Bsize, k = 0, size; char *p; if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B"); Bsize = bam_aux_type2size(str->s[5]); // the size of each element for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array if (*p == ',') ++n; p = str->s + 7; // now p points to the first number in the array size = 6 + Bsize * n; // total number of bytes allocated to this tag s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory *s++ = 'B'; *s++ = str->s[5]; memcpy(s, &n, 4); s += 4; // write the number of elements if (str->s[5] == 'c') while (p < str->s + str->l) ((int8_t*)s)[k++] = (int8_t)strtol(p, &p, 0), ++p; else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++] = (uint8_t)strtol(p, &p, 0), ++p; else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++] = (int16_t)strtol(p, &p, 0), ++p; // FIXME: avoid unaligned memory else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p; else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++] = (int32_t)strtol(p, &p, 0), ++p; else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p; else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++] = (float)strtod(p, &p), ++p; else parse_error(fp->n_lines, "unrecognized array type"); s += Bsize * n; doff += size; } else parse_error(fp->n_lines, "unrecognized type"); if (dret == '\n' || dret == '\r') break; } } b->l_aux = doff - doff0; b->data_len = doff; if (bam_no_B) bam_remove_B(b); return z; } tamFile sam_open(const char *fn) { tamFile fp; gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb"); if (gzfp == 0) return 0; fp = (tamFile)calloc(1, sizeof(struct __tamFile_t)); fp->str = (kstring_t*)calloc(1, sizeof(kstring_t)); fp->fp = gzfp; fp->ks = ks_init(fp->fp); return fp; } void sam_close(tamFile fp) { if (fp) { ks_destroy(fp->ks); gzclose(fp->fp); free(fp->str->s); free(fp->str); free(fp); } } pysam-0.7.7/samtools/bam_index.c.pysam.c0000664000076400007650000005205512162637166020032 0ustar andreasandreas#include "pysam.h" #include #include #include "bam.h" #include "khash.h" #include "ksort.h" #include "bam_endian.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif /*! @header Alignment indexing. Before indexing, BAM must be sorted based on the leftmost coordinate of alignments. In indexing, BAM uses two indices: a UCSC binning index and a simple linear index. The binning index is efficient for alignments spanning long distance, while the auxiliary linear index helps to reduce unnecessary seek calls especially for short alignments. The UCSC binning scheme was suggested by Richard Durbin and Lincoln Stein and is explained by Kent et al. (2002). In this scheme, each bin represents a contiguous genomic region which can be fully contained in another bin; each alignment is associated with a bin which represents the smallest region containing the entire alignment. The binning scheme is essentially another representation of R-tree. A distinct bin uniquely corresponds to a distinct internal node in a R-tree. Bin A is a child of Bin B if region A is contained in B. In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin 0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp, 585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to find the alignments overlapped with a region [rbeg,rend), we need to calculate the list of bins that may be overlapped the region and test the alignments in the bins to confirm the overlaps. If the specified region is short, typically only a few alignments in six bins need to be retrieved. The overlapping alignments can be quickly fetched. */ #define BAM_MIN_CHUNK_GAP 32768 // 1<<14 is the size of minimum bin. #define BAM_LIDX_SHIFT 14 #define BAM_MAX_BIN 37450 // =(8^6-1)/7+1 typedef struct { uint64_t u, v; } pair64_t; #define pair64_lt(a,b) ((a).u < (b).u) KSORT_INIT(off, pair64_t, pair64_lt) typedef struct { uint32_t m, n; pair64_t *list; } bam_binlist_t; typedef struct { int32_t n, m; uint64_t *offset; } bam_lidx_t; KHASH_MAP_INIT_INT(i, bam_binlist_t) struct __bam_index_t { int32_t n; uint64_t n_no_coor; // unmapped reads without coordinate khash_t(i) **index; bam_lidx_t *index2; }; // requirement: len <= LEN_MASK static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end) { khint_t k; bam_binlist_t *l; int ret; k = kh_put(i, h, bin, &ret); l = &kh_value(h, k); if (ret) { // not present l->m = 1; l->n = 0; l->list = (pair64_t*)calloc(l->m, 16); } if (l->n == l->m) { l->m <<= 1; l->list = (pair64_t*)realloc(l->list, l->m * 16); } l->list[l->n].u = beg; l->list[l->n++].v = end; } static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset) { int i, beg, end; beg = b->core.pos >> BAM_LIDX_SHIFT; end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_LIDX_SHIFT; if (index2->m < end + 1) { int old_m = index2->m; index2->m = end + 1; kroundup32(index2->m); index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); } if (beg == end) { if (index2->offset[beg] == 0) index2->offset[beg] = offset; } else { for (i = beg; i <= end; ++i) if (index2->offset[i] == 0) index2->offset[i] = offset; } index2->n = end + 1; } static void merge_chunks(bam_index_t *idx) { #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16) khash_t(i) *index; int i, l, m; khint_t k; for (i = 0; i < idx->n; ++i) { index = idx->index[i]; for (k = kh_begin(index); k != kh_end(index); ++k) { bam_binlist_t *p; if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue; p = &kh_value(index, k); m = 0; for (l = 1; l < p->n; ++l) { #ifdef BAM_TRUE_OFFSET if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v; #else if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v; #endif else p->list[++m] = p->list[l]; } // ~for(l) p->n = m + 1; } // ~for(k) } // ~for(i) #endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF) } static void fill_missing(bam_index_t *idx) { int i, j; for (i = 0; i < idx->n; ++i) { bam_lidx_t *idx2 = &idx->index2[i]; for (j = 1; j < idx2->n; ++j) if (idx2->offset[j] == 0) idx2->offset[j] = idx2->offset[j-1]; } } bam_index_t *bam_index_core(bamFile fp) { bam1_t *b; bam_header_t *h; int i, ret; bam_index_t *idx; uint32_t last_bin, save_bin; int32_t last_coor, last_tid, save_tid; bam1_core_t *c; uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor; h = bam_header_read(fp); if(h == 0) { fprintf(pysamerr, "[bam_index_core] Invalid BAM header."); return NULL; } idx = (bam_index_t*)calloc(1, sizeof(bam_index_t)); b = (bam1_t*)calloc(1, sizeof(bam1_t)); c = &b->core; idx->n = h->n_targets; bam_header_destroy(h); idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i); idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t)); save_bin = save_tid = last_tid = last_bin = 0xffffffffu; save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu; n_mapped = n_unmapped = n_no_coor = off_end = 0; off_beg = off_end = bam_tell(fp); while ((ret = bam_read1(fp, b)) >= 0) { if (c->tid < 0) ++n_no_coor; if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes last_tid = c->tid; last_bin = 0xffffffffu; } else if ((uint32_t)last_tid > (uint32_t)c->tid) { fprintf(pysamerr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n", bam1_qname(b), last_tid+1, c->tid+1); return NULL; } else if ((int32_t)c->tid >= 0 && last_coor > c->pos) { fprintf(pysamerr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n", bam1_qname(b), last_coor, c->pos, c->tid+1); return NULL; } if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off); if (c->bin != last_bin) { // then possibly write the binning index if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record insert_offset(idx->index[save_tid], save_bin, save_off, last_off); if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element off_end = last_off; insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end); insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped); n_mapped = n_unmapped = 0; off_beg = off_end; } save_off = last_off; save_bin = last_bin = c->bin; save_tid = c->tid; if (save_tid < 0) break; } if (bam_tell(fp) <= last_off) { fprintf(pysamerr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n", (unsigned long long)bam_tell(fp), (unsigned long long)last_off); return NULL; } if (c->flag & BAM_FUNMAP) ++n_unmapped; else ++n_mapped; last_off = bam_tell(fp); last_coor = b->core.pos; } if (save_tid >= 0) { insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp)); insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp)); insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped); } merge_chunks(idx); fill_missing(idx); if (ret >= 0) { while ((ret = bam_read1(fp, b)) >= 0) { ++n_no_coor; if (c->tid >= 0 && n_no_coor) { fprintf(pysamerr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n"); return NULL; } } } if (ret < -1) fprintf(pysamerr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret); free(b->data); free(b); idx->n_no_coor = n_no_coor; return idx; } void bam_index_destroy(bam_index_t *idx) { khint_t k; int i; if (idx == 0) return; for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; bam_lidx_t *index2 = idx->index2 + i; for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) free(kh_value(index, k).list); } kh_destroy(i, index); free(index2->offset); } free(idx->index); free(idx->index2); free(idx); } void bam_index_save(const bam_index_t *idx, FILE *fp) { int32_t i, size; khint_t k; fwrite("BAI\1", 1, 4, fp); if (bam_is_be) { uint32_t x = idx->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); } else fwrite(&idx->n, 4, 1, fp); for (i = 0; i < idx->n; ++i) { khash_t(i) *index = idx->index[i]; bam_lidx_t *index2 = idx->index2 + i; // write binning index size = kh_size(index); if (bam_is_be) { // big endian uint32_t x = size; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); } else fwrite(&size, 4, 1, fp); for (k = kh_begin(index); k != kh_end(index); ++k) { if (kh_exist(index, k)) { bam_binlist_t *p = &kh_value(index, k); if (bam_is_be) { // big endian uint32_t x; x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp); x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } fwrite(p->list, 16, p->n, fp); for (x = 0; (int)x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } else { fwrite(&kh_key(index, k), 4, 1, fp); fwrite(&p->n, 4, 1, fp); fwrite(p->list, 16, p->n, fp); } } } // write linear index (index2) if (bam_is_be) { int x = index2->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); } else fwrite(&index2->n, 4, 1, fp); if (bam_is_be) { // big endian int x; for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); fwrite(index2->offset, 8, index2->n, fp); for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); } else fwrite(index2->offset, 8, index2->n, fp); } { // write the number of reads coor-less records. uint64_t x = idx->n_no_coor; if (bam_is_be) bam_swap_endian_8p(&x); fwrite(&x, 8, 1, fp); } fflush(fp); } static bam_index_t *bam_index_load_core(FILE *fp) { int i; char magic[4]; bam_index_t *idx; if (fp == 0) { fprintf(pysamerr, "[bam_index_load_core] fail to load index.\n"); return 0; } fread(magic, 1, 4, fp); if (strncmp(magic, "BAI\1", 4)) { fprintf(pysamerr, "[bam_index_load] wrong magic number.\n"); fclose(fp); return 0; } idx = (bam_index_t*)calloc(1, sizeof(bam_index_t)); fread(&idx->n, 4, 1, fp); if (bam_is_be) bam_swap_endian_4p(&idx->n); idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t)); for (i = 0; i < idx->n; ++i) { khash_t(i) *index; bam_lidx_t *index2 = idx->index2 + i; uint32_t key, size; khint_t k; int j, ret; bam_binlist_t *p; index = idx->index[i] = kh_init(i); // load binning index fread(&size, 4, 1, fp); if (bam_is_be) bam_swap_endian_4p(&size); for (j = 0; j < (int)size; ++j) { fread(&key, 4, 1, fp); if (bam_is_be) bam_swap_endian_4p(&key); k = kh_put(i, index, key, &ret); p = &kh_value(index, k); fread(&p->n, 4, 1, fp); if (bam_is_be) bam_swap_endian_4p(&p->n); p->m = p->n; p->list = (pair64_t*)malloc(p->m * 16); fread(p->list, 16, p->n, fp); if (bam_is_be) { int x; for (x = 0; x < p->n; ++x) { bam_swap_endian_8p(&p->list[x].u); bam_swap_endian_8p(&p->list[x].v); } } } // load linear index fread(&index2->n, 4, 1, fp); if (bam_is_be) bam_swap_endian_4p(&index2->n); index2->m = index2->n; index2->offset = (uint64_t*)calloc(index2->m, 8); fread(index2->offset, index2->n, 8, fp); if (bam_is_be) for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); } if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0; if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor); return idx; } bam_index_t *bam_index_load_local(const char *_fn) { FILE *fp; char *fnidx, *fn; if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) { const char *p; int l = strlen(_fn); for (p = _fn + l - 1; p >= _fn; --p) if (*p == '/') break; fn = strdup(p + 1); } else fn = strdup(_fn); fnidx = (char*)calloc(strlen(fn) + 5, 1); strcpy(fnidx, fn); strcat(fnidx, ".bai"); fp = fopen(fnidx, "rb"); if (fp == 0) { // try "{base}.bai" char *s = strstr(fn, "bam"); if (s == fn + strlen(fn) - 3) { strcpy(fnidx, fn); fnidx[strlen(fn)-1] = 'i'; fp = fopen(fnidx, "rb"); } } free(fnidx); free(fn); if (fp) { bam_index_t *idx = bam_index_load_core(fp); fclose(fp); return idx; } else return 0; } #ifdef _USE_KNETFILE static void download_from_remote(const char *url) { const int buf_size = 1 * 1024 * 1024; char *fn; FILE *fp; uint8_t *buf; knetFile *fp_remote; int l; if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; l = strlen(url); for (fn = (char*)url + l - 1; fn >= url; --fn) if (*fn == '/') break; ++fn; // fn now points to the file name fp_remote = knet_open(url, "r"); if (fp_remote == 0) { fprintf(pysamerr, "[download_from_remote] fail to open remote file.\n"); return; } if ((fp = fopen(fn, "wb")) == 0) { fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory.\n"); knet_close(fp_remote); return; } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) fwrite(buf, 1, l, fp); free(buf); fclose(fp); knet_close(fp_remote); } #else static void download_from_remote(const char *url) { return; } #endif bam_index_t *bam_index_load(const char *fn) { bam_index_t *idx; idx = bam_index_load_local(fn); if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) { char *fnidx = calloc(strlen(fn) + 5, 1); strcat(strcpy(fnidx, fn), ".bai"); fprintf(pysamerr, "[bam_index_load] attempting to download the remote index file.\n"); download_from_remote(fnidx); free(fnidx); idx = bam_index_load_local(fn); } if (idx == 0) fprintf(pysamerr, "[bam_index_load] fail to load BAM index.\n"); return idx; } int bam_index_build2(const char *fn, const char *_fnidx) { char *fnidx; FILE *fpidx; bamFile fp; bam_index_t *idx; if ((fp = bam_open(fn, "r")) == 0) { fprintf(pysamerr, "[bam_index_build2] fail to open the BAM file.\n"); return -1; } idx = bam_index_core(fp); bam_close(fp); if(idx == 0) { fprintf(pysamerr, "[bam_index_build2] fail to index the BAM file.\n"); return -1; } if (_fnidx == 0) { fnidx = (char*)calloc(strlen(fn) + 5, 1); strcpy(fnidx, fn); strcat(fnidx, ".bai"); } else fnidx = strdup(_fnidx); fpidx = fopen(fnidx, "wb"); if (fpidx == 0) { fprintf(pysamerr, "[bam_index_build2] fail to create the index file.\n"); free(fnidx); bam_index_destroy(idx); return -1; } bam_index_save(idx, fpidx); bam_index_destroy(idx); fclose(fpidx); free(fnidx); return 0; } int bam_index_build(const char *fn) { return bam_index_build2(fn, 0); } int bam_index(int argc, char *argv[]) { if (argc < 2) { fprintf(pysamerr, "Usage: samtools index [out.index]\n"); return 1; } if (argc >= 3) bam_index_build2(argv[1], argv[2]); else bam_index_build(argv[1]); return 0; } int bam_idxstats(int argc, char *argv[]) { bam_index_t *idx; bam_header_t *header; bamFile fp; int i; if (argc < 2) { fprintf(pysamerr, "Usage: samtools idxstats \n"); return 1; } fp = bam_open(argv[1], "r"); if (fp == 0) { fprintf(pysamerr, "[%s] fail to open BAM.\n", __func__); return 1; } header = bam_header_read(fp); bam_close(fp); idx = bam_index_load(argv[1]); if (idx == 0) { fprintf(pysamerr, "[%s] fail to load the index.\n", __func__); return 1; } for (i = 0; i < idx->n; ++i) { khint_t k; khash_t(i) *h = idx->index[i]; printf("%s\t%d", header->target_name[i], header->target_len[i]); k = kh_get(i, h, BAM_MAX_BIN); if (k != kh_end(h)) printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v); else printf("\t0\t0"); putchar('\n'); } printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor); bam_header_destroy(header); bam_index_destroy(idx); return 0; } static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_MAX_BIN]) { int i = 0, k; if (beg >= end) return 0; if (end >= 1u<<29) end = 1u<<29; --end; list[i++] = 0; for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; return i; } static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b) { uint32_t rbeg = b->core.pos; uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1; return (rend > beg && rbeg < end); } struct __bam_iter_t { int from_first; // read from the first record; no random access int tid, beg, end, n_off, i, finished; uint64_t curr_off; pair64_t *off; }; // bam_fetch helper function retrieves bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end) { uint16_t *bins; int i, n_bins, n_off; pair64_t *off; khint_t k; khash_t(i) *index; uint64_t min_off; bam_iter_t iter = 0; if (beg < 0) beg = 0; if (end < beg) return 0; // initialize iter iter = calloc(1, sizeof(struct __bam_iter_t)); iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1; // bins = (uint16_t*)calloc(BAM_MAX_BIN, 2); n_bins = reg2bins(beg, end, bins); index = idx->index[tid]; if (idx->index2[tid].n > 0) { min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1] : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT]; if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4 int n = beg>>BAM_LIDX_SHIFT; if (n > idx->index2[tid].n) n = idx->index2[tid].n; for (i = n - 1; i >= 0; --i) if (idx->index2[tid].offset[i] != 0) break; if (i >= 0) min_off = idx->index2[tid].offset[i]; } } else min_off = 0; // tabix 0.1.2 may produce such index files for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) n_off += kh_value(index, k).n; } if (n_off == 0) { free(bins); return iter; } off = (pair64_t*)calloc(n_off, 16); for (i = n_off = 0; i < n_bins; ++i) { if ((k = kh_get(i, index, bins[i])) != kh_end(index)) { int j; bam_binlist_t *p = &kh_value(index, k); for (j = 0; j < p->n; ++j) if (p->list[j].v > min_off) off[n_off++] = p->list[j]; } } free(bins); if (n_off == 0) { free(off); return iter; } { bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t)); int l; ks_introsort(off, n_off, off); // resolve completely contained adjacent blocks for (i = 1, l = 0; i < n_off; ++i) if (off[l].v < off[i].v) off[++l] = off[i]; n_off = l + 1; // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing for (i = 1; i < n_off; ++i) if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; { // merge adjacent blocks #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16) for (i = 1, l = 0; i < n_off; ++i) { #ifdef BAM_TRUE_OFFSET if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v; #else if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; #endif else off[++l] = off[i]; } n_off = l + 1; #endif } bam_destroy1(b); } iter->n_off = n_off; iter->off = off; return iter; } pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off) { // for pysam compatibility bam_iter_t iter; pair64_t *off; iter = bam_iter_query(idx, tid, beg, end); off = iter->off; *cnt_off = iter->n_off; free(iter); return off; } void bam_iter_destroy(bam_iter_t iter) { if (iter) { free(iter->off); free(iter); } } int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b) { int ret; if (iter && iter->finished) return -1; if (iter == 0 || iter->from_first) { ret = bam_read1(fp, b); if (ret < 0 && iter) iter->finished = 1; return ret; } if (iter->off == 0) return -1; for (;;) { if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET); iter->curr_off = bam_tell(fp); } ++iter->i; } if ((ret = bam_read1(fp, b)) >= 0) { iter->curr_off = bam_tell(fp); if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error break; } else if (is_overlap(iter->beg, iter->end, b)) return ret; } else break; // end of file or error } iter->finished = 1; return ret; } int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) { int ret; bam_iter_t iter; bam1_t *b; b = bam_init1(); iter = bam_iter_query(idx, tid, beg, end); while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data); bam_iter_destroy(iter); bam_destroy1(b); return (ret == -1)? 0 : ret; } pysam-0.7.7/samtools/errmod.c.pysam.c0000664000076400007650000000666112162637166017376 0ustar andreasandreas#include "pysam.h" #include #include "errmod.h" #include "ksort.h" KSORT_INIT_GENERIC(uint16_t) typedef struct __errmod_coef_t { double *fk, *beta, *lhet; } errmod_coef_t; typedef struct { double fsum[16], bsum[16]; uint32_t c[16]; } call_aux_t; static errmod_coef_t *cal_coef(double depcorr, double eta) { int k, n, q; long double sum, sum1; double *lC; errmod_coef_t *ec; ec = calloc(1, sizeof(errmod_coef_t)); // initialize ->fk ec->fk = (double*)calloc(256, sizeof(double)); ec->fk[0] = 1.0; for (n = 1; n != 256; ++n) ec->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta; // initialize ->coef ec->beta = (double*)calloc(256 * 256 * 64, sizeof(double)); lC = (double*)calloc(256 * 256, sizeof(double)); for (n = 1; n != 256; ++n) { double lgn = lgamma(n+1); for (k = 1; k <= n; ++k) lC[n<<8|k] = lgn - lgamma(k+1) - lgamma(n-k+1); } for (q = 1; q != 64; ++q) { double e = pow(10.0, -q/10.0); double le = log(e); double le1 = log(1.0 - e); for (n = 1; n <= 255; ++n) { double *beta = ec->beta + (q<<16|n<<8); sum1 = sum = 0.0; for (k = n; k >= 0; --k, sum1 = sum) { sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1); beta[k] = -10. / M_LN10 * logl(sum1 / sum); } } } // initialize ->lhet ec->lhet = (double*)calloc(256 * 256, sizeof(double)); for (n = 0; n < 256; ++n) for (k = 0; k < 256; ++k) ec->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n; free(lC); return ec; } errmod_t *errmod_init(float depcorr) { errmod_t *em; em = (errmod_t*)calloc(1, sizeof(errmod_t)); em->depcorr = depcorr; em->coef = cal_coef(depcorr, 0.03); return em; } void errmod_destroy(errmod_t *em) { if (em == 0) return; free(em->coef->lhet); free(em->coef->fk); free(em->coef->beta); free(em->coef); free(em); } // qual:6, strand:1, base:4 int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q) { call_aux_t aux; int i, j, k, w[32]; if (m > m) return -1; memset(q, 0, m * m * sizeof(float)); if (n == 0) return 0; // calculate aux.esum and aux.fsum if (n > 255) { // then sample 255 bases ks_shuffle(uint16_t, n, bases); n = 255; } ks_introsort(uint16_t, n, bases); memset(w, 0, 32 * sizeof(int)); memset(&aux, 0, sizeof(call_aux_t)); for (j = n - 1; j >= 0; --j) { // calculate esum and fsum uint16_t b = bases[j]; int q = b>>5 < 4? 4 : b>>5; if (q > 63) q = 63; k = b&0x1f; aux.fsum[k&0xf] += em->coef->fk[w[k]]; aux.bsum[k&0xf] += em->coef->fk[w[k]] * em->coef->beta[q<<16|n<<8|aux.c[k&0xf]]; ++aux.c[k&0xf]; ++w[k]; } // generate likelihood for (j = 0; j != m; ++j) { float tmp1, tmp3; int tmp2, bar_e; // homozygous for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != m; ++k) { if (k == j) continue; tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k]; } if (tmp2) { bar_e = (int)(tmp1 / tmp3 + 0.499); if (bar_e > 63) bar_e = 63; q[j*m+j] = tmp1; } // heterozygous for (k = j + 1; k < m; ++k) { int cjk = aux.c[j] + aux.c[k]; for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) { if (i == j || i == k) continue; tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i]; } if (tmp2) { bar_e = (int)(tmp1 / tmp3 + 0.499); if (bar_e > 63) bar_e = 63; q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]] + tmp1; } else q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]]; // all the bases are either j or k } for (k = 0; k != m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0; } return 0; } pysam-0.7.7/samtools/bedcov.c.pysam.c0000664000076400007650000000614112163141656017334 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include "kstring.h" #include "bgzf.h" #include "bam.h" #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) typedef struct { bamFile fp; bam_iter_t iter; int min_mapQ; } aux_t; static int read_bam(void *data, bam1_t *b) { aux_t *aux = (aux_t*)data; int ret = bam_iter_read(aux->fp, aux->iter, b); if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP; return ret; } int main_bedcov(int argc, char *argv[]) { extern void bam_init_header_hash(bam_header_t*); gzFile fp; kstring_t str; kstream_t *ks; bam_index_t **idx; bam_header_t *h = 0; aux_t **aux; int *n_plp, dret, i, n, c, min_mapQ = 0; int64_t *cnt; const bam_pileup1_t **plp; while ((c = getopt(argc, argv, "Q:")) >= 0) { switch (c) { case 'Q': min_mapQ = atoi(optarg); break; } } if (optind + 2 > argc) { fprintf(pysamerr, "Usage: samtools bedcov [...]\n"); return 1; } memset(&str, 0, sizeof(kstring_t)); n = argc - optind - 1; aux = calloc(n, sizeof(void*)); idx = calloc(n, sizeof(void*)); for (i = 0; i < n; ++i) { aux[i] = calloc(1, sizeof(aux_t)); aux[i]->min_mapQ = min_mapQ; aux[i]->fp = bam_open(argv[i+optind+1], "r"); idx[i] = bam_index_load(argv[i+optind+1]); if (aux[i]->fp == 0 || idx[i] == 0) { fprintf(pysamerr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]); return 2; } bgzf_set_cache_size(aux[i]->fp, 20); if (i == 0) h = bam_header_read(aux[0]->fp); } bam_init_header_hash(h); cnt = calloc(n, 8); fp = gzopen(argv[optind], "rb"); ks = ks_init(fp); n_plp = calloc(n, sizeof(int)); plp = calloc(n, sizeof(void*)); while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) { char *p, *q; int tid, beg, end, pos; bam_mplp_t mplp; for (p = q = str.s; *p && *p != '\t'; ++p); if (*p != '\t') goto bed_error; *p = 0; tid = bam_get_tid(h, q); *p = '\t'; if (tid < 0) goto bed_error; for (q = p = p + 1; isdigit(*p); ++p); if (*p != '\t') goto bed_error; *p = 0; beg = atoi(q); *p = '\t'; for (q = p = p + 1; isdigit(*p); ++p); if (*p == '\t' || *p == 0) { int c = *p; *p = 0; end = atoi(q); *p = c; } else goto bed_error; for (i = 0; i < n; ++i) { if (aux[i]->iter) bam_iter_destroy(aux[i]->iter); aux[i]->iter = bam_iter_query(idx[i], tid, beg, end); } mplp = bam_mplp_init(n, read_bam, (void**)aux); bam_mplp_set_maxcnt(mplp, 64000); memset(cnt, 0, 8 * n); while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) if (pos >= beg && pos < end) for (i = 0; i < n; ++i) cnt[i] += n_plp[i]; for (i = 0; i < n; ++i) { kputc('\t', &str); kputl(cnt[i], &str); } puts(str.s); bam_mplp_destroy(mplp); continue; bed_error: fprintf(pysamerr, "Errors in BED line '%s'\n", str.s); } free(n_plp); free(plp); ks_destroy(ks); gzclose(fp); free(cnt); for (i = 0; i < n; ++i) { if (aux[i]->iter) bam_iter_destroy(aux[i]->iter); bam_index_destroy(idx[i]); bam_close(aux[i]->fp); free(aux[i]); } bam_header_destroy(h); free(aux); free(idx); free(str.s); return 0; } pysam-0.7.7/samtools/sample.c.pysam.c0000664000076400007650000000567412162637166017372 0ustar andreasandreas#include "pysam.h" #include #include #include "sample.h" #include "khash.h" KHASH_MAP_INIT_STR(sm, int) bam_sample_t *bam_smpl_init(void) { bam_sample_t *s; s = calloc(1, sizeof(bam_sample_t)); s->rg2smid = kh_init(sm); s->sm2id = kh_init(sm); return s; } void bam_smpl_destroy(bam_sample_t *sm) { int i; khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (sm == 0) return; for (i = 0; i < sm->n; ++i) free(sm->smpl[i]); free(sm->smpl); for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k) if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k)); kh_destroy(sm, sm->rg2smid); kh_destroy(sm, sm->sm2id); free(sm); } static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val) { khint_t k_rg, k_sm; int ret; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; k_rg = kh_get(sm, rg2smid, key); if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID k_rg = kh_put(sm, rg2smid, strdup(key), &ret); k_sm = kh_get(sm, sm2id, val); if (k_sm == kh_end(sm2id)) { // absent if (sm->n == sm->m) { sm->m = sm->m? sm->m<<1 : 1; sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m); } sm->smpl[sm->n] = strdup(val); k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret); kh_val(sm2id, k_sm) = sm->n++; } kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm); } int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt) { const char *p = txt, *q, *r; kstring_t buf, first_sm; int n = 0; khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id; if (txt == 0) { add_pair(sm, sm2id, fn, fn); return 0; } memset(&buf, 0, sizeof(kstring_t)); memset(&first_sm, 0, sizeof(kstring_t)); while ((q = strstr(p, "@RG")) != 0) { p = q + 3; r = q = 0; if ((q = strstr(p, "\tID:")) != 0) q += 4; if ((r = strstr(p, "\tSM:")) != 0) r += 4; if (r && q) { char *u, *v; int oq, or; for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u); for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v); oq = *u; or = *v; *u = *v = '\0'; buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf); add_pair(sm, sm2id, buf.s, r); if ( !first_sm.s ) kputs(r,&first_sm); *u = oq; *v = or; } else break; p = q > r? q : r; ++n; } if (n == 0) add_pair(sm, sm2id, fn, fn); // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but // use the tag instead. else if ( n==1 && first_sm.s ) add_pair(sm,sm2id,fn,first_sm.s); if ( first_sm.s ) free(first_sm.s); // add_pair(sm, sm2id, fn, fn); free(buf.s); return 0; } int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str) { khint_t k; khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid; if (rg) { str->l = 0; kputs(fn, str); kputc('/', str); kputs(rg, str); k = kh_get(sm, rg2smid, str->s); } else k = kh_get(sm, rg2smid, fn); return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k); } pysam-0.7.7/samtools/klist.h0000664000076400007650000000662012162637166015663 0ustar andreasandreas#ifndef _LH3_KLIST_H #define _LH3_KLIST_H #include #define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f) \ typedef struct { \ size_t cnt, n, max; \ kmptype_t **buf; \ } kmp_##name##_t; \ static inline kmp_##name##_t *kmp_init_##name() { \ return calloc(1, sizeof(kmp_##name##_t)); \ } \ static inline void kmp_destroy_##name(kmp_##name##_t *mp) { \ size_t k; \ for (k = 0; k < mp->n; ++k) { \ kmpfree_f(mp->buf[k]); free(mp->buf[k]); \ } \ free(mp->buf); free(mp); \ } \ static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) { \ ++mp->cnt; \ if (mp->n == 0) return calloc(1, sizeof(kmptype_t)); \ return mp->buf[--mp->n]; \ } \ static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \ --mp->cnt; \ if (mp->n == mp->max) { \ mp->max = mp->max? mp->max<<1 : 16; \ mp->buf = realloc(mp->buf, sizeof(void*) * mp->max); \ } \ mp->buf[mp->n++] = p; \ } #define kmempool_t(name) kmp_##name##_t #define kmp_init(name) kmp_init_##name() #define kmp_destroy(name, mp) kmp_destroy_##name(mp) #define kmp_alloc(name, mp) kmp_alloc_##name(mp) #define kmp_free(name, mp, p) kmp_free_##name(mp, p) #define KLIST_INIT(name, kltype_t, kmpfree_t) \ struct __kl1_##name { \ kltype_t data; \ struct __kl1_##name *next; \ }; \ typedef struct __kl1_##name kl1_##name; \ KMEMPOOL_INIT(name, kl1_##name, kmpfree_t) \ typedef struct { \ kl1_##name *head, *tail; \ kmp_##name##_t *mp; \ size_t size; \ } kl_##name##_t; \ static inline kl_##name##_t *kl_init_##name() { \ kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t)); \ kl->mp = kmp_init(name); \ kl->head = kl->tail = kmp_alloc(name, kl->mp); \ kl->head->next = 0; \ return kl; \ } \ static inline void kl_destroy_##name(kl_##name##_t *kl) { \ kl1_##name *p; \ for (p = kl->head; p != kl->tail; p = p->next) \ kmp_free(name, kl->mp, p); \ kmp_free(name, kl->mp, p); \ kmp_destroy(name, kl->mp); \ free(kl); \ } \ static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) { \ kl1_##name *q, *p = kmp_alloc(name, kl->mp); \ q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p; \ ++kl->size; \ return &q->data; \ } \ static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \ kl1_##name *p; \ if (kl->head->next == 0) return -1; \ --kl->size; \ p = kl->head; kl->head = kl->head->next; \ if (d) *d = p->data; \ kmp_free(name, kl->mp, p); \ return 0; \ } #define kliter_t(name) kl1_##name #define klist_t(name) kl_##name##_t #define kl_val(iter) ((iter)->data) #define kl_next(iter) ((iter)->next) #define kl_begin(kl) ((kl)->head) #define kl_end(kl) ((kl)->tail) #define kl_init(name) kl_init_##name() #define kl_destroy(name, kl) kl_destroy_##name(kl) #define kl_pushp(name, kl) kl_pushp_##name(kl) #define kl_shift(name, kl, d) kl_shift_##name(kl, d) #endif pysam-0.7.7/samtools/bam_tview.c.pysam.c0000664000076400007650000002625312162637166020062 0ustar andreasandreas#include "pysam.h" #include #include "bam_tview.h" int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples) { assert(tv!=NULL); assert(fn!=NULL); tv->mrow = 24; tv->mcol = 80; tv->color_for = TV_COLOR_MAPQ; tv->is_dot = 1; tv->fp = bam_open(fn, "r"); if(tv->fp==0) { fprintf(pysamerr,"bam_open %s. %s\n", fn,fn_fa); exit(EXIT_FAILURE); } bgzf_set_cache_size(tv->fp, 8 * 1024 *1024); assert(tv->fp); tv->header = bam_header_read(tv->fp); if(tv->header==0) { fprintf(pysamerr,"Cannot read '%s'.\n", fn); exit(EXIT_FAILURE); } tv->idx = bam_index_load(fn); if (tv->idx == 0) { fprintf(pysamerr,"Cannot read index for '%s'.\n", fn); exit(EXIT_FAILURE); } tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv); if (fn_fa) tv->fai = fai_load(fn_fa); tv->bca = bcf_call_init(0.83, 13); tv->ins = 1; if ( samples ) { if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text); void *iter = tv->header->dict; const char *key, *val; int n = 0; tv->rg_hash = kh_init(kh_rg); while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) ) { if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) ) { khiter_t k = kh_get(kh_rg, tv->rg_hash, key); if ( k != kh_end(tv->rg_hash) ) continue; int ret; k = kh_put(kh_rg, tv->rg_hash, key, &ret); kh_value(tv->rg_hash, k) = val; n++; } } if ( !n ) { fprintf(pysamerr,"The sample or read group \"%s\" not present.\n", samples); exit(EXIT_FAILURE); } } return 0; } void base_tv_destroy(tview_t* tv) { bam_lplbuf_destroy(tv->lplbuf); bcf_call_destroy(tv->bca); bam_index_destroy(tv->idx); if (tv->fai) fai_destroy(tv->fai); free(tv->ref); bam_header_destroy(tv->header); bam_close(tv->fp); } int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) { extern unsigned char bam_nt16_table[256]; tview_t *tv = (tview_t*)data; int i, j, c, rb, attr, max_ins = 0; uint32_t call = 0; if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen // print referece rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N'; for (i = tv->last_pos + 1; i < pos; ++i) { if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1); c = tv->ref? tv->ref[i - tv->left_pos] : 'N'; tv->my_mvaddch(tv,1, tv->ccol++, c); } if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1); { // call consensus bcf_callret1_t bcr; int qsum[4], a1, a2, tmp; double p[3], prior = 30; bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr); for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i; for (i = 1; i < 4; ++i) // insertion sort for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j) tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp; a1 = qsum[0]&3; a2 = qsum[1]&3; p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2]; if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3; if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3; if (p[0] < p[1] && p[0] < p[2]) call = (1<my_underline(tv); c = ",ACMGRSVTWYHKDBN"[call>>16&0xf]; i = (call&0xffff)/10+1; if (i > 4) i = 4; attr |= tv->my_colorpair(tv,i); if (c == toupper(rb)) c = '.'; tv->my_attron(tv,attr); tv->my_mvaddch(tv,2, tv->ccol, c); tv->my_attroff(tv,attr); if(tv->ins) { // calculate maximum insert for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel; } } // core loop for (j = 0; j <= max_ins; ++j) { for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; int row = TV_MIN_ALNROW + p->level - tv->row_shift; if (j == 0) { if (!p->is_del) { if (tv->base_for == TV_BASE_COLOR_SPACE && (c = bam_aux_getCSi(p->b, p->qpos))) { // assume that if we found one color, we will be able to get the color error if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.'; } else { if (tv->show_name) { char *name = bam1_qname(p->b); c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos]; } else { c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.'; } } } else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*'; } else { // padding if (j > p->indel) c = '*'; else { // insertion if (tv->base_for == TV_BASE_NUCL) { if (tv->show_name) { char *name = bam1_qname(p->b); c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j]; } else { c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)]; if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.'; } } else { c = bam_aux_getCSi(p->b, p->qpos + j); if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.'; } } } if (row > TV_MIN_ALNROW && row < tv->mrow) { int x; attr = 0; if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR)) || (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv); if (tv->color_for == TV_COLOR_BASEQ) { x = bam1_qual(p->b)[p->qpos]/10 + 1; if (x > 4) x = 4; attr |= tv->my_colorpair(tv,x); } else if (tv->color_for == TV_COLOR_MAPQ) { x = p->b->core.qual/10 + 1; if (x > 4) x = 4; attr |= tv->my_colorpair(tv,x); } else if (tv->color_for == TV_COLOR_NUCL) { x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5; attr |= tv->my_colorpair(tv,x); } else if(tv->color_for == TV_COLOR_COL) { x = 0; switch(bam_aux_getCSi(p->b, p->qpos)) { case '0': x = 0; break; case '1': x = 1; break; case '2': x = 2; break; case '3': x = 3; break; case '4': x = 4; break; default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break; } x+=5; attr |= tv->my_colorpair(tv,x); } else if(tv->color_for == TV_COLOR_COLQ) { x = bam_aux_getCQi(p->b, p->qpos); if(0 == x) x = bam1_qual(p->b)[p->qpos]; x = x/10 + 1; if (x > 4) x = 4; attr |= tv->my_colorpair(tv,x); } tv->my_attron(tv,attr); tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c)); tv->my_attroff(tv,attr); } } c = j? '*' : rb; if (c == '*') { attr = tv->my_colorpair(tv,8); tv->my_attron(tv,attr); tv->my_mvaddch(tv,1, tv->ccol++, c); tv->my_attroff(tv,attr); } else tv->my_mvaddch(tv,1, tv->ccol++, c); } tv->last_pos = pos; return 0; } int tv_fetch_func(const bam1_t *b, void *data) { tview_t *tv = (tview_t*)data; if ( tv->rg_hash ) { const uint8_t *rg = bam_aux_get(b, "RG"); if ( !rg ) return 0; khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1)); if ( k == kh_end(tv->rg_hash) ) return 0; } if (tv->no_skip) { uint32_t *cigar = bam1_cigar(b); // this is cheating... int i; for (i = 0; i core.n_cigar; ++i) { if ((cigar[i]&0xf) == BAM_CREF_SKIP) cigar[i] = cigar[i]>>4<<4 | BAM_CDEL; } } bam_lplbuf_push(b, tv->lplbuf); return 0; } int base_draw_aln(tview_t *tv, int tid, int pos) { assert(tv!=NULL); // reset tv->my_clear(tv); tv->curr_tid = tid; tv->left_pos = pos; tv->last_pos = tv->left_pos - 1; tv->ccol = 0; // print ref and consensus if (tv->fai) { char *str; if (tv->ref) free(tv->ref); assert(tv->curr_tid>=0); str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1); assert(str!=NULL); sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol); tv->ref = fai_fetch(tv->fai, str, &tv->l_ref); free(str); } // draw aln bam_lplbuf_reset(tv->lplbuf); bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func); bam_lplbuf_push(0, tv->lplbuf); while (tv->ccol < tv->mcol) { int pos = tv->last_pos + 1; if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1); tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N'); ++tv->last_pos; } return 0; } static void error(const char *format, ...) { if ( !format ) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: bamtk tview [options] [ref.fasta]\n"); fprintf(pysamerr, "Options:\n"); fprintf(pysamerr, " -d display output as (H)tml or (C)urses or (T)ext \n"); fprintf(pysamerr, " -p chr:pos go directly to this position\n"); fprintf(pysamerr, " -s STR display only reads from this sample or group\n"); fprintf(pysamerr, "\n\n"); } else { va_list ap; va_start(ap, format); vfprintf(pysamerr, format, ap); va_end(ap); } exit(-1); } enum dipsay_mode {display_ncurses,display_html,display_text}; extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples); extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples); extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples); int bam_tview_main(int argc, char *argv[]) { int view_mode=display_ncurses; tview_t* tv=NULL; char *samples=NULL, *position=NULL; int c; while ((c = getopt(argc, argv, "s:p:d:")) >= 0) { switch (c) { case 's': samples=optarg; break; case 'p': position=optarg; break; case 'd': { switch(optarg[0]) { case 'H': case 'h': view_mode=display_html;break; case 'T': case 't': view_mode=display_text;break; case 'C': case 'c': view_mode=display_ncurses;break; default: view_mode=display_ncurses;break; } break; } default: error(NULL); } } if (argc==optind) error(NULL); switch(view_mode) { case display_ncurses: { tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); break; } case display_text: { tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); break; } case display_html: { tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples); break; } } if(tv==NULL) { error("cannot create view"); return EXIT_FAILURE; } if ( position ) { int _tid = -1, _beg, _end; bam_parse_region(tv->header, position, &_tid, &_beg, &_end); if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; } } tv->my_drawaln(tv, tv->curr_tid, tv->left_pos); tv->my_loop(tv); tv->my_destroy(tv); return EXIT_SUCCESS; } pysam-0.7.7/samtools/razf.h0000664000076400007650000001005112162637166015470 0ustar andreasandreas /*- * RAZF : Random Access compressed(Z) File * Version: 1.0 * Release Date: 2008-10-27 * * Copyright 2008, Jue Ruan , Heng Li * * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF * SUCH DAMAGE. */ #ifndef __RAZF_RJ_H #define __RAZF_RJ_H #include #include #include "zlib.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #if ZLIB_VERNUM < 0x1221 #define _RZ_READONLY struct _gz_header_s; typedef struct _gz_header_s _gz_header; #define gz_header _gz_header #endif #define WINDOW_BITS 15 #ifndef RZ_BLOCK_SIZE #define RZ_BLOCK_SIZE (1<mode from HEAD to TYPE after call inflateReset */ int buf_off, buf_len; int z_err, z_eof; int seekable; /* Indice where the source is seekable */ int load_index; /* set has_index to 0 in mode 'w', then index will be discarded */ } RAZF; #ifdef __cplusplus extern "C" { #endif RAZF* razf_dopen(int data_fd, const char *mode); RAZF *razf_open(const char *fn, const char *mode); int razf_write(RAZF* rz, const void *data, int size); int razf_read(RAZF* rz, void *data, int size); int64_t razf_seek(RAZF* rz, int64_t pos, int where); void razf_close(RAZF* rz); #define razf_tell(rz) ((rz)->out) RAZF* razf_open2(const char *filename, const char *mode); RAZF* razf_dopen2(int fd, const char *mode); uint64_t razf_tell2(RAZF *rz); int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bam_mate.c.pysam.c0000664000076400007650000001074312162637166017647 0ustar andreasandreas#include "pysam.h" #include #include #include #include "kstring.h" #include "bam.h" void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str) { bam1_t *swap; int i, end; uint32_t *cigar; str->l = 0; if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } end = bam_calend(&b1->core, cigar); kputw(b2->core.pos - end, str); kputc('T', str); kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) { kputw(bam_cigar_oplen(cigar[i]), str); kputc(bam_cigar_opchr(cigar[i]), str); } bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s); } // currently, this function ONLY works if each read has one hit void bam_mating_core(bamFile in, bamFile out, int remove_reads) { bam_header_t *header; bam1_t *b[2]; int curr, has_prev, pre_end = 0, cur_end; kstring_t str; str.l = str.m = 0; str.s = 0; header = bam_header_read(in); bam_header_write(out, header); b[0] = bam_init1(); b[1] = bam_init1(); curr = 0; has_prev = 0; while (bam_read1(in, b[curr]) >= 0) { bam1_t *cur = b[curr], *pre = b[1-curr]; if (cur->core.tid < 0) { if ( !remove_reads ) bam_write1(out, cur); continue; } cur_end = bam_calend(&cur->core, bam1_cigar(cur)); if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP; if (cur->core.flag & BAM_FSECONDARY) { if ( !remove_reads ) bam_write1(out, cur); continue; // skip secondary alignments } if (has_prev) { if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos; pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos; if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)) && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE { uint32_t cur5, pre5; cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos; pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos; cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5; } else cur->core.isize = pre->core.isize = 0; if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE; else cur->core.flag &= ~BAM_FMREVERSE; if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE; else pre->core.flag &= ~BAM_FMREVERSE; if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; } if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; } bam_template_cigar(pre, cur, &str); bam_write1(out, pre); bam_write1(out, cur); has_prev = 0; } else { // unpaired or singleton pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0; if (pre->core.flag & BAM_FPAIRED) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR; } bam_write1(out, pre); } } else has_prev = 1; curr = 1 - curr; pre_end = cur_end; } if (has_prev) bam_write1(out, b[1-curr]); bam_header_destroy(header); bam_destroy1(b[0]); bam_destroy1(b[1]); free(str.s); } void usage() { fprintf(pysamerr,"Usage: samtools fixmate \n"); fprintf(pysamerr,"Options:\n"); fprintf(pysamerr," -r remove unmapped reads and secondary alignments\n"); exit(1); } int bam_mating(int argc, char *argv[]) { bamFile in, out; int c, remove_reads=0; while ((c = getopt(argc, argv, "r")) >= 0) { switch (c) { case 'r': remove_reads=1; break; } } if (optind+1 >= argc) usage(); in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r"); out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w"); bam_mating_core(in, out, remove_reads); bam_close(in); bam_close(out); return 0; } pysam-0.7.7/samtools/sam_header.h0000664000076400007650000000307512162637166016626 0ustar andreasandreas#ifndef __SAM_HEADER_H__ #define __SAM_HEADER_H__ #ifdef __cplusplus extern "C" { #endif void *sam_header_parse2(const char *headerText); void *sam_header_merge(int n, const void **dicts); void sam_header_free(void *header); char *sam_header_write(const void *headerDict); // returns a newly allocated string /* // Usage example const char *key, *val; void *iter = sam_header_parse2(bam->header->text); while ( iter = sam_header_key_val(iter, "RG","ID","SM" &key,&val) ) printf("%s\t%s\n", key,val); */ void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **key, const char **value); char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n); /* // Usage example int i, j, n; const char *tags[] = {"SN","LN","UR","M5",NULL}; void *dict = sam_header_parse2(bam->header->text); char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &n); for (i=0; i #include #include "faidx.h" #include "sam.h" #define TYPE_BAM 1 #define TYPE_READ 2 bam_header_t *bam_header_dup(const bam_header_t *h0) { bam_header_t *h; int i; h = bam_header_init(); *h = *h0; h->hash = h->dict = h->rg2lib = 0; h->text = (char*)calloc(h->l_text + 1, 1); memcpy(h->text, h0->text, h->l_text); h->target_len = (uint32_t*)calloc(h->n_targets, 4); h->target_name = (char**)calloc(h->n_targets, sizeof(void*)); for (i = 0; i < h->n_targets; ++i) { h->target_len[i] = h0->target_len[i]; h->target_name[i] = strdup(h0->target_name[i]); } return h; } static void append_header_text(bam_header_t *header, char* text, int len) { int x = header->l_text + 1; int y = header->l_text + len + 1; // 1 byte null if (text == 0) return; kroundup32(x); kroundup32(y); if (x < y) header->text = (char*)realloc(header->text, y); strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here. header->l_text += len; header->text[header->l_text] = 0; } int samthreads(samfile_t *fp, int n_threads, int n_sub_blks) { if (!(fp->type&1) || (fp->type&2)) return -1; bgzf_mt(fp->x.bam, n_threads, n_sub_blks); return 0; } samfile_t *samopen(const char *fn, const char *mode, const void *aux) { samfile_t *fp; fp = (samfile_t*)calloc(1, sizeof(samfile_t)); if (strchr(mode, 'r')) { // read fp->type |= TYPE_READ; if (strchr(mode, 'b')) { // binary fp->type |= TYPE_BAM; fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r"); if (fp->x.bam == 0) goto open_err_ret; fp->header = bam_header_read(fp->x.bam); } else { // text fp->x.tamr = sam_open(fn); if (fp->x.tamr == 0) goto open_err_ret; fp->header = sam_header_read(fp->x.tamr); if (fp->header->n_targets == 0) { // no @SQ fields if (aux) { // check if aux is present bam_header_t *textheader = fp->header; fp->header = sam_header_read2((const char*)aux); if (fp->header == 0) goto open_err_ret; append_header_text(fp->header, textheader->text, textheader->l_text); bam_header_destroy(textheader); } if (fp->header->n_targets == 0 && bam_verbose >= 1) fprintf(pysamerr, "[samopen] no @SQ lines in the header.\n"); } else if (bam_verbose >= 2) fprintf(pysamerr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets); } } else if (strchr(mode, 'w')) { // write fp->header = bam_header_dup((const bam_header_t*)aux); if (strchr(mode, 'b')) { // binary char bmode[3]; int i, compress_level = -1; for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; if (mode[i]) compress_level = mode[i] - '0'; if (strchr(mode, 'u')) compress_level = 0; bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0; fp->type |= TYPE_BAM; fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode); if (fp->x.bam == 0) goto open_err_ret; bam_header_write(fp->x.bam, fp->header); } else { // text // open file fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout; if (fp->x.tamw == 0) goto open_err_ret; if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2; else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2; else fp->type |= BAM_OFDEC<<2; // write header if (strchr(mode, 'h')) { int i; bam_header_t *alt; // parse the header text alt = bam_header_init(); alt->l_text = fp->header->l_text; alt->text = fp->header->text; sam_header_parse(alt); alt->l_text = 0; alt->text = 0; // check if there are @SQ lines in the header fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL if (alt->n_targets) { // then write the header text without dumping ->target_{name,len} if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1) fprintf(pysamerr, "[samopen] inconsistent number of target sequences. Output the text header.\n"); } else { // then dump ->target_{name,len} for (i = 0; i < fp->header->n_targets; ++i) fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]); } bam_header_destroy(alt); } } } return fp; open_err_ret: free(fp); return 0; } void samclose(samfile_t *fp) { if (fp == 0) return; if (fp->header) bam_header_destroy(fp->header); if (fp->type & TYPE_BAM) bam_close(fp->x.bam); else if (fp->type & TYPE_READ) sam_close(fp->x.tamr); else fclose(fp->x.tamw); free(fp); } int samread(samfile_t *fp, bam1_t *b) { if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b); else return sam_read1(fp->x.tamr, fp->header, b); } int samwrite(samfile_t *fp, const bam1_t *b) { if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b); else { char *s = bam_format1_core(fp->header, b, fp->type>>2&3); int l = strlen(s); fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw); free(s); return l + 1; } } int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data) { bam_plbuf_t *buf; int ret; bam1_t *b; b = bam_init1(); buf = bam_plbuf_init(func, func_data); bam_plbuf_set_mask(buf, mask); while ((ret = samread(fp, b)) >= 0) bam_plbuf_push(b, buf); bam_plbuf_push(0, buf); bam_plbuf_destroy(buf); bam_destroy1(b); return 0; } char *samfaipath(const char *fn_ref) { char *fn_list = 0; if (fn_ref == 0) return 0; fn_list = calloc(strlen(fn_ref) + 5, 1); strcat(strcpy(fn_list, fn_ref), ".fai"); if (access(fn_list, R_OK) == -1) { // fn_list is unreadable if (access(fn_ref, R_OK) == -1) { fprintf(pysamerr, "[samfaipath] fail to read file %s.\n", fn_ref); } else { if (bam_verbose >= 3) fprintf(pysamerr, "[samfaipath] build FASTA index...\n"); if (fai_build(fn_ref) == -1) { fprintf(pysamerr, "[samfaipath] fail to build FASTA index.\n"); free(fn_list); fn_list = 0; } } } return fn_list; } pysam-0.7.7/samtools/kprobaln.h0000664000076400007650000000304012162637166016336 0ustar andreasandreas/* The MIT License Copyright (c) 2003-2006, 2008, 2009 by Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef LH3_KPROBALN_H_ #define LH3_KPROBALN_H_ #include typedef struct { float d, e; int bw; } kpa_par_t; #ifdef __cplusplus extern "C" { #endif int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual, const kpa_par_t *c, int *state, uint8_t *q); #ifdef __cplusplus } #endif extern kpa_par_t kpa_par_def, kpa_par_alt; #endif pysam-0.7.7/samtools/bcftools/0000775000076400007650000000000012241575073016167 5ustar andreasandreaspysam-0.7.7/samtools/bcftools/prob1.h0000660000076400007650000000266112162637166017370 0ustar andreasandreas#ifndef BCF_PROB1_H #define BCF_PROB1_H #include "bcf.h" struct __bcf_p1aux_t; typedef struct __bcf_p1aux_t bcf_p1aux_t; typedef struct { int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal() int ac; // ML alternative allele count double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var; double cil, cih; double cmp[3], p_chi2, lrt; // used by contrast2() } bcf_p1rst_t; typedef struct { double p[4]; int mq, depth, is_tested, d[4]; } anno16_t; #define MC_PTYPE_FULL 1 #define MC_PTYPE_COND2 2 #define MC_PTYPE_FLAT 3 #ifdef __cplusplus extern "C" { #endif bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy); void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta); void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta); void bcf_p1_destroy(bcf_p1aux_t *ma); void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma); int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst); int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only); int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k); void bcf_p1_dump_afs(bcf_p1aux_t *ma); int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn); int bcf_p1_set_n1(bcf_p1aux_t *b, int n1); void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bcftools/kmin.c.pysam.c0000664000076400007650000001617112162637166020654 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008, 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Hooke-Jeeves algorithm for nonlinear minimization Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM 6(6):313-314). The original algorithm was designed by Hooke and Jeeves (ACM 8:212-229). This program is further revised according to Johnson's implementation at Netlib (opt/hooke.c). Hooke-Jeeves algorithm is very simple and it works quite well on a few examples. However, it might fail to converge due to its heuristic nature. A possible improvement, as is suggested by Johnson, may be to choose a small r at the beginning to quickly approach to the minimum and a large r at later step to hit the minimum. */ #include #include #include #include "kmin.h" static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls) { int k, j = *n_calls; double ftmp; for (k = 0; k != n; ++k) { x1[k] += dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else { /* search the opposite direction */ dx[k] = 0.0 - dx[k]; x1[k] += dx[k] + dx[k]; ftmp = func(n, x1, data); ++j; if (ftmp < fx1) fx1 = ftmp; else x1[k] -= dx[k]; /* back to the original x[k] */ } } *n_calls = j; return fx1; /* here: fx1=f(n,x1) */ } double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls) { double fx, fx1, *x1, *dx, radius; int k, n_calls = 0; x1 = (double*)calloc(n, sizeof(double)); dx = (double*)calloc(n, sizeof(double)); for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */ dx[k] = fabs(x[k]) * r; if (dx[k] == 0) dx[k] = r; } radius = r; fx1 = fx = func(n, x, data); ++n_calls; for (;;) { memcpy(x1, x, n * sizeof(double)); /* x1 = x */ fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls); while (fx1 < fx) { for (k = 0; k != n; ++k) { double t = x[k]; dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]); x[k] = x1[k]; x1[k] = x1[k] + x1[k] - t; } fx = fx1; if (n_calls >= max_calls) break; fx1 = func(n, x1, data); ++n_calls; fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls); if (fx1 >= fx) break; for (k = 0; k != n; ++k) if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break; if (k == n) break; } if (radius >= eps) { if (n_calls >= max_calls) break; radius *= r; for (k = 0; k != n; ++k) dx[k] *= r; } else break; /* converge */ } free(x1); free(dx); return fx1; } // I copied this function somewhere several years ago with some of my modifications, but I forgot the source. double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin) { double bound, u, r, q, fu, tmp, fa, fb, fc, c; const double gold1 = 1.6180339887; const double gold2 = 0.3819660113; const double tiny = 1e-20; const int max_iter = 100; double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw; int iter; fa = func(a, data); fb = func(b, data); if (fb > fa) { // swap, such that f(a) > f(b) tmp = a; a = b; b = tmp; tmp = fa; fa = fb; fb = tmp; } c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation while (fb > fc) { bound = b + 100.0 * (c - b); // the farthest point where we want to go r = (b - a) * (fb - fc); q = (b - c) * (fb - fa); if (fabs(q - r) < tiny) { // avoid 0 denominator tmp = q > r? tiny : 0.0 - tiny; } else tmp = q - r; u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c fu = func(u, data); if (fu < fc) { // (b,u,c) bracket the minimum a = b; b = u; fa = fb; fb = fu; break; } else if (fu > fb) { // (a,b,u) bracket the minimum c = u; fc = fu; break; } u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation } else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound fu = func(u, data); if (fu < fc) { // fb > fc > fu b = c; c = u; u = c + gold1 * (c - b); fb = fc; fc = fu; fu = func(u, data); } else { // (b,c,u) bracket the minimum a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; break; } } else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound u = bound; fu = func(u, data); } else { // u goes the other way around, use golden section extrapolation u = c + gold1 * (c - b); fu = func(u, data); } a = b; b = c; c = u; fa = fb; fb = fc; fc = fu; } if (a > c) u = a, a = c, c = u; // swap // now, afb and fb tol1) { // related to parabolic interpolation r = (b - w) * (fb - fv); q = (b - v) * (fb - fw); p = (b - v) * q - (b - w) * r; q = 2.0 * (q - r); if (q > 0.0) p = 0.0 - p; else q = 0.0 - q; eold = e; e = d; if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) { d = gold2 * (e = (b >= mid ? a - b : c - b)); } else { d = p / q; u = b + d; // actual parabolic interpolation happens here if (u - a < tol2 || c - u < tol2) d = (mid > b)? tol1 : 0.0 - tol1; } } else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1); fu = func(u, data); if (fu <= fb) { // u is the minimum point so far if (u >= b) a = b; else c = b; v = w; w = b; b = u; fv = fw; fw = fb; fb = fu; } else { // adjust (a,c) and (u,v,w) if (u < b) a = u; else c = u; if (fu <= fw || w == b) { v = w; w = u; fv = fw; fw = fu; } else if (fu <= fv || v == b || v == w) { v = u; fv = fu; } } } *xmin = b; return fb; } pysam-0.7.7/samtools/bcftools/kmin.h0000660000076400007650000000312312162637166017275 0ustar andreasandreas/* Copyright (c) 2008, 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KMIN_H #define KMIN_H #define KMIN_RADIUS 0.5 #define KMIN_EPS 1e-7 #define KMIN_MAXCALL 50000 typedef double (*kmin_f)(int, double*, void*); typedef double (*kmin1_f)(double, void*); #ifdef __cplusplus extern "C" { #endif double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls); double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bcftools/bcfutils.c.pysam.c0000664000076400007650000003173112162637166021530 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bcf.h" #include "kstring.h" #include "khash.h" KHASH_MAP_INIT_STR(str2id, int) #ifdef _WIN32 #define srand48(x) srand(x) #define drand48() ((double)rand() / RAND_MAX) #endif // FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated... void *bcf_build_refhash(bcf_hdr_t *h) { khash_t(str2id) *hash; int i, ret; hash = kh_init(str2id); for (i = 0; i < h->n_ref; ++i) { khint_t k; k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret kh_val(hash, k) = i; } return hash; } void *bcf_str2id_init() { return kh_init(str2id); } void bcf_str2id_destroy(void *_hash) { khash_t(str2id) *hash = (khash_t(str2id)*)_hash; if (hash) kh_destroy(str2id, hash); // Note that strings are not freed. } void bcf_str2id_thorough_destroy(void *_hash) { khash_t(str2id) *hash = (khash_t(str2id)*)_hash; khint_t k; if (hash == 0) return; for (k = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_destroy(str2id, hash); } int bcf_str2id(void *_hash, const char *str) { khash_t(str2id) *hash = (khash_t(str2id)*)_hash; khint_t k; if (!hash) return -1; k = kh_get(str2id, hash, str); return k == kh_end(hash)? -1 : kh_val(hash, k); } int bcf_str2id_add(void *_hash, const char *str) { khint_t k; int ret; khash_t(str2id) *hash = (khash_t(str2id)*)_hash; if (!hash) return -1; k = kh_put(str2id, hash, str, &ret); if (ret == 0) return kh_val(hash, k); kh_val(hash, k) = kh_size(hash) - 1; return kh_val(hash, k); } void bcf_fit_alt(bcf1_t *b, int mask) { mask |= 1; // REF must be always present int i,j,nals=0; for (i=0; in_alleles <= nals ) return; // update ALT, in principle any of the alleles can be removed char *p; if ( nals>1 ) { char *dst, *src; int n=0, nalts=nals-1; for (src=dst=p=b->alt, i=1; *p; p++) { if ( *p!=',' ) continue; if ( mask&1<=nalts ) { *dst=0; break; } src = p+1; } if ( nalt, *p = '\0'; p++; memmove(p, b->flt, b->str + b->l_str - b->flt); b->l_str -= b->flt - p; // update PL and GT int ipl=-1, igt=-1; for (i = 0; i < b->n_gi; ++i) { bcf_ginfo_t *g = b->gi + i; if (g->fmt == bcf_str2int("PL", 2)) ipl = i; if (g->fmt == bcf_str2int("GT", 2)) igt = i; } // .. create mapping between old and new indexes int npl = nals * (nals+1) / 2; int *map = malloc(sizeof(int)*(npl>b->n_alleles ? npl : b->n_alleles)); int kori=0,knew=0; for (i=0; in_alleles; i++) { for (j=0; j<=i; j++) { int skip=0; if ( i && !(mask&1<n_smpl; for (i = 0; i < b->n_gi; ++i) { bcf_ginfo_t *g = b->gi + i; if (g->fmt == bcf_str2int("PL", 2)) { g->len = npl; uint8_t *d = (uint8_t*)g->data; int ismpl, npl_ori = b->n_alleles * (b->n_alleles + 1) / 2; for (knew=ismpl=0; ismpln_alleles; i++) map[i] = mask&1<gi[igt].data)[i]; int a1 = (gt>>3)&7; int a2 = gt&7; assert( map[a1]>=0 && map[a2]>=0 ); ((uint8_t*)b->gi[igt].data)[i] = ((1<<7|1<<6)>) | map[a1]<<3 | map[a2]; } free(map); b->n_alleles = nals; bcf_sync(b); } int bcf_shrink_alt(bcf1_t *b, int n) { char *p; int i, j, k, n_smpl = b->n_smpl; if (b->n_alleles <= n) return -1; // update ALT if (n > 1) { for (p = b->alt, k = 1; *p; ++p) if (*p == ',' && ++k == n) break; *p = '\0'; } else p = b->alt, *p = '\0'; ++p; memmove(p, b->flt, b->str + b->l_str - b->flt); b->l_str -= b->flt - p; // update PL for (i = 0; i < b->n_gi; ++i) { bcf_ginfo_t *g = b->gi + i; if (g->fmt == bcf_str2int("PL", 2)) { int l, x = b->n_alleles * (b->n_alleles + 1) / 2; uint8_t *d = (uint8_t*)g->data; g->len = n * (n + 1) / 2; for (l = k = 0; l < n_smpl; ++l) { uint8_t *dl = d + l * x; for (j = 0; j < g->len; ++j) d[k++] = dl[j]; } } // FIXME: to add GL } b->n_alleles = n; bcf_sync(b); return 0; } int bcf_gl2pl(bcf1_t *b) { char *p; int i, n_smpl = b->n_smpl; bcf_ginfo_t *g; float *d0; uint8_t *d1; if (strstr(b->fmt, "PL")) return -1; if ((p = strstr(b->fmt, "GL")) == 0) return -1; *p = 'P'; for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("GL", 2)) break; g = b->gi + i; g->fmt = bcf_str2int("PL", 2); g->len /= 4; // 4 == sizeof(float) d0 = (float*)g->data; d1 = (uint8_t*)g->data; for (i = 0; i < n_smpl * g->len; ++i) { int x = (int)(-10. * d0[i] + .499); if (x > 255) x = 255; if (x < 0) x = 0; d1[i] = x; } return 0; } /* FIXME: this function will fail given AB:GTX:GT. BCFtools never * produces such FMT, but others may do. */ int bcf_fix_gt(bcf1_t *b) { char *s; int i; uint32_t tmp; bcf_ginfo_t gt; // check the presence of the GT FMT if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first assert(s[3] == '\0' || s[3] == ':'); // :GTX in fact tmp = bcf_str2int("GT", 2); for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == tmp) break; if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug... gt = b->gi[i]; // move GT to the first for (; i > 0; --i) b->gi[i] = b->gi[i-1]; b->gi[0] = gt; if ( s[3]==0 ) memmove(b->fmt + 3, b->fmt, s - b->fmt); // :GT else memmove(b->fmt + 3, b->fmt, s - b->fmt + 1); // :GT: b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; return 0; } int bcf_fix_pl(bcf1_t *b) { int i; uint32_t tmp; uint8_t *PL, *swap; bcf_ginfo_t *gi; // pinpoint PL tmp = bcf_str2int("PL", 2); for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == tmp) break; if (i == b->n_gi) return 0; // prepare gi = b->gi + i; PL = (uint8_t*)gi->data; swap = alloca(gi->len); // loop through individuals for (i = 0; i < b->n_smpl; ++i) { int k, l, x; uint8_t *PLi = PL + i * gi->len; memcpy(swap, PLi, gi->len); for (k = x = 0; k < b->n_alleles; ++k) for (l = k; l < b->n_alleles; ++l) PLi[l*(l+1)/2 + k] = swap[x++]; } return 0; } int bcf_smpl_covered(const bcf1_t *b) { int i, j, n = 0; uint32_t tmp; bcf_ginfo_t *gi; // pinpoint PL tmp = bcf_str2int("PL", 2); for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == tmp) break; if (i == b->n_gi) return 0; // count how many samples having PL!=[0..0] gi = b->gi + i; for (i = 0; i < b->n_smpl; ++i) { uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len; for (j = 0; j < gi->len; ++j) if (PLi[j]) break; if (j < gi->len) ++n; } return n; } static void *locate_field(const bcf1_t *b, const char *fmt, int l) { int i; uint32_t tmp; tmp = bcf_str2int(fmt, l); for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == tmp) break; return i == b->n_gi? 0 : b->gi[i].data; } int bcf_anno_max(bcf1_t *b) { int k, max_gq, max_sp, n_het; kstring_t str; uint8_t *gt, *gq; int32_t *sp; max_gq = max_sp = n_het = 0; gt = locate_field(b, "GT", 2); if (gt == 0) return -1; gq = locate_field(b, "GQ", 2); sp = locate_field(b, "SP", 2); if (sp) for (k = 0; k < b->n_smpl; ++k) if (gt[k]&0x3f) max_sp = max_sp > (int)sp[k]? max_sp : sp[k]; if (gq) for (k = 0; k < b->n_smpl; ++k) if (gt[k]&0x3f) max_gq = max_gq > (int)gq[k]? max_gq : gq[k]; for (k = 0; k < b->n_smpl; ++k) { int a1, a2; a1 = gt[k]&7; a2 = gt[k]>>3&7; if ((!a1 && a2) || (!a2 && a1)) { // a het if (gq == 0) ++n_het; else if (gq[k] >= 20) ++n_het; } } if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499); if (max_sp < 0) max_sp = 0; memset(&str, 0, sizeof(kstring_t)); if (*b->info) kputc(';', &str); ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq); bcf_append_info(b, str.s, str.l); free(str.s); return 0; } // FIXME: only data are shuffled; the header is NOT int bcf_shuffle(bcf1_t *b, int seed) { int i, j, *a; if (seed > 0) srand48(seed); a = malloc(b->n_smpl * sizeof(int)); for (i = 0; i < b->n_smpl; ++i) a[i] = i; for (i = b->n_smpl; i > 1; --i) { int tmp; j = (int)(drand48() * i); tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; } for (j = 0; j < b->n_gi; ++j) { bcf_ginfo_t *gi = b->gi + j; uint8_t *swap, *data = (uint8_t*)gi->data; swap = malloc(gi->len * b->n_smpl); for (i = 0; i < b->n_smpl; ++i) memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len); free(gi->data); gi->data = swap; } free(a); return 0; } bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list) { int i, ret, j; khint_t k; bcf_hdr_t *h; khash_t(str2id) *hash; kstring_t s; s.l = s.m = 0; s.s = 0; hash = kh_init(str2id); for (i = 0; i < h0->n_smpl; ++i) { k = kh_put(str2id, hash, h0->sns[i], &ret); kh_val(hash, k) = i; } for (i = j = 0; i < n; ++i) { k = kh_get(str2id, hash, samples[i]); if (k != kh_end(hash)) { list[j++] = kh_val(hash, k); kputs(samples[i], &s); kputc('\0', &s); } } if (j < n) { fprintf(pysamerr, "<%s> %d samples in the list but not in BCF.", __func__, n - j); exit(1); } kh_destroy(str2id, hash); h = calloc(1, sizeof(bcf_hdr_t)); *h = *h0; h->ns = 0; h->sns = 0; h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm); h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt); h->l_smpl = s.l; h->sname = s.s; bcf_hdr_sync(h); return h; } int bcf_subsam(int n_smpl, int *list, bcf1_t *b) { int i, j; for (j = 0; j < b->n_gi; ++j) { bcf_ginfo_t *gi = b->gi + j; uint8_t *swap; swap = malloc(gi->len * b->n_smpl); for (i = 0; i < n_smpl; ++i) memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len); free(gi->data); gi->data = swap; } b->n_smpl = n_smpl; return 0; } static int8_t nt4_table[128] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4 }; int bcf_gl10(const bcf1_t *b, uint8_t *gl) { int a[4], k, l, map[4], k1, j, i; const bcf_ginfo_t *PL; char *s; if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL PL = b->gi + i; a[0] = nt4_table[(int)b->ref[0]]; if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T a[1] = a[2] = a[3] = -2; // -1 has a special meaning if (b->alt[0] == 0) return -1; // no alternate allele map[0] = map[1] = map[2] = map[3] = -2; map[a[0]] = 0; for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) { if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base a[k+1] = nt4_table[(int)*s]; if (a[k+1] >= 0) map[a[k+1]] = k+1; else k1 = k + 1; if (s[1] == 0) break; // the end of the ALT string } for (k = 0; k < 4; ++k) if (map[k] < 0) map[k] = k1; for (i = 0; i < b->n_smpl; ++i) { const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual uint8_t *g = gl + 10 * i; for (k = j = 0; k < 4; ++k) { for (l = k; l < 4; ++l) { int t, x = map[k], y = map[l]; if (x > y) t = x, x = y, y = t; // make sure x is the smaller g[j++] = p[y * (y+1) / 2 + x]; } } } return 0; } int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl) { int k, l, j, i; const bcf_ginfo_t *PL; if (b->alt[0] == 0) return -1; // no alternate allele for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL PL = b->gi + i; for (i = 0; i < b->n_smpl; ++i) { const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual uint8_t *g = gl + 10 * i; for (k = j = 0; k < 4; ++k) { for (l = k; l < 4; ++l) { int t, x = k, y = l; if (x > y) t = x, x = y, y = t; // make sure x is the smaller x = y * (y+1) / 2 + x; g[j++] = x < PL->len? p[x] : 255; } } } return 0; } pysam-0.7.7/samtools/bcftools/kfunc.c.pysam.c0000664000076400007650000001156412162637166021025 0ustar andreasandreas#include "pysam.h" #include /* Log gamma function * \log{\Gamma(z)} * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245 */ double kf_lgamma(double z) { double x = 0; x += 0.1659470187408462e-06 / (z+7); x += 0.9934937113930748e-05 / (z+6); x -= 0.1385710331296526 / (z+5); x += 12.50734324009056 / (z+4); x -= 176.6150291498386 / (z+3); x += 771.3234287757674 / (z+2); x -= 1259.139216722289 / (z+1); x += 676.5203681218835 / z; x += 0.9999999999995183; return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5); } /* complementary error function * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66 */ double kf_erfc(double x) { const double p0 = 220.2068679123761; const double p1 = 221.2135961699311; const double p2 = 112.0792914978709; const double p3 = 33.912866078383; const double p4 = 6.37396220353165; const double p5 = .7003830644436881; const double p6 = .03526249659989109; const double q0 = 440.4137358247522; const double q1 = 793.8265125199484; const double q2 = 637.3336333788311; const double q3 = 296.5642487796737; const double q4 = 86.78073220294608; const double q5 = 16.06417757920695; const double q6 = 1.755667163182642; const double q7 = .08838834764831844; double expntl, z, p; z = fabs(x) * M_SQRT2; if (z > 37.) return x > 0.? 0. : 2.; expntl = exp(z * z * - .5); if (z < 10. / M_SQRT2) // for small z p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0) / (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0); else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65))))); return x > 0.? 2. * p : 2. * (1. - p); } /* The following computes regularized incomplete gamma functions. * Formulas are taken from Wiki, with additional input from Numerical * Recipes in C (for modified Lentz's algorithm) and AS245 * (http://lib.stat.cmu.edu/apstat/245). * * A good online calculator is available at: * * http://www.danielsoper.com/statcalc/calc23.aspx * * It calculates upper incomplete gamma function, which equals * kf_gammaq(s,z)*tgamma(s). */ #define KF_GAMMA_EPS 1e-14 #define KF_TINY 1e-290 // regularized lower incomplete gamma function, by series expansion static double _kf_gammap(double s, double z) { double sum, x; int k; for (k = 1, sum = x = 1.; k < 100; ++k) { sum += (x *= z / (s + k)); if (x / sum < KF_GAMMA_EPS) break; } return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum)); } // regularized upper incomplete gamma function, by continued fraction static double _kf_gammaq(double s, double z) { int j; double C, D, f; f = 1. + z - s; C = f; D = 0.; // Modified Lentz's algorithm for computing continued fraction // See Numerical Recipes in C, 2nd edition, section 5.2 for (j = 1; j < 100; ++j) { double a = j * (s - j), b = (j<<1) + 1 + z - s, d; D = b + a * D; if (D < KF_TINY) D = KF_TINY; C = b + a / C; if (C < KF_TINY) C = KF_TINY; D = 1. / D; d = C * D; f *= d; if (fabs(d - 1.) < KF_GAMMA_EPS) break; } return exp(s * log(z) - z - kf_lgamma(s) - log(f)); } double kf_gammap(double s, double z) { return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z); } double kf_gammaq(double s, double z) { return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z); } /* Regularized incomplete beta function. The method is taken from * Numerical Recipe in C, 2nd edition, section 6.4. The following web * page calculates the incomplete beta function, which equals * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b): * * http://www.danielsoper.com/statcalc/calc36.aspx */ static double kf_betai_aux(double a, double b, double x) { double C, D, f; int j; if (x == 0.) return 0.; if (x == 1.) return 1.; f = 1.; C = f; D = 0.; // Modified Lentz's algorithm for computing continued fraction for (j = 1; j < 200; ++j) { double aa, d; int m = j>>1; aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1)) : m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m)); D = 1. + aa * D; if (D < KF_TINY) D = KF_TINY; C = 1. + aa / C; if (C < KF_TINY) C = KF_TINY; D = 1. / D; d = C * D; f *= d; if (fabs(d - 1.) < KF_GAMMA_EPS) break; } return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f; } double kf_betai(double a, double b, double x) { return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x); } #ifdef KF_MAIN #include int main(int argc, char *argv[]) { double x = 5.5, y = 3; double a, b; printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x)); printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y)); a = 2; b = 2; x = 0.5; printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b))); return 0; } #endif pysam-0.7.7/samtools/bcftools/index.c.pysam.c0000664000076400007650000002014612162637166021022 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bam_endian.h" #include "kstring.h" #include "bcf.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #define TAD_LIDX_SHIFT 13 typedef struct { int32_t n, m; uint64_t *offset; } bcf_lidx_t; struct __bcf_idx_t { int32_t n; bcf_lidx_t *index2; }; /************ * indexing * ************/ static inline void insert_offset2(bcf_lidx_t *index2, int _beg, int _end, uint64_t offset) { int i, beg, end; beg = _beg >> TAD_LIDX_SHIFT; end = (_end - 1) >> TAD_LIDX_SHIFT; if (index2->m < end + 1) { int old_m = index2->m; index2->m = end + 1; kroundup32(index2->m); index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); } if (beg == end) { if (index2->offset[beg] == 0) index2->offset[beg] = offset; } else { for (i = beg; i <= end; ++i) if (index2->offset[i] == 0) index2->offset[i] = offset; } if (index2->n < end + 1) index2->n = end + 1; } bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h) { bcf_idx_t *idx; int32_t last_coor, last_tid; uint64_t last_off; kstring_t *str; BGZF *fp = bp->fp; bcf1_t *b; int ret; b = calloc(1, sizeof(bcf1_t)); str = calloc(1, sizeof(kstring_t)); idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t)); idx->n = h->n_ref; idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t)); last_tid = 0xffffffffu; last_off = bgzf_tell(fp); last_coor = 0xffffffffu; while ((ret = bcf_read(bp, h, b)) > 0) { int end, tmp; if (last_tid != b->tid) { // change of chromosomes last_tid = b->tid; } else if (last_coor > b->pos) { fprintf(pysamerr, "[bcf_idx_core] the input is out of order\n"); free(str->s); free(str); free(idx); bcf_destroy(b); return 0; } tmp = strlen(b->ref); end = b->pos + (tmp > 0? tmp : 1); insert_offset2(&idx->index2[b->tid], b->pos, end, last_off); last_off = bgzf_tell(fp); last_coor = b->pos; } free(str->s); free(str); bcf_destroy(b); return idx; } void bcf_idx_destroy(bcf_idx_t *idx) { int i; if (idx == 0) return; for (i = 0; i < idx->n; ++i) free(idx->index2[i].offset); free(idx->index2); free(idx); } /****************** * index file I/O * ******************/ void bcf_idx_save(const bcf_idx_t *idx, BGZF *fp) { int32_t i, ti_is_be; ti_is_be = bam_is_big_endian(); bgzf_write(fp, "BCI\4", 4); if (ti_is_be) { uint32_t x = idx->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &idx->n, 4); for (i = 0; i < idx->n; ++i) { bcf_lidx_t *index2 = idx->index2 + i; // write linear index (index2) if (ti_is_be) { int x = index2->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4); } else bgzf_write(fp, &index2->n, 4); if (ti_is_be) { // big endian int x; for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); bgzf_write(fp, index2->offset, 8 * index2->n); for (x = 0; (int)x < index2->n; ++x) bam_swap_endian_8p(&index2->offset[x]); } else bgzf_write(fp, index2->offset, 8 * index2->n); } } static bcf_idx_t *bcf_idx_load_core(BGZF *fp) { int i, ti_is_be; char magic[4]; bcf_idx_t *idx; ti_is_be = bam_is_big_endian(); if (fp == 0) { fprintf(pysamerr, "[%s] fail to load index.\n", __func__); return 0; } bgzf_read(fp, magic, 4); if (strncmp(magic, "BCI\4", 4)) { fprintf(pysamerr, "[%s] wrong magic number.\n", __func__); return 0; } idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t)); bgzf_read(fp, &idx->n, 4); if (ti_is_be) bam_swap_endian_4p(&idx->n); idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t)); for (i = 0; i < idx->n; ++i) { bcf_lidx_t *index2 = idx->index2 + i; int j; bgzf_read(fp, &index2->n, 4); if (ti_is_be) bam_swap_endian_4p(&index2->n); index2->m = index2->n; index2->offset = (uint64_t*)calloc(index2->m, 8); bgzf_read(fp, index2->offset, index2->n * 8); if (ti_is_be) for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); } return idx; } bcf_idx_t *bcf_idx_load_local(const char *fnidx) { BGZF *fp; fp = bgzf_open(fnidx, "r"); if (fp) { bcf_idx_t *idx = bcf_idx_load_core(fp); bgzf_close(fp); return idx; } else return 0; } #ifdef _USE_KNETFILE static void download_from_remote(const char *url) { const int buf_size = 1 * 1024 * 1024; char *fn; FILE *fp; uint8_t *buf; knetFile *fp_remote; int l; if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; l = strlen(url); for (fn = (char*)url + l - 1; fn >= url; --fn) if (*fn == '/') break; ++fn; // fn now points to the file name fp_remote = knet_open(url, "r"); if (fp_remote == 0) { fprintf(pysamerr, "[download_from_remote] fail to open remote file.\n"); return; } if ((fp = fopen(fn, "w")) == 0) { fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory.\n"); knet_close(fp_remote); return; } buf = (uint8_t*)calloc(buf_size, 1); while ((l = knet_read(fp_remote, buf, buf_size)) != 0) fwrite(buf, 1, l, fp); free(buf); fclose(fp); knet_close(fp_remote); } #else static void download_from_remote(const char *url) { return; } #endif static char *get_local_version(const char *fn) { struct stat sbuf; char *fnidx = (char*)calloc(strlen(fn) + 5, 1); strcat(strcpy(fnidx, fn), ".bci"); if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) { char *p, *url; int l = strlen(fnidx); for (p = fnidx + l - 1; p >= fnidx; --p) if (*p == '/') break; url = fnidx; fnidx = strdup(p + 1); if (stat(fnidx, &sbuf) == 0) { free(url); return fnidx; } fprintf(pysamerr, "[%s] downloading the index file...\n", __func__); download_from_remote(url); free(url); } if (stat(fnidx, &sbuf) == 0) return fnidx; free(fnidx); return 0; } bcf_idx_t *bcf_idx_load(const char *fn) { bcf_idx_t *idx; char *fname = get_local_version(fn); if (fname == 0) return 0; idx = bcf_idx_load_local(fname); free(fname); return idx; } int bcf_idx_build2(const char *fn, const char *_fnidx) { char *fnidx; BGZF *fpidx; bcf_t *bp; bcf_idx_t *idx; bcf_hdr_t *h; if ((bp = bcf_open(fn, "r")) == 0) { fprintf(pysamerr, "[bcf_idx_build2] fail to open the BAM file.\n"); return -1; } h = bcf_hdr_read(bp); idx = bcf_idx_core(bp, h); bcf_close(bp); if (_fnidx == 0) { fnidx = (char*)calloc(strlen(fn) + 5, 1); strcpy(fnidx, fn); strcat(fnidx, ".bci"); } else fnidx = strdup(_fnidx); fpidx = bgzf_open(fnidx, "w"); if (fpidx == 0) { fprintf(pysamerr, "[bcf_idx_build2] fail to create the index file.\n"); free(fnidx); bcf_idx_destroy(idx); return -1; } bcf_idx_save(idx, fpidx); bcf_idx_destroy(idx); bgzf_close(fpidx); free(fnidx); return 0; } int bcf_idx_build(const char *fn) { return bcf_idx_build2(fn, 0); } /******************************************** * parse a region in the format chr:beg-end * ********************************************/ int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end) { char *s, *p; int i, l, k; l = strlen(str); p = s = (char*)malloc(l+1); /* squeeze out "," */ for (i = k = 0; i != l; ++i) if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i]; s[k] = 0; for (i = 0; i != k; ++i) if (s[i] == ':') break; s[i] = 0; if ((*tid = bcf_str2id(str2id, s)) < 0) { free(s); return -1; } if (i == k) { /* dump the whole sequence */ *begin = 0; *end = 1<<29; free(s); return 0; } for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break; *begin = atoi(p); if (i < k) { p = s + i + 1; *end = atoi(p); } else *end = 1<<29; if (*begin > 0) --*begin; free(s); if (*begin > *end) return -1; return 0; } /******************************* * retrieve a specified region * *******************************/ uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg) { uint64_t min_off, *offset; int i; if (beg < 0) beg = 0; offset = idx->index2[tid].offset; for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i); min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i]; return min_off; } int bcf_main_index(int argc, char *argv[]) { if (argc == 1) { fprintf(pysamerr, "Usage: bcftools index \n"); return 1; } bcf_idx_build(argv[1]); return 0; } pysam-0.7.7/samtools/bcftools/bcf.c.pysam.c0000664000076400007650000002453712162637166020455 0ustar andreasandreas#include "pysam.h" #include #include #include #include "kstring.h" #include "bcf.h" bcf_t *bcf_open(const char *fn, const char *mode) { bcf_t *b; b = calloc(1, sizeof(bcf_t)); if (strchr(mode, 'w')) { b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode); } else { b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode); } return b; } int bcf_close(bcf_t *b) { int ret; if (b == 0) return 0; ret = bgzf_close(b->fp); free(b); return ret; } int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h) { if (b == 0 || h == 0) return -1; bgzf_write(b->fp, "BCF\4", 4); bgzf_write(b->fp, &h->l_nm, 4); bgzf_write(b->fp, h->name, h->l_nm); bgzf_write(b->fp, &h->l_smpl, 4); bgzf_write(b->fp, h->sname, h->l_smpl); bgzf_write(b->fp, &h->l_txt, 4); bgzf_write(b->fp, h->txt, h->l_txt); bgzf_flush(b->fp); return 16 + h->l_nm + h->l_smpl + h->l_txt; } bcf_hdr_t *bcf_hdr_read(bcf_t *b) { uint8_t magic[4]; bcf_hdr_t *h; if (b == 0) return 0; h = calloc(1, sizeof(bcf_hdr_t)); bgzf_read(b->fp, magic, 4); bgzf_read(b->fp, &h->l_nm, 4); h->name = malloc(h->l_nm); bgzf_read(b->fp, h->name, h->l_nm); bgzf_read(b->fp, &h->l_smpl, 4); h->sname = malloc(h->l_smpl); bgzf_read(b->fp, h->sname, h->l_smpl); bgzf_read(b->fp, &h->l_txt, 4); h->txt = malloc(h->l_txt); bgzf_read(b->fp, h->txt, h->l_txt); bcf_hdr_sync(h); return h; } void bcf_hdr_destroy(bcf_hdr_t *h) { if (h == 0) return; free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns); free(h); } static inline char **cnt_null(int l, char *str, int *_n) { int n = 0; char *p, **list; *_n = 0; if (l == 0 || str == 0) return 0; for (p = str; p != str + l; ++p) if (*p == 0) ++n; *_n = n; list = calloc(n, sizeof(void*)); list[0] = str; for (p = str, n = 1; p < str + l - 1; ++p) if (*p == 0) list[n++] = p + 1; return list; } int bcf_hdr_sync(bcf_hdr_t *b) { if (b == 0) return -1; if (b->ns) free(b->ns); if (b->sns) free(b->sns); if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref); else b->ns = 0, b->n_ref = 0; b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl); return 0; } int bcf_sync(bcf1_t *b) { char *p, *tmp[5]; int i, n, n_smpl = b->n_smpl; ks_tokaux_t aux; // set ref, alt, flt, info, fmt b->ref = b->alt = b->flt = b->info = b->fmt = 0; for (p = b->str, n = 0; p < b->str + b->l_str; ++p) { if (*p == 0 && p+1 != b->str + b->l_str) { if (n == 5) { ++n; break; } else tmp[n++] = p + 1; } } if (n != 5) { fprintf(pysamerr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos); return -1; } b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4]; // set n_alleles if (*b->alt == 0) b->n_alleles = 1; else { for (p = b->alt, n = 1; *p; ++p) if (*p == ',') ++n; b->n_alleles = n + 1; } // set n_gi and gi[i].fmt for (p = b->fmt, n = 1; *p; ++p) if (*p == ':') ++n; if (n > b->m_gi) { int old_m = b->m_gi; b->m_gi = n; kroundup32(b->m_gi); b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t)); memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t)); } b->n_gi = n; for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux)) b->gi[n++].fmt = bcf_str2int(p, aux.p - p); // set gi[i].len for (i = 0; i < b->n_gi; ++i) { if (b->gi[i].fmt == bcf_str2int("PL", 2)) { b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2; } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) { b->gi[i].len = 2; } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) { b->gi[i].len = 1; } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) { b->gi[i].len = 4; } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) { b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4; } b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len); } return 0; } int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b) { int i, l = 0; if (b == 0) return -1; bgzf_write(bp->fp, &b->tid, 4); bgzf_write(bp->fp, &b->pos, 4); bgzf_write(bp->fp, &b->qual, 4); bgzf_write(bp->fp, &b->l_str, 4); bgzf_write(bp->fp, b->str, b->l_str); l = 12 + b->l_str; for (i = 0; i < b->n_gi; ++i) { bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl); l += b->gi[i].len * h->n_smpl; } return l; } int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b) { int i, l = 0; if (b == 0) return -1; if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1; b->n_smpl = h->n_smpl; bgzf_read(bp->fp, &b->pos, 4); bgzf_read(bp->fp, &b->qual, 4); bgzf_read(bp->fp, &b->l_str, 4); if (b->l_str > b->m_str) { b->m_str = b->l_str; kroundup32(b->m_str); b->str = realloc(b->str, b->m_str); } bgzf_read(bp->fp, b->str, b->l_str); l = 12 + b->l_str; if (bcf_sync(b) < 0) return -2; for (i = 0; i < b->n_gi; ++i) { bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl); l += b->gi[i].len * h->n_smpl; } return l; } int bcf_destroy(bcf1_t *b) { int i; if (b == 0) return -1; free(b->str); for (i = 0; i < b->m_gi; ++i) free(b->gi[i].data); free(b->gi); free(b); return 0; } static inline void fmt_str(const char *p, kstring_t *s) { if (*p == 0) kputc('.', s); else kputs(p, s); } void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s) { int i, j, x; s->l = 0; if (h->n_ref) kputs(h->ns[b->tid], s); else kputw(b->tid, s); kputc('\t', s); kputw(b->pos + 1, s); kputc('\t', s); fmt_str(b->str, s); kputc('\t', s); fmt_str(b->ref, s); kputc('\t', s); fmt_str(b->alt, s); kputc('\t', s); ksprintf(s, "%.3g", b->qual); kputc('\t', s); fmt_str(b->flt, s); kputc('\t', s); fmt_str(b->info, s); if (b->fmt[0]) { kputc('\t', s); fmt_str(b->fmt, s); } x = b->n_alleles * (b->n_alleles + 1) / 2; if (b->n_gi == 0) return; int iPL = -1; if ( b->n_alleles > 2 ) { for (i=0; in_gi; i++) { if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) { iPL = i; break; } } } for (j = 0; j < h->n_smpl; ++j) { int ploidy = b->ploidy ? b->ploidy[j] : 2; kputc('\t', s); for (i = 0; i < b->n_gi; ++i) { if (i) kputc(':', s); if (b->gi[i].fmt == bcf_str2int("PL", 2)) { uint8_t *d = (uint8_t*)b->gi[i].data + j * x; int k; if ( ploidy==1 ) for (k=0; kn_alleles; k++) { if (k>0) kputc(',', s); kputw(d[(k+1)*(k+2)/2-1], s); } else for (k = 0; k < x; ++k) { if (k > 0) kputc(',', s); kputw(d[k], s); } } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) { kputw(((uint16_t*)b->gi[i].data)[j], s); } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) { kputw(((uint8_t*)b->gi[i].data)[j], s); } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) { kputw(((int32_t*)b->gi[i].data)[j], s); } else if (b->gi[i].fmt == bcf_str2int("GT", 2)) { int y = ((uint8_t*)b->gi[i].data)[j]; if ( ploidy==1 ) { if ( y>>7&1 ) kputc('.', s); else kputc('0' + (y>>3&7), s); } else { if ( y>>7&1 ) kputsn("./.", 3, s); else { kputc('0' + (y>>3&7), s); kputc("/|"[y>>6&1], s); kputc('0' + (y&7), s); } } } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) { float *d = (float*)b->gi[i].data + j * x; int k; //printf("- %lx\n", d); for (k = 0; k < x; ++k) { if (k > 0) kputc(',', s); ksprintf(s, "%.2f", d[k]); } } else kputc('.', s); // custom fields } } } char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b) { kstring_t s; s.l = s.m = 0; s.s = 0; bcf_fmt_core(h, b, &s); return s.s; } int bcf_append_info(bcf1_t *b, const char *info, int l) { int shift = b->fmt - b->str; int l_fmt = b->l_str - shift; char *ori = b->str; if (b->l_str + l > b->m_str) { // enlarge if necessary b->m_str = b->l_str + l; kroundup32(b->m_str); b->str = realloc(b->str, b->m_str); } memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field memcpy(b->str + shift - 1, info, l); // append to the INFO field b->str[shift + l - 1] = '\0'; b->fmt = b->str + shift + l; b->l_str += l; if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer return 0; } int remove_tag(char *str, const char *tag, char delim) { char *tmp = str, *p; int len_diff = 0, ori_len = strlen(str); while ( *tmp && (p = strstr(tmp,tag)) ) { if ( p>str ) { if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring p--; } char *q=p+1; while ( *q && *q!=delim ) q++; if ( p==str && *q ) q++; // the tag is first, don't move the delim char len_diff += q-p; if ( ! *q ) { *p = 0; break; } // the tag was last, no delim follows else memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)); // *q==delim } if ( len_diff==ori_len ) str[0]='.', str[1]=0, len_diff--; return len_diff; } void rm_info(kstring_t *s, const char *key) { char *p = s->s; int n = 0; while ( n<4 ) { if ( !*p ) n++; p++; } char *q = p+1; while ( *q && q-s->sl ) q++; int nrm = remove_tag(p, key, ';'); if ( nrm ) memmove(q-nrm, q, s->s+s->l-q+1); s->l -= nrm; } int bcf_cpy(bcf1_t *r, const bcf1_t *b) { char *t1 = r->str; bcf_ginfo_t *t2 = r->gi; int i, t3 = r->m_str, t4 = r->m_gi; *r = *b; r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4; if (r->m_str < b->m_str) { r->m_str = b->m_str; r->str = realloc(r->str, r->m_str); } memcpy(r->str, b->str, r->m_str); bcf_sync(r); // calling bcf_sync() is simple but inefficient for (i = 0; i < r->n_gi; ++i) memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len); return 0; } int bcf_is_indel(const bcf1_t *b) { char *p; if (strlen(b->ref) > 1) return 1; for (p = b->alt; *p; ++p) if (*p != ',' && p[1] != ',' && p[1] != '\0') return 1; return 0; } pysam-0.7.7/samtools/bcftools/bcf2qcall.c.pysam.c0000664000076400007650000000575012162637166021550 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include "bcf.h" static int8_t nt4_table[256] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, -1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 }; static int read_I16(bcf1_t *b, int anno[16]) { char *p; int i; if ((p = strstr(b->info, "I16=")) == 0) return -1; p += 4; for (i = 0; i < 16; ++i) { anno[i] = strtol(p, &p, 10); if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2; ++p; } return 0; } int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b) { int a[4], k, g[10], l, map[4], k1, j, i, i0, anno[16], dp, mq, d_rest; char *s; if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL if (read_I16(b, anno) != 0) return -1; // no I16; FIXME: can be improved d_rest = dp = anno[0] + anno[1] + anno[2] + anno[3]; if (dp == 0) return -1; // depth is zero mq = (int)(sqrt((double)(anno[9] + anno[11]) / dp) + .499); i0 = i; a[0] = nt4_table[(int)b->ref[0]]; if (a[0] > 3) return -1; // ref is not A/C/G/T a[1] = a[2] = a[3] = -2; // -1 has a special meaning if (b->alt[0] == 0) return -1; // no alternate allele map[0] = map[1] = map[2] = map[3] = -2; map[a[0]] = 0; for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) { if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base a[k+1] = nt4_table[(int)*s]; if (a[k+1] >= 0) map[a[k+1]] = k+1; else k1 = k+1; if (s[1] == 0) break; } for (k = 0; k < 4; ++k) if (map[k] < 0) map[k] = k1; for (i = 0; i < h->n_smpl; ++i) { int d; uint8_t *p = b->gi[i0].data + i * b->gi[i0].len; for (j = 0; j < b->gi[i0].len; ++j) if (p[j]) break; d = (int)((double)d_rest / (h->n_smpl - i) + .499); if (d == 0) d = 1; if (j == b->gi[i0].len) d = 0; d_rest -= d; for (k = j = 0; k < 4; ++k) { for (l = k; l < 4; ++l) { int t, x = map[k], y = map[l]; if (x > y) t = x, x = y, y = t; // swap g[j++] = p[y * (y+1) / 2 + x]; } } printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref); printf("\t%d\t%d\t0", d, mq); for (j = 0; j < 10; ++j) printf("\t%d", g[j]); printf("\t%s\n", h->sns[i]); } return 0; } pysam-0.7.7/samtools/bcftools/prob1.c.pysam.c0000664000076400007650000010130112162637166020727 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include #include #include "prob1.h" #include "kstring.h" #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define MC_MAX_EM_ITER 16 #define MC_EM_EPS 1e-5 #define MC_DEF_INDEL 0.15 gzFile bcf_p1_fp_lk; unsigned char seq_nt4_table[256] = { 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 /*'-'*/, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 }; struct __bcf_p1aux_t { int n, M, n1, is_indel; uint8_t *ploidy; // haploid or diploid ONLY double *q2p, *pdg; // pdg -> P(D|g) double *phi, *phi_indel; double *z, *zswap; // aux for afs double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set double **hg; // hypergeometric distribution double *lf; // log factorial double t, t1, t2; double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution const uint8_t *PL; // point to PL int PL_len; }; void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x) { int i; for (i = 0; i < ma->M; ++i) ma->phi_indel[i] = ma->phi[i] * x; ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x; } static void init_prior(int type, double theta, int M, double *phi) { int i; if (type == MC_PTYPE_COND2) { for (i = 0; i <= M; ++i) phi[i] = 2. * (i + 1) / (M + 1) / (M + 2); } else if (type == MC_PTYPE_FLAT) { for (i = 0; i <= M; ++i) phi[i] = 1. / (M + 1); } else { double sum; for (i = 0, sum = 0.; i < M; ++i) sum += (phi[i] = theta / (M - i)); phi[M] = 1. - sum; } } void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta) { init_prior(type, theta, ma->M, ma->phi); bcf_p1_indel_prior(ma, MC_DEF_INDEL); } void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta) { if (ma->n1 <= 0 || ma->n1 >= ma->M) return; init_prior(type, theta, 2*ma->n1, ma->phi1); init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2); } int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn) { gzFile fp; kstring_t s; kstream_t *ks; long double sum; int dret, k; memset(&s, 0, sizeof(kstring_t)); fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); ks = ks_init(fp); memset(ma->phi, 0, sizeof(double) * (ma->M + 1)); while (ks_getuntil(ks, '\n', &s, &dret) >= 0) { if (strstr(s.s, "[afs] ") == s.s) { char *p = s.s + 6; for (k = 0; k <= ma->M; ++k) { int x; double y; x = strtol(p, &p, 10); if (x != k && (errno == EINVAL || errno == ERANGE)) return -1; ++p; y = strtod(p, &p); if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1; ma->phi[ma->M - k] += y; } } } ks_destroy(ks); gzclose(fp); free(s.s); for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k]; fprintf(pysamerr, "[prior]"); for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum; for (k = 0; k <= ma->M; ++k) fprintf(pysamerr, " %d:%.3lg", k, ma->phi[ma->M - k]); fputc('\n', pysamerr); for (sum = 0., k = 1; k < ma->M; ++k) sum += ma->phi[ma->M - k] * (2.* k * (ma->M - k) / ma->M / (ma->M - 1)); fprintf(pysamerr, "[%s] heterozygosity=%lf, ", __func__, (double)sum); for (sum = 0., k = 1; k <= ma->M; ++k) sum += k * ma->phi[ma->M - k] / ma->M; fprintf(pysamerr, "theta=%lf\n", (double)sum); bcf_p1_indel_prior(ma, MC_DEF_INDEL); return 0; } bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy) { bcf_p1aux_t *ma; int i; ma = calloc(1, sizeof(bcf_p1aux_t)); ma->n1 = -1; ma->n = n; ma->M = 2 * n; if (ploidy) { ma->ploidy = malloc(n); memcpy(ma->ploidy, ploidy, n); for (i = 0, ma->M = 0; i < n; ++i) ma->M += ploidy[i]; if (ma->M == 2 * n) { free(ma->ploidy); ma->ploidy = 0; } } ma->q2p = calloc(256, sizeof(double)); ma->pdg = calloc(3 * ma->n, sizeof(double)); ma->phi = calloc(ma->M + 1, sizeof(double)); ma->phi_indel = calloc(ma->M + 1, sizeof(double)); ma->phi1 = calloc(ma->M + 1, sizeof(double)); ma->phi2 = calloc(ma->M + 1, sizeof(double)); ma->z = calloc(ma->M + 1, sizeof(double)); ma->zswap = calloc(ma->M + 1, sizeof(double)); ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large ma->z2 = calloc(ma->M + 1, sizeof(double)); ma->afs = calloc(ma->M + 1, sizeof(double)); ma->afs1 = calloc(ma->M + 1, sizeof(double)); ma->lf = calloc(ma->M + 1, sizeof(double)); for (i = 0; i < 256; ++i) ma->q2p[i] = pow(10., -i / 10.); for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1); bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior return ma; } int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; } int bcf_p1_set_n1(bcf_p1aux_t *b, int n1) { if (n1 == 0 || n1 >= b->n) return -1; if (b->M != b->n * 2) { fprintf(pysamerr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__); return -1; } b->n1 = n1; return 0; } void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma) { // bcf_p1aux_t fields are not visible outside of prob1.c, hence this wrapper. // Ideally, this should set ploidy per site to allow pseudo-autosomal regions b->ploidy = ma->ploidy; } void bcf_p1_destroy(bcf_p1aux_t *ma) { if (ma) { int k; free(ma->lf); if (ma->hg && ma->n1 > 0) { for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]); free(ma->hg); } free(ma->ploidy); free(ma->q2p); free(ma->pdg); free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2); free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2); free(ma->afs); free(ma->afs1); free(ma); } } extern double kf_gammap(double s, double z); int test16(bcf1_t *b, anno16_t *a); // Wigginton 2005, PMID: 15789306 // written by Jan Wigginton double calc_hwe(int obs_hom1, int obs_hom2, int obs_hets) { if (obs_hom1 + obs_hom2 + obs_hets == 0 ) return 1; assert(obs_hom1 >= 0 && obs_hom2 >= 0 && obs_hets >= 0); int obs_homc = obs_hom1 < obs_hom2 ? obs_hom2 : obs_hom1; int obs_homr = obs_hom1 < obs_hom2 ? obs_hom1 : obs_hom2; int rare_copies = 2 * obs_homr + obs_hets; int genotypes = obs_hets + obs_homc + obs_homr; double *het_probs = (double*) calloc(rare_copies+1, sizeof(double)); /* start at midpoint */ int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes); /* check to ensure that midpoint and rare alleles have same parity */ if ((rare_copies & 1) ^ (mid & 1)) mid++; int curr_hets = mid; int curr_homr = (rare_copies - mid) / 2; int curr_homc = genotypes - curr_hets - curr_homr; het_probs[mid] = 1.0; double sum = het_probs[mid]; for (curr_hets = mid; curr_hets > 1; curr_hets -= 2) { het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0) / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0)); sum += het_probs[curr_hets - 2]; /* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */ curr_homr++; curr_homc++; } curr_hets = mid; curr_homr = (rare_copies - mid) / 2; curr_homc = genotypes - curr_hets - curr_homr; for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2) { het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc /((curr_hets + 2.0) * (curr_hets + 1.0)); sum += het_probs[curr_hets + 2]; /* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */ curr_homr--; curr_homc--; } int i; for (i = 0; i <= rare_copies; i++) het_probs[i] /= sum; /* p-value calculation for p_hwe */ double p_hwe = 0.0; for (i = 0; i <= rare_copies; i++) { if (het_probs[i] > het_probs[obs_hets]) continue; p_hwe += het_probs[i]; } p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe; free(het_probs); return p_hwe; } static void _bcf1_set_ref(bcf1_t *b, int idp) { kstring_t s; int old_n_gi = b->n_gi; s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str; kputs(":GT", &s); kputc('\0', &s); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); // Call GTs int isample, an = 0; for (isample = 0; isample < b->n_smpl; isample++) { if ( idp>=0 && ((uint16_t*)b->gi[idp].data)[isample]==0 ) ((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7; else { ((uint8_t*)b->gi[old_n_gi].data)[isample] = 0; an += b->ploidy ? b->ploidy[isample] : 2; } } bcf_fit_alt(b,1); b->qual = 999; // Prepare BCF for output: ref, alt, filter, info, format memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s); kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s); { ksprintf(&s, "AN=%d;", an); kputs(b->info, &s); anno16_t a; int has_I16 = test16(b, &a) >= 0? 1 : 0; if (has_I16 ) { if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]); ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq); } kputc('\0', &s); rm_info(&s, "I16="); rm_info(&s, "QS="); } kputs(b->fmt, &s); kputc('\0', &s); free(b->str); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); } int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only) { int nals = 1; char *p; for (p=b->alt; *p; p++) { if ( *p=='X' || p[0]=='.' ) break; if ( p[0]==',' ) nals++; } if ( b->alt[0] && !*p ) nals++; if ( nals>4 ) { if ( *b->ref=='N' ) return 0; fprintf(pysamerr,"Not ready for this, more than 4 alleles at %d: %s, %s\n", b->pos+1, b->ref,b->alt); exit(1); } // find PL, DV and DP FORMAT indexes uint8_t *pl = NULL; int i, npl = 0, idp = -1, idv = -1; for (i = 0; i < b->n_gi; ++i) { if (b->gi[i].fmt == bcf_str2int("PL", 2)) { pl = (uint8_t*)b->gi[i].data; npl = b->gi[i].len; } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) idp=i; else if (b->gi[i].fmt == bcf_str2int("DV", 2)) idv=i; } if ( nals==1 ) { if ( !var_only ) _bcf1_set_ref(b, idp); return 1; } if ( !pl ) return -1; assert(ma->q2p[0] == 1); // Init P(D|G) int npdg = nals*(nals+1)/2; double *pdg,*_pdg; _pdg = pdg = malloc(sizeof(double)*ma->n*npdg); for (i=0; in; i++) { int j; double sum = 0; for (j=0; jq2p[pl[j]]; sum += _pdg[j]; } if ( sum ) for (j=0; jinfo, "QS=")) == 0) { fprintf(pysamerr,"INFO/QS is required with -m, exiting\n"); exit(1); } double qsum[4]; if ( sscanf(p+3,"%lf,%lf,%lf,%lf",&qsum[0],&qsum[1],&qsum[2],&qsum[3])!=4 ) { fprintf(pysamerr,"Could not parse %s\n",p); exit(1); } // Calculate the most likely combination of alleles, remembering the most and second most likely set int ia,ib,ic, max_als=0, max_als2=0; double ref_lk = 0, max_lk = INT_MIN, max_lk2 = INT_MIN, lk_sum = INT_MIN, lk_sums[3]; for (ia=0; ian; isample++) { double *p = pdg + isample*npdg; // assert( log(p[iaa]) <= 0 ); lk_tot += log(p[iaa]); } if ( ia==0 ) ref_lk = lk_tot; if ( max_lklk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum)); } lk_sums[0] = lk_sum; if ( nals>1 ) { for (ia=0; ian; isample++) { double *p = pdg + isample*npdg; //assert( log(fa*p[iaa] + fb*p[ibb] + fab*p[iab]) <= 0 ); if ( b->ploidy && b->ploidy[isample]==1 ) lk_tot += log(fa*p[iaa] + fb*p[ibb]); else lk_tot += log(fa*p[iaa] + fb*p[ibb] + fab*p[iab]); } if ( max_lklk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum)); } } lk_sums[1] = lk_sum; } if ( nals>2 ) { for (ia=0; ian; isample++) { double *p = pdg + isample*npdg; //assert( log(fa*p[iaa] + fb*p[ibb] + fc*p[icc] + fab*p[iab] + fac*p[iac] + fbc*p[ibc]) <= 0 ); if ( b->ploidy && b->ploidy[isample]==1 ) lk_tot += log(fa*p[iaa] + fb*p[ibb] + fc*p[icc]); else lk_tot += log(fa*p[iaa] + fb*p[ibb] + fc*p[icc] + fab*p[iab] + fac*p[iac] + fbc*p[ibc]); } if ( max_lklk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum)); } } } lk_sums[2] = lk_sum; } // Should we add another allele, does it increase the likelihood significantly? int n1=0, n2=0; for (i=0; in_gi; s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str; kputs(":GT:GQ", &s); kputc('\0', &s); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); // Call GTs int isample, gts=0, ac[4] = {0,0,0,0}; int nRR = 0, nAA = 0, nRA = 0, max_dv = 0; for (isample = 0; isample < b->n_smpl; isample++) { int ploidy = b->ploidy ? b->ploidy[isample] : 2; double *p = pdg + isample*npdg; int ia, als = 0; double lk = 0, lk_s = 0; for (ia=0; ia lk ) { lk = _lk; als = ia<<3 | ia; } lk_s += _lk; } if ( ploidy==2 ) { for (ia=0; ia lk ) { lk = _lk; als = ib<<3 | ia; } lk_s += _lk; } } } lk = -log(1-lk/lk_s)/0.2302585; int dp = 0; if ( idp>=0 && (dp=((uint16_t*)b->gi[idp].data)[isample])==0 ) { // no coverage ((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7; ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = 0; continue; } if ( lk>99 ) lk = 99; ((uint8_t*)b->gi[old_n_gi].data)[isample] = als; ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = (int)lk; // For MDV annotation int dv; if ( als && idv>=0 && (dv=((uint16_t*)b->gi[idv].data)[isample]) ) { if ( max_dv < dv ) max_dv = dv; } // For HWE annotation; multiple ALT alleles treated as one if ( !als ) nRR++; else if ( !(als>>3&7) || !(als&7) ) nRA++; else nAA++; gts |= 1<<(als>>3&7) | 1<<(als&7); ac[ als>>3&7 ]++; ac[ als&7 ]++; } free(pdg); bcf_fit_alt(b,max_als); // The VCF spec is ambiguous about QUAL: is it the probability of anything else // (that is QUAL(non-ref) = P(ref)+P(any non-ref other than ALT)) or is it // QUAL(non-ref)=P(ref) and QUAL(ref)=1-P(ref)? Assuming the latter. b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*log(1-exp(ref_lk - lk_sum)); if ( b->qual>999 ) b->qual = 999; // Prepare BCF for output: ref, alt, filter, info, format memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s); kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s); { int an=0, nalts=0; for (i=0; i0 && ac[i] ) nalts++; } ksprintf(&s, "AN=%d;", an); if ( nalts ) { kputs("AC=", &s); for (i=1; i0 ) kputc(',', &s); } kputc(';', &s); } kputs(b->info, &s); anno16_t a; int has_I16 = test16(b, &a) >= 0? 1 : 0; if (has_I16 ) { if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]); ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq); ksprintf(&s, ";QBD=%e", b->qual/(a.d[0] + a.d[1] + a.d[2] + a.d[3])); if ( max_dv ) ksprintf(&s, ";MDV=%d", max_dv); } if ( nAA+nRA ) { double hwe = calc_hwe(nAA, nRR, nRA); ksprintf(&s, ";HWE=%e", hwe); } kputc('\0', &s); rm_info(&s, "I16="); rm_info(&s, "QS="); } kputs(b->fmt, &s); kputc('\0', &s); free(b->str); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); return gts; } static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma) { int i, j; long *p, tmp; p = alloca(b->n_alleles * sizeof(long)); memset(p, 0, sizeof(long) * b->n_alleles); for (j = 0; j < ma->n; ++j) { const uint8_t *pi = ma->PL + j * ma->PL_len; double *pdg = ma->pdg + j * 3; pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]]; for (i = 0; i < b->n_alleles; ++i) p[i] += (int)pi[(i+1)*(i+2)/2-1]; } for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i; for (i = 1; i < b->n_alleles; ++i) // insertion sort for (j = i; j > 0 && p[j] < p[j-1]; --j) tmp = p[j], p[j] = p[j-1], p[j-1] = tmp; for (i = b->n_alleles - 1; i >= 0; --i) if ((p[i]&0xf) == 0) break; return i; } int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k) { double sum, g[3]; double max, f3[3], *pdg = ma->pdg + k * 3; int q, i, max_i, ploidy; ploidy = ma->ploidy? ma->ploidy[k] : 2; if (ploidy == 2) { f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; } else { f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0; } for (i = 0, sum = 0.; i < 3; ++i) sum += (g[i] = pdg[i] * f3[i]); for (i = 0, max = -1., max_i = 0; i < 3; ++i) { g[i] /= sum; if (g[i] > max) max = g[i], max_i = i; } max = 1. - max; if (max < 1e-308) max = 1e-308; q = (int)(-4.343 * log(max) + .499); if (q > 99) q = 99; return q<<2|max_i; } #define TINY 1e-20 static void mc_cal_y_core(bcf_p1aux_t *ma, int beg) { double *z[2], *tmp, *pdg; int _j, last_min, last_max; assert(beg == 0 || ma->M == ma->n*2); z[0] = ma->z; z[1] = ma->zswap; pdg = ma->pdg; memset(z[0], 0, sizeof(double) * (ma->M + 1)); memset(z[1], 0, sizeof(double) * (ma->M + 1)); z[0][0] = 1.; last_min = last_max = 0; ma->t = 0.; if (ma->M == ma->n * 2) { int M = 0; for (_j = beg; _j < ma->n; ++_j) { int k, j = _j - beg, _min = last_min, _max = last_max, M0; double p[3], sum; M0 = M; M += 2; pdg = ma->pdg + _j * 3; p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2]; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset ma->t1 = ma->t; memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1)); } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } //for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary? //for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.; } else { // this block is very similar to the block above; these two might be merged in future int j, M = 0; for (j = 0; j < ma->n; ++j) { int k, M0, _min = last_min, _max = last_max; double p[3], sum; pdg = ma->pdg + j * 3; for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.; for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.; M0 = M; M += ma->ploidy[j]; if (ma->ploidy[j] == 1) { p[0] = pdg[0]; p[1] = pdg[2]; _max++; if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k]; for (k = _min < 1? 1 : _min; k <= _max; ++k) z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / M); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (j < ma->n - 1) z[1][_max+1] = 0.; } else if (ma->ploidy[j] == 2) { p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2]; _max += 2; if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k]; if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1]; for (k = _min < 2? 2 : _min; k <= _max; ++k) z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2]; for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k]; ma->t += log(sum / (M * (M - 1.))); for (k = _min; k <= _max; ++k) z[1][k] /= sum; if (_min >= 1) z[1][_min-1] = 0.; if (_min >= 2) z[1][_min-2] = 0.; if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.; } tmp = z[0]; z[0] = z[1]; z[1] = tmp; last_min = _min; last_max = _max; } } if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1)); if (bcf_p1_fp_lk) gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1)); } static void mc_cal_y(bcf_p1aux_t *ma) { if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples int k; long double x; memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1)); memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); ma->t1 = ma->t2 = 0.; mc_cal_y_core(ma, ma->n1); ma->t2 = ma->t; memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1)); mc_cal_y_core(ma, 0); // rescale z x = expl(ma->t - (ma->t1 + ma->t2)); for (k = 0; k <= ma->M; ++k) ma->z[k] *= x; } else mc_cal_y_core(ma, 0); } #define CONTRAST_TINY 1e-30 extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test static inline double chi2_test(int a, int b, int c, int d) { double x, z; x = (double)(a+b) * (c+d) * (b+d) * (a+c); if (x == 0.) return 1; z = a * d - b * c; return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x); } // chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)] static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3]) { double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2]; int n1 = p1->n1, n2 = p1->n - p1->n1; if (p < CONTRAST_TINY) return -1; if (.5*k1/n1 < .5*k2/n2) x[1] += p; else if (.5*k1/n1 > .5*k2/n2) x[2] += p; else x[0] += p; return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2); } static double contrast2(bcf_p1aux_t *p1, double ret[3]) { int k, k1, k2, k10, k20, n1, n2; double sum; // get n1 and n2 n1 = p1->n1; n2 = p1->n - p1->n1; if (n1 <= 0 || n2 <= 0) return 0.; if (p1->hg == 0) { // initialize the hypergeometric distribution /* NB: the hg matrix may take a lot of memory when there are many samples. There is a way to avoid precomputing this matrix, but it is slower and quite intricate. The following computation in this block can be accelerated with a similar strategy, but perhaps this is not a serious concern for now. */ double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1)); p1->hg = calloc(2*n1+1, sizeof(void*)); for (k1 = 0; k1 <= 2*n1; ++k1) { p1->hg[k1] = calloc(2*n2+1, sizeof(double)); for (k2 = 0; k2 <= 2*n2; ++k2) p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp)); } } { // compute long double suml = 0; for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k]; sum = suml; } { // get the max k1 and k2 double max; int max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) { double x = p1->phi1[k] * p1->z1[k]; if (x > max) max = x, max_k = k; } k10 = max_k; for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) { double x = p1->phi2[k] * p1->z2[k]; if (x > max) max = x, max_k = k; } k20 = max_k; } { // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N. double x[3], y; long double z = 0., L[2]; x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0; for (k1 = k10; k1 >= 0; --k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2]; x[0] = x[1] = x[2] = 0; for (k1 = k10 + 1; k1 <= 2*n1; ++k1) { for (k2 = k20; k2 >= 0; --k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } for (k2 = k20 + 1; k2 <= 2*n2; ++k2) { if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break; else z += y; } } ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2]; if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0; for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1) for (k2 = 0; k2 <= 2*n2; ++k2) if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y; if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why... z = 1.0, ret[0] = ret[1] = ret[2] = 1./3; } return (double)z; } } static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded) { int k; long double sum = 0., sum2; double *phi = ma->is_indel? ma->phi_indel : ma->phi; memset(ma->afs1, 0, sizeof(double) * (ma->M + 1)); mc_cal_y(ma); // compute AFS for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)phi[k] * ma->z[k]; for (k = 0; k <= ma->M; ++k) { ma->afs1[k] = phi[k] * ma->z[k] / sum; if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.; } // compute folded variant probability for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; for (k = 1, sum2 = 0.; k < ma->M; ++k) sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k]; *p_var_folded = sum2 / sum; *p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum; // the expected frequency for (k = 0, sum = 0.; k <= ma->M; ++k) { ma->afs[k] += ma->afs1[k]; sum += k * ma->afs1[k]; } return sum / ma->M; } int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst) { int i, k; long double sum = 0.; ma->is_indel = bcf_is_indel(b); rst->perm_rank = -1; // set PL and PL_len for (i = 0; i < b->n_gi; ++i) { if (b->gi[i].fmt == bcf_str2int("PL", 2)) { ma->PL = (uint8_t*)b->gi[i].data; ma->PL_len = b->gi[i].len; break; } } if (i == b->n_gi) return -1; // no PL if (b->n_alleles < 2) return -1; // FIXME: find a better solution // rst->rank0 = cal_pdg(b, ma); rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded); rst->p_ref = ma->afs1[ma->M]; for (k = 0, sum = 0.; k < ma->M; ++k) sum += ma->afs1[k]; rst->p_var = (double)sum; { // compute the allele count double max = -1; rst->ac = -1; for (k = 0; k <= ma->M; ++k) if (max < ma->z[k]) max = ma->z[k], rst->ac = k; rst->ac = ma->M - rst->ac; } // calculate f_flat and f_em for (k = 0, sum = 0.; k <= ma->M; ++k) sum += (long double)ma->z[k]; rst->f_flat = 0.; for (k = 0; k <= ma->M; ++k) { double p = ma->z[k] / sum; rst->f_flat += k * p; } rst->f_flat /= ma->M; { // estimate equal-tail credible interval (95% level) int l, h; double p; for (i = 0, p = 0.; i <= ma->M; ++i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; l = i; for (i = ma->M, p = 0.; i >= 0; --i) if (p + ma->afs1[i] > 0.025) break; else p += ma->afs1[i]; h = i; rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M; } if (ma->n1 > 0) { // compute LRT double max0, max1, max2; for (k = 0, max0 = -1; k <= ma->M; ++k) if (max0 < ma->z[k]) max0 = ma->z[k]; for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k) if (max1 < ma->z1[k]) max1 = ma->z1[k]; for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k) if (max2 < ma->z2[k]) max2 = ma->z2[k]; rst->lrt = log(max1 * max2 / max0); rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt); } else rst->lrt = -1.0; rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0; if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant rst->p_chi2 = contrast2(ma, rst->cmp); return 0; } void bcf_p1_dump_afs(bcf_p1aux_t *ma) { int k; fprintf(pysamerr, "[afs]"); for (k = 0; k <= ma->M; ++k) fprintf(pysamerr, " %d:%.3lf", k, ma->afs[ma->M - k]); fprintf(pysamerr, "\n"); memset(ma->afs, 0, sizeof(double) * (ma->M + 1)); } pysam-0.7.7/samtools/bcftools/fet.c.pysam.c0000664000076400007650000000610612162637166020471 0ustar andreasandreas#include "pysam.h" #include #include /* This program is implemented with ideas from this web page: * * http://www.langsrud.com/fisher.htm */ // log\binom{n}{k} static double lbinom(int n, int k) { if (k == 0 || n == k) return 0; return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1); } // n11 n12 | n1_ // n21 n22 | n2_ //-----------+---- // n_1 n_2 | n // hypergeometric distribution static double hypergeo(int n11, int n1_, int n_1, int n) { return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1)); } typedef struct { int n11, n1_, n_1, n; double p; } hgacc_t; // incremental version of hypergenometric distribution static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux) { if (n1_ || n_1 || n) { aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n; } else { // then only n11 changed; the rest fixed if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) { if (n11 == aux->n11 + 1) { // incremental aux->p *= (double)(aux->n1_ - aux->n11) / n11 * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1); aux->n11 = n11; return aux->p; } if (n11 == aux->n11 - 1) { // incremental aux->p *= (double)aux->n11 / (aux->n1_ - n11) * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11); aux->n11 = n11; return aux->p; } } aux->n11 = n11; } aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n); return aux->p; } double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two) { int i, j, max, min; double p, q, left, right; hgacc_t aux; int n1_, n_1, n; n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail min = n1_ + n_1 - n; if (min < 0) min = 0; // min n11, for left tail *two = *_left = *_right = 1.; if (min == max) return 1.; // no need to do test q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table // left tail p = hypergeo_acc(min, 0, 0, 0, &aux); for (left = 0., i = min + 1; p < 0.99999999 * q; ++i) // loop until underflow left += p, p = hypergeo_acc(i, 0, 0, 0, &aux); --i; if (p < 1.00000001 * q) left += p; else --i; // right tail p = hypergeo_acc(max, 0, 0, 0, &aux); for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow right += p, p = hypergeo_acc(j, 0, 0, 0, &aux); ++j; if (p < 1.00000001 * q) right += p; else ++j; // two-tail *two = left + right; if (*two > 1.) *two = 1.; // adjust left and right if (abs(i - n11) < abs(j - n11)) right = 1. - left + q; else left = 1.0 - right + q; *_left = left; *_right = right; return q; } #ifdef FET_MAIN #include int main(int argc, char *argv[]) { char id[1024]; int n11, n12, n21, n22; double left, right, twotail, prob; while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) { prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail); printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22, prob, left, right, twotail); } return 0; } #endif pysam-0.7.7/samtools/bcftools/bcf.h0000660000076400007650000001606712162637166017104 0ustar andreasandreas/* The MIT License Copyright (c) 2010 Broad Institute Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ #ifndef BCF_H #define BCF_H #define BCF_VERSION "0.1.19-44428cd" #include #include #ifndef BCF_LITE #include "bgzf.h" typedef BGZF *bcfFile; #else typedef gzFile bcfFile; #define bgzf_open(fn, mode) gzopen(fn, mode) #define bgzf_fdopen(fd, mode) gzdopen(fd, mode) #define bgzf_close(fp) gzclose(fp) #define bgzf_read(fp, buf, len) gzread(fp, buf, len) #define bgzf_write(fp, buf, len) #define bgzf_flush(fp) #endif /* A member in the structs below is said to "primary" if its content cannot be inferred from other members in any of structs below; a member is said to be "derived" if its content can be derived from other members. For example, bcf1_t::str is primary as this comes from the input data, while bcf1_t::info is derived as it can always be correctly set if we know bcf1_t::str. Derived members are for quick access to the content and must be synchronized with the primary data. */ typedef struct { uint32_t fmt; // format of the block, set by bcf_str2int(). int len; // length of data for each individual void *data; // concatenated data // derived info: fmt, len (<-bcf1_t::fmt) } bcf_ginfo_t; typedef struct { int32_t tid, pos; // refID and 0-based position int32_t l_str, m_str; // length and the allocated size of ->str float qual; // SNP quality char *str; // concatenated string of variable length strings in VCF (from col.2 to col.7) char *ref, *alt, *flt, *info, *fmt; // they all point to ->str; no memory allocation int n_gi, m_gi; // number and the allocated size of geno fields bcf_ginfo_t *gi; // array of geno fields int n_alleles, n_smpl; // number of alleles and samples // derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl) uint8_t *ploidy; // ploidy of all samples; if NULL, ploidy of 2 is assumed. } bcf1_t; typedef struct { int32_t n_ref, n_smpl; // number of reference sequences and samples int32_t l_nm; // length of concatenated sequence names; 0 padded int32_t l_smpl; // length of concatenated sample names; 0 padded int32_t l_txt; // length of header text (lines started with ##) char *name, *sname, *txt; // concatenated sequence names, sample names and header text char **ns, **sns; // array of sequence and sample names; point to name and sname, respectively // derived info: n_ref (<-name), n_smpl (<-sname), ns (<-name), sns (<-sname) } bcf_hdr_t; typedef struct { int is_vcf; // if the file in operation is a VCF void *v; // auxillary data structure for VCF bcfFile fp; // file handler for BCF } bcf_t; struct __bcf_idx_t; typedef struct __bcf_idx_t bcf_idx_t; #ifdef __cplusplus extern "C" { #endif // open a BCF file; for BCF file only bcf_t *bcf_open(const char *fn, const char *mode); // close file int bcf_close(bcf_t *b); // read one record from BCF; return -1 on end-of-file, and <-1 for errors int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b); // call this function if b->str is changed int bcf_sync(bcf1_t *b); // write a BCF record int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b); // read the BCF header; BCF only bcf_hdr_t *bcf_hdr_read(bcf_t *b); // write the BCF header int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h); // set bcf_hdr_t::ns and bcf_hdr_t::sns int bcf_hdr_sync(bcf_hdr_t *b); // destroy the header void bcf_hdr_destroy(bcf_hdr_t *h); // destroy a record int bcf_destroy(bcf1_t *b); // BCF->VCF conversion char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b); // append more info int bcf_append_info(bcf1_t *b, const char *info, int l); // remove tag int remove_tag(char *string, const char *tag, char delim); // remove info tag, string is the kstring holder of bcf1_t.str void rm_info(kstring_t *string, const char *key); // copy int bcf_cpy(bcf1_t *r, const bcf1_t *b); // open a VCF or BCF file if "b" is set in "mode" bcf_t *vcf_open(const char *fn, const char *mode); // close a VCF/BCF file int vcf_close(bcf_t *bp); // read the VCF/BCF header bcf_hdr_t *vcf_hdr_read(bcf_t *bp); // read the sequence dictionary from a separate file; required for VCF->BCF conversion int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn); // read a VCF/BCF record; return -1 on end-of-file and <-1 for errors int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b); // write the VCF header int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h); // write a VCF record int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b); // keep the first n alleles and discard the rest int bcf_shrink_alt(bcf1_t *b, int n); // keep the masked alleles and discard the rest void bcf_fit_alt(bcf1_t *b, int mask); // convert GL to PL int bcf_gl2pl(bcf1_t *b); // if the site is an indel int bcf_is_indel(const bcf1_t *b); bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list); int bcf_subsam(int n_smpl, int *list, bcf1_t *b); // move GT to the first FORMAT field int bcf_fix_gt(bcf1_t *b); // update PL generated by old samtools int bcf_fix_pl(bcf1_t *b); // convert PL to GLF-like 10-likelihood GL int bcf_gl10(const bcf1_t *b, uint8_t *gl); // convert up to 4 INDEL alleles to GLF-like 10-likelihood GL int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl); // string hash table void *bcf_build_refhash(bcf_hdr_t *h); void bcf_str2id_destroy(void *_hash); void bcf_str2id_thorough_destroy(void *_hash); int bcf_str2id_add(void *_hash, const char *str); int bcf_str2id(void *_hash, const char *str); void *bcf_str2id_init(); // indexing related functions int bcf_idx_build(const char *fn); uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg); int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end); bcf_idx_t *bcf_idx_load(const char *fn); void bcf_idx_destroy(bcf_idx_t *idx); #ifdef __cplusplus } #endif static inline uint32_t bcf_str2int(const char *str, int l) { int i; uint32_t x = 0; for (i = 0; i < l && i < 4; ++i) { if (str[i] == 0) return x; x = x<<8 | str[i]; } return x; } #endif pysam-0.7.7/samtools/bcftools/em.c.pysam.c0000664000076400007650000002145512162637166020320 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bcf.h" #include "kmin.h" static double g_q2p[256]; #define ITER_MAX 50 #define ITER_TRY 10 #define EPS 1e-5 extern double kf_gammaq(double, double); /* Generic routines */ // get the 3 genotype likelihoods static double *get_pdg3(const bcf1_t *b) { double *pdg; const uint8_t *PL = 0; int i, PL_len = 0; // initialize g_q2p if necessary if (g_q2p[0] == 0.) for (i = 0; i < 256; ++i) g_q2p[i] = pow(10., -i / 10.); // set PL and PL_len for (i = 0; i < b->n_gi; ++i) { if (b->gi[i].fmt == bcf_str2int("PL", 2)) { PL = (const uint8_t*)b->gi[i].data; PL_len = b->gi[i].len; break; } } if (i == b->n_gi) return 0; // no PL // fill pdg pdg = malloc(3 * b->n_smpl * sizeof(double)); for (i = 0; i < b->n_smpl; ++i) { const uint8_t *pi = PL + i * PL_len; double *p = pdg + i * 3; p[0] = g_q2p[pi[2]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]]; } return pdg; } // estimate site allele frequency in a very naive and inaccurate way static double est_freq(int n, const double *pdg) { int i, gcnt[3], tmp1; // get a rough estimate of the genotype frequency gcnt[0] = gcnt[1] = gcnt[2] = 0; for (i = 0; i < n; ++i) { const double *p = pdg + i * 3; if (p[0] != 1. || p[1] != 1. || p[2] != 1.) { int which = p[0] > p[1]? 0 : 1; which = p[which] > p[2]? which : 2; ++gcnt[which]; } } tmp1 = gcnt[0] + gcnt[1] + gcnt[2]; return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1; } /* Single-locus EM */ typedef struct { int beg, end; const double *pdg; } minaux1_t; static double prob1(double f, void *data) { minaux1_t *a = (minaux1_t*)data; double p = 1., l = 0., f3[3]; int i; // printf("brent %lg\n", f); if (f < 0 || f > 1) return 1e300; f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f; for (i = a->beg; i < a->end; ++i) { const double *pdg = a->pdg + i * 3; p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]; if (p < 1e-200) l -= log(p), p = 1.; } return l - log(p); } // one EM iteration for allele frequency estimate static double freq_iter(double *f, const double *_pdg, int beg, int end) { double f0 = *f, f3[3], err; int i; // printf("em %lg\n", *f); f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0; for (i = beg, f0 = 0.; i < end; ++i) { const double *pdg = _pdg + i * 3; f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2]) / (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]); } f0 /= (end - beg) * 2; err = fabs(f0 - *f); *f = f0; return err; } /* The following function combines EM and Brent's method. When the signal from * the data is strong, EM is faster but sometimes, EM may converge very slowly. * When this happens, we switch to Brent's method. The idea is learned from * Rasmus Nielsen. */ static double freqml(double f0, int beg, int end, const double *pdg) { int i; double f; for (i = 0, f = f0; i < ITER_TRY; ++i) if (freq_iter(&f, pdg, beg, end) < EPS) break; if (i == ITER_TRY) { // haven't converged yet; try Brent's method minaux1_t a; a.beg = beg; a.end = end; a.pdg = pdg; kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f); } return f; } // one EM iteration for genotype frequency estimate static double g3_iter(double g[3], const double *_pdg, int beg, int end) { double err, gg[3]; int i; gg[0] = gg[1] = gg[2] = 0.; // printf("%lg,%lg,%lg\n", g[0], g[1], g[2]); for (i = beg; i < end; ++i) { double sum, tmp[3]; const double *pdg = _pdg + i * 3; tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2]; sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg); gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum; } err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]); err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]); g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2]; return err; } // perform likelihood ratio test static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3]) { double r; int i; for (i = 0, r = 1.; i < n1; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } for (; i < n; ++i) { const double *p = pdg + i * 3; r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2]) / (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]); } return r; } // x[0]: ref frequency // x[1..3]: alt-alt, alt-ref, ref-ref frequenc // x[4]: HWE P-value // x[5..6]: group1 freq, group2 freq // x[7]: 1-degree P-value // x[8]: 2-degree P-value int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]) { double *pdg; int i, n, n2; if (b->n_alleles < 2) return -1; // one allele only // initialization if (n1 < 0 || n1 > b->n_smpl) n1 = 0; if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required if (flag & 0xf<<1) flag |= 0xf<<1; n = b->n_smpl; n2 = n - n1; pdg = get_pdg3(b); if (pdg == 0) return -1; for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative { if ((x[0] = est_freq(n, pdg)) < 0.) { free(pdg); return -1; // no data } x[0] = freqml(x[0], 0, n, pdg); } if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE double *g = x + 1, f3[3], r; f3[0] = g[0] = (1 - x[0]) * (1 - x[0]); f3[1] = g[1] = 2 * x[0] * (1 - x[0]); f3[2] = g[2] = x[0] * x[0]; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g, pdg, 0, n) < EPS) break; // Hardy-Weinberg equilibrium (HWE) for (i = 0, r = 1.; i < n; ++i) { double *p = pdg + i * 3; r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]); } x[4] = kf_gammaq(.5, log(r)); } if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency x[5] = freqml(x[0], 0, n1, pdg); x[6] = freqml(x[0], n1, n, pdg); } if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value double f[3], f3[3][3], tmp; f[0] = x[0]; f[1] = x[5]; f[2] = x[6]; for (i = 0; i < 3; ++i) f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i]; tmp = log(lk_ratio_test(n, n1, pdg, f3)); if (tmp < 0) tmp = 0; x[7] = kf_gammaq(.5, tmp); } if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value double g[3][3], tmp; for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double)); for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[1], pdg, 0, n1) < EPS) break; for (i = 0; i < ITER_MAX; ++i) if (g3_iter(g[2], pdg, n1, n) < EPS) break; tmp = log(lk_ratio_test(n, n1, pdg, g)); if (tmp < 0) tmp = 0; x[8] = kf_gammaq(1., tmp); } // free free(pdg); return 0; } /* Two-locus EM (LD) */ #define _G1(h, k) ((h>>1&1) + (k>>1&1)) #define _G2(h, k) ((h&1) + (k&1)) // 0: the previous site; 1: the current site static int pair_freq_iter(int n, double *pdg[2], double f[4]) { double ff[4]; int i, k, h; // printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]); memset(ff, 0, 4 * sizeof(double)); for (i = 0; i < n; ++i) { double *p[2], sum, tmp; p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3; for (k = 0, sum = 0.; k < 4; ++k) for (h = 0; h < 4; ++h) sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)]; for (k = 0; k < 4; ++k) { tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)]) + f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)]) + f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)]) + f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]); ff[k] += f[k] * tmp / sum; } } for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n); return 0; } double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]) { const bcf1_t *b[2]; int i, j, n_smpl; double *pdg[2], flast[4], r, f0[2]; // initialize others if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples n_smpl = b0->n_smpl; b[0] = b0; b[1] = b1; f[0] = f[1] = f[2] = f[3] = -1.; if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only pdg[0] = get_pdg3(b0); pdg[1] = get_pdg3(b1); if (pdg[0] == 0 || pdg[1] == 0) { free(pdg[0]); free(pdg[1]); return -1; } // set the initial value f0[0] = est_freq(n_smpl, pdg[0]); f0[1] = est_freq(n_smpl, pdg[1]); f[0] = (1 - f0[0]) * (1 - f0[1]); f[3] = f0[0] * f0[1]; f[1] = (1 - f0[0]) * f0[1]; f[2] = f0[0] * (1 - f0[1]); // iteration for (j = 0; j < ITER_MAX; ++j) { double eps = 0; memcpy(flast, f, 4 * sizeof(double)); pair_freq_iter(n_smpl, pdg, f); for (i = 0; i < 4; ++i) { double x = fabs(f[i] - flast[i]); if (x > eps) eps = x; } if (eps < EPS) break; } // free free(pdg[0]); free(pdg[1]); { // calculate r^2 double p[2], q[2], D; p[0] = f[0] + f[1]; q[0] = 1 - p[0]; p[1] = f[0] + f[2]; q[1] = 1 - p[1]; D = f[0] * f[3] - f[1] * f[2]; r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1])); // printf("R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r); if (isnan(r)) r = -1.; } return r; } pysam-0.7.7/samtools/bcftools/vcf.c.pysam.c0000664000076400007650000001562412162637166020476 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include "bcf.h" #include "kstring.h" #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 4096) typedef struct { gzFile fp; FILE *fpout; kstream_t *ks; void *refhash; kstring_t line; int max_ref; } vcf_t; bcf_hdr_t *vcf_hdr_read(bcf_t *bp) { kstring_t meta, smpl; int dret; vcf_t *v; bcf_hdr_t *h; if (!bp->is_vcf) return bcf_hdr_read(bp); h = calloc(1, sizeof(bcf_hdr_t)); v = (vcf_t*)bp->v; v->line.l = 0; memset(&meta, 0, sizeof(kstring_t)); memset(&smpl, 0, sizeof(kstring_t)); while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) { if (v->line.l < 2) continue; if (v->line.s[0] != '#') { free(meta.s); free(smpl.s); free(h); return 0; // no sample line } if (v->line.s[0] == '#' && v->line.s[1] == '#') { kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta); } else if (v->line.s[0] == '#') { int k; ks_tokaux_t aux; char *p; for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) { if (k >= 9) { kputsn(p, aux.p - p, &smpl); kputc('\0', &smpl); } } break; } } kputc('\0', &meta); h->name = 0; h->sname = smpl.s; h->l_smpl = smpl.l; h->txt = meta.s; h->l_txt = meta.l; bcf_hdr_sync(h); return h; } bcf_t *vcf_open(const char *fn, const char *mode) { bcf_t *bp; vcf_t *v; if (strchr(mode, 'b')) return bcf_open(fn, mode); bp = calloc(1, sizeof(bcf_t)); v = calloc(1, sizeof(vcf_t)); bp->is_vcf = 1; bp->v = v; v->refhash = bcf_str2id_init(); if (strchr(mode, 'r')) { v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); v->ks = ks_init(v->fp); } else if (strchr(mode, 'w')) v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout; return bp; } int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn) { vcf_t *v; gzFile fp; kstream_t *ks; kstring_t s, rn; int dret; if (bp == 0) return -1; if (!bp->is_vcf) return 0; s.l = s.m = 0; s.s = 0; rn.m = rn.l = h->l_nm; rn.s = h->name; v = (vcf_t*)bp->v; fp = gzopen(fn, "r"); ks = ks_init(fp); while (ks_getuntil(ks, 0, &s, &dret) >= 0) { bcf_str2id_add(v->refhash, strdup(s.s)); kputs(s.s, &rn); kputc('\0', &rn); if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); } ks_destroy(ks); gzclose(fp); h->l_nm = rn.l; h->name = rn.s; bcf_hdr_sync(h); free(s.s); return 0; } int vcf_close(bcf_t *bp) { vcf_t *v; if (bp == 0) return -1; if (!bp->is_vcf) return bcf_close(bp); v = (vcf_t*)bp->v; if (v->fp) { ks_destroy(v->ks); gzclose(v->fp); } if (v->fpout) fclose(v->fpout); free(v->line.s); bcf_str2id_thorough_destroy(v->refhash); free(v); free(bp); return 0; } int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h) { vcf_t *v = (vcf_t*)bp->v; int i, has_ver = 0; if (!bp->is_vcf) return bcf_hdr_write(bp, h); if (h->l_txt > 0) { if (strstr(h->txt, "##fileformat=")) has_ver = 1; if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n"); fwrite(h->txt, 1, h->l_txt - 1, v->fpout); } if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n"); fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"); for (i = 0; i < h->n_smpl; ++i) fprintf(v->fpout, "\t%s", h->sns[i]); fputc('\n', v->fpout); return 0; } int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b) { vcf_t *v = (vcf_t*)bp->v; extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s); if (!bp->is_vcf) return bcf_write(bp, h, b); bcf_fmt_core(h, b, &v->line); fwrite(v->line.s, 1, v->line.l, v->fpout); fputc('\n', v->fpout); return v->line.l + 1; } int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b) { int dret, k, i, sync = 0; vcf_t *v = (vcf_t*)bp->v; char *p, *q; kstring_t str, rn; ks_tokaux_t aux, a2; if (!bp->is_vcf) return bcf_read(bp, h, b); v->line.l = 0; str.l = 0; str.m = b->m_str; str.s = b->str; rn.l = rn.m = h->l_nm; rn.s = h->name; if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1; b->n_smpl = h->n_smpl; for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) { *(char*)aux.p = 0; if (k == 0) { // ref int tid = bcf_str2id(v->refhash, p); if (tid < 0) { tid = bcf_str2id_add(v->refhash, strdup(p)); kputs(p, &rn); kputc('\0', &rn); sync = 1; } b->tid = tid; } else if (k == 1) { // pos b->pos = atoi(p) - 1; } else if (k == 5) { // qual b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0; } else if (k <= 8) { // variable length strings kputs(p, &str); kputc('\0', &str); b->l_str = str.l; b->m_str = str.m; b->str = str.s; if (k == 8) bcf_sync(b); } else { // k > 9 if (strncmp(p, "./.", 3) == 0) { for (i = 0; i < b->n_gi; ++i) { if (b->gi[i].fmt == bcf_str2int("GT", 2)) { ((uint8_t*)b->gi[i].data)[k-9] = 1<<7; } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) { ((uint8_t*)b->gi[i].data)[k-9] = 0; } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) { ((int32_t*)b->gi[i].data)[k-9] = 0; } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) { ((uint16_t*)b->gi[i].data)[k-9] = 0; } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) { int y = b->n_alleles * (b->n_alleles + 1) / 2; memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y); } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) { int y = b->n_alleles * (b->n_alleles + 1) / 2; memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4); } } goto endblock; } for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) { if (b->gi[i].fmt == bcf_str2int("GT", 2)) { ((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6; } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) { double _x = strtod(q, &q); int x = (int)(_x + .499); if (x > 255) x = 255; ((uint8_t*)b->gi[i].data)[k-9] = x; } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) { int x = strtol(q, &q, 10); if (x > 0xffff) x = 0xffff; ((uint32_t*)b->gi[i].data)[k-9] = x; } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) { int x = strtol(q, &q, 10); if (x > 0xffff) x = 0xffff; ((uint16_t*)b->gi[i].data)[k-9] = x; } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) { int x, y, j; uint8_t *data = (uint8_t*)b->gi[i].data; y = b->n_alleles * (b->n_alleles + 1) / 2; for (j = 0; j < y; ++j) { x = strtol(q, &q, 10); if (x > 255) x = 255; data[(k-9) * y + j] = x; ++q; } } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) { int j, y; float x, *data = (float*)b->gi[i].data; y = b->n_alleles * (b->n_alleles + 1) / 2; for (j = 0; j < y; ++j) { x = strtod(q, &q); data[(k-9) * y + j] = x > 0? -x/10. : x; ++q; } } } endblock: i = i; } } h->l_nm = rn.l; h->name = rn.s; if (sync) bcf_hdr_sync(h); return v->line.l + 1; } pysam-0.7.7/samtools/bcftools/call1.c.pysam.c0000664000076400007650000006343012162637166020712 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "bcf.h" #include "prob1.h" #include "kstring.h" #include "time.h" #ifdef _WIN32 #define srand48(x) srand(x) #define lrand48() rand() #endif #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define VC_NO_GENO 2 #define VC_BCFOUT 4 #define VC_CALL 8 #define VC_VARONLY 16 #define VC_VCFIN 32 #define VC_UNCOMP 64 #define VC_KEEPALT 256 #define VC_ACGT_ONLY 512 #define VC_QCALL 1024 #define VC_CALL_GT 2048 #define VC_ADJLD 4096 #define VC_NO_INDEL 8192 #define VC_ANNO_MAX 16384 #define VC_FIX_PL 32768 #define VC_EM 0x10000 #define VC_PAIRCALL 0x20000 #define VC_QCNT 0x40000 #define VC_INDEL_ONLY 0x80000 typedef struct { int flag, prior_type, n1, n_sub, *sublist, n_perm; uint32_t *trio_aux; char *prior_file, **subsam, *fn_dict; uint8_t *ploidy; double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt, min_ma_lrt; void *bed; } viewconf_t; void *bed_read(const char *fn); void bed_destroy(void *_h); int bed_overlap(const void *_h, const char *chr, int beg, int end); static double ttest(int n1, int n2, int a[4]) { extern double kf_betai(double a, double b, double x); double t, v, u1, u2; if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0; u1 = (double)a[0] / n1; u2 = (double)a[2] / n2; if (u1 <= u2) return 1.; t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2)); v = n1 + n2 - 2; // printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2); return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t)); } static int test16_core(int anno[16], anno16_t *a) { extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); double left, right; int i; a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; memcpy(a->d, anno, 4 * sizeof(int)); a->depth = anno[0] + anno[1] + anno[2] + anno[3]; a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0); if (a->depth == 0) return -1; a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499); kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]); for (i = 1; i < 4; ++i) a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i); return 0; } int test16(bcf1_t *b, anno16_t *a) { char *p; int i, anno[16]; a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.; a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.; a->mq = a->depth = a->is_tested = 0; if ((p = strstr(b->info, "I16=")) == 0) return -1; p += 4; for (i = 0; i < 16; ++i) { errno = 0; anno[i] = strtol(p, &p, 10); if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2; ++p; } return test16_core(anno, a); } static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt) { kstring_t s; int has_I16, is_var; double fq, r; anno16_t a; has_I16 = test16(b, &a) >= 0? 1 : 0; //rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed! memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s); kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s); kputs(b->info, &s); if (b->info[0]) kputc(';', &s); { // print EM if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]); if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]); if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]); if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]); if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]); } if (cons_llr > 0) { ksprintf(&s, ";CLR=%d", cons_llr); if (cons_gt > 0) ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff, cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff); } if (pr == 0) { // if pr is unset, return kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s); free(b->str); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); return 1; } is_var = (pr->p_ref < pref); r = is_var? pr->p_ref : pr->p_var; // ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted! ksprintf(&s, ";AC1=%d", pr->ac); if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq); fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded); if (fq < -999) fq = -999; if (fq > 999) fq = 999; ksprintf(&s, ";FQ=%.3g", fq); if (pr->cmp[0] >= 0.) { // two sample groups int i, q[3]; for (i = 1; i < 3; ++i) { double x = pr->cmp[i] + pr->cmp[0]/2.; q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499); if (q[i] > 255) q[i] = 255; } if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank); // ksprintf(&s, ";LRT3=%.3g", pr->lrt); ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2); } if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]); kputc('\0', &s); rm_info(&s, "QS="); rm_info(&s, "I16="); kputs(b->fmt, &s); kputc('\0', &s); free(b->str); b->m_str = s.m; b->l_str = s.l; b->str = s.s; b->qual = r < 1e-100? 999 : -4.343 * log(r); if (b->qual > 999) b->qual = 999; bcf_sync(b); if (!is_var) bcf_shrink_alt(b, 1); else if (!(flag&VC_KEEPALT)) bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1); if (is_var && (flag&VC_CALL_GT)) { // call individual genotype int i, x, old_n_gi = b->n_gi; s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str; kputs(":GT:GQ", &s); kputc('\0', &s); b->m_str = s.m; b->l_str = s.l; b->str = s.s; bcf_sync(b); for (i = 0; i < b->n_smpl; ++i) { x = bcf_p1_call_gt(pa, pr->f_exp, i); ((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0; ((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2; } } return is_var; } static char **read_samples(const char *fn, int *_n) { gzFile fp; kstream_t *ks; kstring_t s; int dret, n = 0, max = 0; char **sam = 0; *_n = 0; s.l = s.m = 0; s.s = 0; fp = gzopen(fn, "r"); if (fp == 0) { // interpret as sample names, not as a file name const char *t = fn, *p = t; while (*t) { t++; if ( *t==',' || !*t ) { sam = realloc(sam, sizeof(void*)*(n+1)); sam[n] = (char*) malloc(sizeof(char)*(t-p+2)); memcpy(sam[n], p, t-p); sam[n][t-p] = 0; sam[n][t-p+1] = 2; // assume diploid p = t+1; n++; } } *_n = n; return sam; // fail to open file } ks = ks_init(fp); while (ks_getuntil(ks, 0, &s, &dret) >= 0) { int l; if (max == n) { max = max? max<<1 : 4; sam = realloc(sam, sizeof(void*)*max); } l = s.l; sam[n] = malloc(s.l + 2); strcpy(sam[n], s.s); sam[n][l+1] = 2; // by default, diploid if (dret != '\n') { if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2 int x = (int)s.s[0] - '0'; if (x == 1 || x == 2) sam[n][l+1] = x; else fprintf(pysamerr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__); } if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); } ++n; } ks_destroy(ks); gzclose(fp); free(s.s); *_n = n; return sam; } static void write_header(bcf_hdr_t *h) { kstring_t str; str.l = h->l_txt? h->l_txt - 1 : 0; str.m = str.l + 1; str.s = h->txt; if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); // if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); //if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##INFO=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); if (!strstr(str.s, "##FORMAT=\n", &str); h->l_txt = str.l + 1; h->txt = str.s; } double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]); int bcfview(int argc, char *argv[]) { extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b); extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x); extern int bcf_fix_gt(bcf1_t *b); extern int bcf_anno_max(bcf1_t *b); extern int bcf_shuffle(bcf1_t *b, int seed); extern uint32_t *bcf_trio_prep(int is_x, int is_son); extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt); extern int bcf_pair_call(const bcf1_t *b); extern int bcf_min_diff(const bcf1_t *b); extern int bcf_p1_get_M(bcf_p1aux_t *b); extern gzFile bcf_p1_fp_lk; bcf_t *bp, *bout = 0; bcf1_t *b, *blast; int c, *seeds = 0; uint64_t n_processed = 0, qcnt[256]; viewconf_t vc; bcf_p1aux_t *p1 = 0; bcf_hdr_t *hin, *hout; int tid, begin, end; char moder[4], modew[4]; tid = begin = end = -1; memset(&vc, 0, sizeof(viewconf_t)); vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; vc.min_ma_lrt = -1; memset(qcnt, 0, 8 * 256); while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) { switch (c) { case '1': vc.n1 = atoi(optarg); break; case 'l': vc.bed = bed_read(optarg); if (!vc.bed) { fprintf(pysamerr,"Could not read \"%s\"\n", optarg); return 1; } break; case 'D': vc.fn_dict = strdup(optarg); break; case 'F': vc.flag |= VC_FIX_PL; break; case 'N': vc.flag |= VC_ACGT_ONLY; break; case 'G': vc.flag |= VC_NO_GENO; break; case 'A': vc.flag |= VC_KEEPALT; break; case 'b': vc.flag |= VC_BCFOUT; break; case 'S': vc.flag |= VC_VCFIN; break; case 'c': vc.flag |= VC_CALL; break; case 'e': vc.flag |= VC_EM; break; case 'v': vc.flag |= VC_VARONLY | VC_CALL; break; case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break; case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break; case 'I': vc.flag |= VC_NO_INDEL; break; case 'w': vc.flag |= VC_INDEL_ONLY; break; case 'M': vc.flag |= VC_ANNO_MAX; break; case 'Y': vc.flag |= VC_QCNT; break; case 'm': vc.min_ma_lrt = atof(optarg); break; case 't': vc.theta = atof(optarg); break; case 'p': vc.pref = atof(optarg); break; case 'i': vc.indel_frac = atof(optarg); break; case 'Q': vc.flag |= VC_QCALL; break; case 'L': vc.flag |= VC_ADJLD; break; case 'U': vc.n_perm = atoi(optarg); break; case 'C': vc.min_lrt = atof(optarg); break; case 'X': vc.min_perm_p = atof(optarg); break; case 'd': vc.min_smpl_frac = atof(optarg); break; case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break; case 's': vc.subsam = read_samples(optarg, &vc.n_sub); vc.ploidy = calloc(vc.n_sub + 1, 1); for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1]; tid = -1; break; case 'T': if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0); else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0); else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1); else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL; else { fprintf(pysamerr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__); return 1; } break; case 'P': if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL; else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2; else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT; else vc.prior_file = strdup(optarg); break; } } if (argc == optind) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: bcftools view [options] [reg]\n\n"); fprintf(pysamerr, "Input/output options:\n\n"); fprintf(pysamerr, " -A keep all possible alternate alleles at variant sites\n"); fprintf(pysamerr, " -b output BCF instead of VCF\n"); fprintf(pysamerr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n"); fprintf(pysamerr, " -F PL generated by r921 or before (which generate old ordering)\n"); fprintf(pysamerr, " -G suppress all individual genotype information\n"); fprintf(pysamerr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n"); fprintf(pysamerr, " -L calculate LD for adjacent sites\n"); fprintf(pysamerr, " -N skip sites where REF is not A/C/G/T\n"); fprintf(pysamerr, " -Q output the QCALL likelihood format\n"); fprintf(pysamerr, " -s FILE list of samples to use [all samples]\n"); fprintf(pysamerr, " -S input is VCF\n"); fprintf(pysamerr, " -u uncompressed BCF output (force -b)\n"); fprintf(pysamerr, "\nConsensus/variant calling options:\n\n"); fprintf(pysamerr, " -c SNP calling (force -e)\n"); fprintf(pysamerr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n"); fprintf(pysamerr, " -e likelihood based analyses\n"); fprintf(pysamerr, " -g call genotypes at variant sites (force -c)\n"); fprintf(pysamerr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac); fprintf(pysamerr, " -I skip indels\n"); fprintf(pysamerr, " -m FLOAT alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT\n"); fprintf(pysamerr, " -p FLOAT variant if P(ref|D)BCF conversion please specify the sequence dictionary with -D\n", __func__); return 1; } if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here! if (vc.n_perm > 0) { seeds = malloc(vc.n_perm * sizeof(int)); srand48(time(0)); for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48(); } b = calloc(1, sizeof(bcf1_t)); blast = calloc(1, sizeof(bcf1_t)); strcpy(moder, "r"); if (!(vc.flag & VC_VCFIN)) strcat(moder, "b"); strcpy(modew, "w"); if (vc.flag & VC_BCFOUT) strcat(modew, "b"); if (vc.flag & VC_UNCOMP) strcat(modew, "u"); bp = vcf_open(argv[optind], moder); hin = hout = vcf_hdr_read(bp); if (vc.fn_dict && (vc.flag & VC_VCFIN)) vcf_dictread(bp, hin, vc.fn_dict); bout = vcf_open("-", modew); if (!(vc.flag & VC_QCALL)) { if (vc.n_sub) { vc.sublist = calloc(vc.n_sub, sizeof(int)); hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist); } write_header(hout); // always print the header vcf_hdr_write(bout, hout); } if (vc.flag & VC_CALL) { p1 = bcf_p1_init(hout->n_smpl, vc.ploidy); if (vc.prior_file) { if (bcf_p1_read_prior(p1, vc.prior_file) < 0) { fprintf(pysamerr, "[%s] fail to read the prior AFS.\n", __func__); return 1; } } else bcf_p1_init_prior(p1, vc.prior_type, vc.theta); if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1 bcf_p1_set_n1(p1, vc.n1); bcf_p1_init_subprior(p1, vc.prior_type, vc.theta); } if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac } if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) { void *str2id = bcf_build_refhash(hout); if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) { bcf_idx_t *idx; idx = bcf_idx_load(argv[optind]); if (idx) { uint64_t off; off = bcf_idx_query(idx, tid, begin); if (off == 0) { fprintf(pysamerr, "[%s] no records in the query region.\n", __func__); return 1; // FIXME: a lot of memory leaks... } bgzf_seek(bp->fp, off, SEEK_SET); bcf_idx_destroy(idx); } } } if (bcf_p1_fp_lk && p1) { int32_t M = bcf_p1_get_M(p1); gzwrite(bcf_p1_fp_lk, &M, 4); } while (vcf_read(bp, hin, b) > 0) { int is_indel, cons_llr = -1; int64_t cons_gt = -1; double em[10]; if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue; if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) { extern int bcf_smpl_covered(const bcf1_t *b); int n = bcf_smpl_covered(b); if ((double)n / b->n_smpl < vc.min_smpl_frac) continue; } if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b); if (vc.flag & VC_FIX_PL) bcf_fix_pl(b); is_indel = bcf_is_indel(b); if ((vc.flag & VC_NO_INDEL) && is_indel) continue; if ((vc.flag & VC_INDEL_ONLY) && !is_indel) continue; if ((vc.flag & VC_ACGT_ONLY) && !is_indel) { int x; if (b->ref[0] == 0 || b->ref[1] != 0) continue; x = toupper(b->ref[0]); if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue; } if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue; if (tid >= 0) { int l = strlen(b->ref); l = b->pos + (l > 0? l : 1); if (b->tid != tid || b->pos >= end) break; if (!(l > begin && end > b->pos)) continue; } ++n_processed; if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference int x = bcf_min_diff(b); if (x > 255) x = 255; if (x >= 0) ++qcnt[x]; } if (vc.flag & VC_QCALL) { // output QCALL format; STOP here bcf_2qcall(hout, b); continue; } if (vc.trio_aux) // do trio calling bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt); else if (vc.flag & VC_PAIRCALL) cons_llr = bcf_pair_call(b); if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b); if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em); else { int i; for (i = 0; i < 9; ++i) em[i] = -1.; } if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 ) { bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY); if ( gts<=1 && vc.flag & VC_VARONLY ) continue; } else if (vc.flag & VC_CALL) { // call variants bcf_p1rst_t pr; int calret; gzwrite(bcf_p1_fp_lk, &b->tid, 4); gzwrite(bcf_p1_fp_lk, &b->pos, 4); gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double)); calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr); if (n_processed % 100000 == 0) { fprintf(pysamerr, "[%s] %ld sites processed.\n", __func__, (long)n_processed); bcf_p1_dump_afs(p1); } if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue; if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test bcf_p1rst_t r; int i, n = 0; for (i = 0; i < vc.n_perm; ++i) { #ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts double x[10]; bcf_shuffle(b, seeds[i]); bcf_em1(b, vc.n1, 1<<7, x); if (x[7] < em[7]) ++n; #else bcf_shuffle(b, seeds[i]); bcf_p1_cal(b, 1, p1, &r); if (pr.p_chi2 >= r.p_chi2) ++n; #endif } pr.perm_rank = n; } if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt); } else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt); if (vc.flag & VC_ADJLD) { // compute LD double f[4], r2; if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) { kstring_t s; s.m = s.l = 0; s.s = 0; if (*b->info) kputc(';', &s); ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]); bcf_append_info(b, s.s, s.l); free(s.s); } bcf_cpy(blast, b); } if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b); if (vc.flag & VC_NO_GENO) { // do not output GENO fields b->n_gi = 0; b->fmt[0] = '\0'; b->l_str = b->fmt - b->str + 1; } else bcf_fix_gt(b); vcf_write(bout, hout, b); } if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk); if (vc.prior_file) free(vc.prior_file); if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1); if (hin != hout) bcf_hdr_destroy(hout); bcf_hdr_destroy(hin); bcf_destroy(b); bcf_destroy(blast); vcf_close(bp); vcf_close(bout); if (vc.fn_dict) free(vc.fn_dict); if (vc.ploidy) free(vc.ploidy); if (vc.trio_aux) free(vc.trio_aux); if (vc.n_sub) { int i; for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]); free(vc.subsam); free(vc.sublist); } if (vc.bed) bed_destroy(vc.bed); if (vc.flag & VC_QCNT) for (c = 0; c < 256; ++c) fprintf(pysamerr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]); if (seeds) free(seeds); if (p1) bcf_p1_destroy(p1); return 0; } pysam-0.7.7/samtools/bcftools/__init__.py0000664000076400007650000000000012162643057020266 0ustar andreasandreaspysam-0.7.7/samtools/bcftools/mut.c.pysam.c0000664000076400007650000000737412162637166020530 0ustar andreasandreas#include "pysam.h" #include #include #include "bcf.h" #define MAX_GENO 359 int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 }; char *seq_nt16rev = "XACMGRSVTWYHKDBN"; uint32_t *bcf_trio_prep(int is_x, int is_son) { int i, j, k, n, map[10]; uint32_t *ret; ret = calloc(MAX_GENO, 4); for (i = 0, k = 0; i < 4; ++i) for (j = i; j < 4; ++j) map[k++] = 1<n_smpl != 3) return -1; // not a trio for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL gl10 = alloca(10 * b->n_smpl); if (bcf_gl10(b, gl10) < 0) { if (bcf_gl10_indel(b, gl10) < 0) return -1; } PL = b->gi + i; for (i = 0, k = 0; i < 4; ++i) for (j = i; j < 4; ++j) map[k++] = seq_nt16rev[1<data)[j * PL->len] != 0) break; if (j < 3) { // we need to go through the complex procedure uint8_t *g[3]; int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0; g[0] = gl10; g[1] = gl10 + 10; g[2] = gl10 + 20; for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff]; if (sum < minc) minc = sum, minc_j = j; } gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16; for (j = 0; j < 3; ++j) { // compute LK without constraint int min = 1<<30, min_k = -1; for (k = 0; k < 10; ++k) if (g[j][k] < min) min = g[j][k], min_k = k; gtf |= map[min_k]<<(j*8); minf += min; } *llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf; } else *llr = 0, *gt = -1; return 0; } int bcf_pair_call(const bcf1_t *b) { int i, j, k; const bcf_ginfo_t *PL; if (b->n_smpl != 2) return -1; // not a pair for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL PL = b->gi + i; for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members if (((uint8_t*)PL->data)[j * PL->len] != 0) break; if (j < 2) { // we need to go through the complex procedure uint8_t *g[2]; int minc = 1<<30, minf = 0; g[0] = PL->data; g[1] = (uint8_t*)PL->data + PL->len; for (j = 0; j < PL->len; ++j) // compute LK with constraint minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j]; for (j = 0; j < 2; ++j) { // compute LK without constraint int min = 1<<30; for (k = 0; k < PL->len; ++k) min = min < g[j][k]? min : g[j][k]; minf += min; } return minc - minf; } else return 0; } int bcf_min_diff(const bcf1_t *b) { int i, min = 1<<30; const bcf_ginfo_t *PL; for (i = 0; i < b->n_gi; ++i) if (b->gi[i].fmt == bcf_str2int("PL", 2)) break; if (i == b->n_gi) return -1; // no PL PL = b->gi + i; for (i = 0; i < b->n_smpl; ++i) { int m1, m2, j; const uint8_t *p = (uint8_t*)PL->data; m1 = m2 = 1<<30; for (j = 0; j < PL->len; ++j) { if ((int)p[j] < m1) m2 = m1, m1 = p[j]; else if ((int)p[j] < m2) m2 = p[j]; } min = min < m2 - m1? min : m2 - m1; } return min; } pysam-0.7.7/samtools/bam2bcf.h0000664000076400007650000000354112162637166016030 0ustar andreasandreas#ifndef BAM2BCF_H #define BAM2BCF_H #include #include "errmod.h" #include "bcftools/bcf.h" #define B2B_INDEL_NULL 10000 #define B2B_FMT_DP 0x1 #define B2B_FMT_SP 0x2 #define B2B_FMT_DV 0x4 typedef struct __bcf_callaux_t { int capQ, min_baseQ; int openQ, extQ, tandemQ; // for indels int min_support, max_support; // for collecting indel candidates double min_frac, max_frac; // for collecting indel candidates int per_sample_flt; // indel filtering strategy int *ref_pos, *alt_pos, npos; // for ReadPosBias // for internal uses int max_bases; int indel_types[4]; int maxins, indelreg; int read_len; char *inscns; uint16_t *bases; errmod_t *e; void *rghash; } bcf_callaux_t; typedef struct { int depth, n_supp, ori_depth, qsum[4]; unsigned int anno[16]; float p[25]; } bcf_callret1_t; typedef struct { int a[5]; // alleles: ref, alt, alt2, alt3 float qsum[4]; int n, n_alleles, shift, ori_ref, unseen; int n_supp; // number of supporting non-reference reads unsigned int anno[16], depth, ori_depth; uint8_t *PL; float vdb; // variant distance bias float read_pos_bias; struct { float avg, var; int dp; } read_pos; } bcf_call_t; #ifdef __cplusplus extern "C" { #endif bcf_callaux_t *bcf_call_init(double theta, int min_baseQ); void bcf_call_destroy(bcf_callaux_t *bca); int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r); int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call); int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref); int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, const void *rghash); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/errmod.h0000664000076400007650000000067212162637166016026 0ustar andreasandreas#ifndef ERRMOD_H #define ERRMOD_H #include struct __errmod_coef_t; typedef struct { double depcorr; struct __errmod_coef_t *coef; } errmod_t; errmod_t *errmod_init(float depcorr); void errmod_destroy(errmod_t *em); /* n: number of bases m: maximum base bases[i]: qual:6, strand:1, base:4 q[i*m+j]: phred-scaled likelihood of (i,j) */ int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q); #endif pysam-0.7.7/samtools/khash.h0000664000076400007650000004262712162637166015642 0ustar andreasandreas/* The MIT License Copyright (c) 2008, 2009, 2011 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* An example: #include "khash.h" KHASH_MAP_INIT_INT(32, char) int main() { int ret, is_missing; khiter_t k; khash_t(32) *h = kh_init(32); k = kh_put(32, h, 5, &ret); if (!ret) kh_del(32, h, k); kh_value(h, k) = 10; k = kh_get(32, h, 10); is_missing = (k == kh_end(h)); k = kh_get(32, h, 5); kh_del(32, h, k); for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k)) kh_value(h, k) = 1; kh_destroy(32, h); return 0; } */ /* 2011-02-14 (0.2.5): * Allow to declare global functions. 2009-09-26 (0.2.4): * Improve portability 2008-09-19 (0.2.3): * Corrected the example * Improved interfaces 2008-09-11 (0.2.2): * Improved speed a little in kh_put() 2008-09-10 (0.2.1): * Added kh_clear() * Fixed a compiling error 2008-09-02 (0.2.0): * Changed to token concatenation which increases flexibility. 2008-08-31 (0.1.2): * Fixed a bug in kh_get(), which has not been tested previously. 2008-08-31 (0.1.1): * Added destructor */ #ifndef __AC_KHASH_H #define __AC_KHASH_H /*! @header Generic hash table library. @copyright Heng Li */ #define AC_VERSION_KHASH_H "0.2.5" #include #include #include /* compipler specific configuration */ #if UINT_MAX == 0xffffffffu typedef unsigned int khint32_t; #elif ULONG_MAX == 0xffffffffu typedef unsigned long khint32_t; #endif #if ULONG_MAX == ULLONG_MAX typedef unsigned long khint64_t; #else typedef unsigned long long khint64_t; #endif #ifdef _MSC_VER #define inline __inline #endif typedef khint32_t khint_t; typedef khint_t khiter_t; #define __ac_HASH_PRIME_SIZE 32 static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] = { 0ul, 3ul, 11ul, 23ul, 53ul, 97ul, 193ul, 389ul, 769ul, 1543ul, 3079ul, 6151ul, 12289ul, 24593ul, 49157ul, 98317ul, 196613ul, 393241ul, 786433ul, 1572869ul, 3145739ul, 6291469ul, 12582917ul, 25165843ul, 50331653ul, 100663319ul, 201326611ul, 402653189ul, 805306457ul, 1610612741ul, 3221225473ul, 4294967291ul }; #define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) #define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) #define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) #define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) #define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) #define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) #define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) static const double __ac_HASH_UPPER = 0.77; #define KHASH_DECLARE(name, khkey_t, khval_t) \ typedef struct { \ khint_t n_buckets, size, n_occupied, upper_bound; \ khint32_t *flags; \ khkey_t *keys; \ khval_t *vals; \ } kh_##name##_t; \ extern kh_##name##_t *kh_init_##name(); \ extern void kh_destroy_##name(kh_##name##_t *h); \ extern void kh_clear_##name(kh_##name##_t *h); \ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \ extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \ extern void kh_del_##name(kh_##name##_t *h, khint_t x); #define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ typedef struct { \ khint_t n_buckets, size, n_occupied, upper_bound; \ khint32_t *flags; \ khkey_t *keys; \ khval_t *vals; \ } kh_##name##_t; \ SCOPE kh_##name##_t *kh_init_##name() { \ return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \ } \ SCOPE void kh_destroy_##name(kh_##name##_t *h) \ { \ if (h) { \ free(h->keys); free(h->flags); \ free(h->vals); \ free(h); \ } \ } \ SCOPE void kh_clear_##name(kh_##name##_t *h) \ { \ if (h && h->flags) { \ memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \ h->size = h->n_occupied = 0; \ } \ } \ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ { \ if (h->n_buckets) { \ khint_t inc, k, i, last; \ k = __hash_func(key); i = k % h->n_buckets; \ inc = 1 + k % (h->n_buckets - 1); last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \ else i += inc; \ if (i == last) return h->n_buckets; \ } \ return __ac_iseither(h->flags, i)? h->n_buckets : i; \ } else return 0; \ } \ SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ { \ khint32_t *new_flags = 0; \ khint_t j = 1; \ { \ khint_t t = __ac_HASH_PRIME_SIZE - 1; \ while (__ac_prime_list[t] > new_n_buckets) --t; \ new_n_buckets = __ac_prime_list[t+1]; \ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; \ else { \ new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \ memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \ if (h->n_buckets < new_n_buckets) { \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) \ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } \ } \ } \ if (j) { \ for (j = 0; j != h->n_buckets; ++j) { \ if (__ac_iseither(h->flags, j) == 0) { \ khkey_t key = h->keys[j]; \ khval_t val; \ if (kh_is_map) val = h->vals[j]; \ __ac_set_isdel_true(h->flags, j); \ while (1) { \ khint_t inc, k, i; \ k = __hash_func(key); \ i = k % new_n_buckets; \ inc = 1 + k % (new_n_buckets - 1); \ while (!__ac_isempty(new_flags, i)) { \ if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \ else i += inc; \ } \ __ac_set_isempty_false(new_flags, i); \ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ __ac_set_isdel_true(h->flags, i); \ } else { \ h->keys[i] = key; \ if (kh_is_map) h->vals[i] = val; \ break; \ } \ } \ } \ } \ if (h->n_buckets > new_n_buckets) { \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) \ h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } \ free(h->flags); \ h->flags = new_flags; \ h->n_buckets = new_n_buckets; \ h->n_occupied = h->size; \ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ } \ } \ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ { \ khint_t x; \ if (h->n_occupied >= h->upper_bound) { \ if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \ else kh_resize_##name(h, h->n_buckets + 1); \ } \ { \ khint_t inc, k, i, site, last; \ x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \ if (__ac_isempty(h->flags, i)) x = i; \ else { \ inc = 1 + k % (h->n_buckets - 1); last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (__ac_isdel(h->flags, i)) site = i; \ if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \ else i += inc; \ if (i == last) { x = site; break; } \ } \ if (x == h->n_buckets) { \ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ else x = i; \ } \ } \ } \ if (__ac_isempty(h->flags, x)) { \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; ++h->n_occupied; \ *ret = 1; \ } else if (__ac_isdel(h->flags, x)) { \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; \ *ret = 2; \ } else *ret = 0; \ return x; \ } \ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ { \ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ __ac_set_isdel_true(h->flags, x); \ --h->size; \ } \ } #define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) /* --- BEGIN OF HASH FUNCTIONS --- */ /*! @function @abstract Integer hash function @param key The integer [khint32_t] @return The hash value [khint_t] */ #define kh_int_hash_func(key) (khint32_t)(key) /*! @function @abstract Integer comparison function */ #define kh_int_hash_equal(a, b) ((a) == (b)) /*! @function @abstract 64-bit integer hash function @param key The integer [khint64_t] @return The hash value [khint_t] */ #define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11) /*! @function @abstract 64-bit integer comparison function */ #define kh_int64_hash_equal(a, b) ((a) == (b)) /*! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */ static inline khint_t __ac_X31_hash_string(const char *s) { khint_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } /*! @function @abstract Another interface to const char* hash function @param key Pointer to a null terminated string [const char*] @return The hash value [khint_t] */ #define kh_str_hash_func(key) __ac_X31_hash_string(key) /*! @function @abstract Const char* comparison function */ #define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) /* --- END OF HASH FUNCTIONS --- */ /* Other necessary macros... */ /*! @abstract Type of the hash table. @param name Name of the hash table [symbol] */ #define khash_t(name) kh_##name##_t /*! @function @abstract Initiate a hash table. @param name Name of the hash table [symbol] @return Pointer to the hash table [khash_t(name)*] */ #define kh_init(name) kh_init_##name() /*! @function @abstract Destroy a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_destroy(name, h) kh_destroy_##name(h) /*! @function @abstract Reset a hash table without deallocating memory. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_clear(name, h) kh_clear_##name(h) /*! @function @abstract Resize a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param s New size [khint_t] */ #define kh_resize(name, h, s) kh_resize_##name(h, s) /*! @function @abstract Insert a key to the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @param r Extra return code: 0 if the key is present in the hash table; 1 if the bucket is empty (never used); 2 if the element in the bucket has been deleted [int*] @return Iterator to the inserted element [khint_t] */ #define kh_put(name, h, k, r) kh_put_##name(h, k, r) /*! @function @abstract Retrieve a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t] */ #define kh_get(name, h, k) kh_get_##name(h, k) /*! @function @abstract Remove a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Iterator to the element to be deleted [khint_t] */ #define kh_del(name, h, k) kh_del_##name(h, k) /*! @function @abstract Test whether a bucket contains data. @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return 1 if containing data; 0 otherwise [int] */ #define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) /*! @function @abstract Get key given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Key [type of keys] */ #define kh_key(h, x) ((h)->keys[x]) /*! @function @abstract Get value given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Value [type of values] @discussion For hash sets, calling this results in segfault. */ #define kh_val(h, x) ((h)->vals[x]) /*! @function @abstract Alias of kh_val() */ #define kh_value(h, x) ((h)->vals[x]) /*! @function @abstract Get the start iterator @param h Pointer to the hash table [khash_t(name)*] @return The start iterator [khint_t] */ #define kh_begin(h) (khint_t)(0) /*! @function @abstract Get the end iterator @param h Pointer to the hash table [khash_t(name)*] @return The end iterator [khint_t] */ #define kh_end(h) ((h)->n_buckets) /*! @function @abstract Get the number of elements in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of elements in the hash table [khint_t] */ #define kh_size(h) ((h)->size) /*! @function @abstract Get the number of buckets in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of buckets in the hash table [khint_t] */ #define kh_n_buckets(h) ((h)->n_buckets) /* More conenient interfaces */ /*! @function @abstract Instantiate a hash set containing integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT(name) \ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT(name, khval_t) \ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT64(name) \ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT64(name, khval_t) \ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) typedef const char *kh_cstr_t; /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_STR(name) \ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_STR(name, khval_t) \ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) #endif /* __AC_KHASH_H */ pysam-0.7.7/samtools/kseq.h0000664000076400007650000002115312162637166015476 0ustar andreasandreas/* The MIT License Copyright (c) 2008, 2009, 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Last Modified: 05MAR2012 */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) #define KS_SEP_MAX 2 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ unsigned char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ { \ if (dret) *dret = 0; \ str->l = append? str->l : 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter == KS_SEP_LINE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == '\n') break; \ } else if (delimiter > KS_SEP_MAX) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (str->s == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ str->s[str->l] = '\0'; \ return str->l; \ } \ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { return ks_getuntil2(ks, delimiter, str, dret, 0); } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) #define __KSEQ_BASIC(SCOPE, type_t) \ SCOPE kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ SCOPE void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string */ #define __KSEQ_READ(SCOPE) \ SCOPE int kseq_read(kseq_t *seq) \ { \ int c; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ if (c == -1) return -1; /* end of file */ \ seq->last_char = c; \ } /* else: the first header char has been read in the previous call */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ seq->seq.m = 256; \ seq->seq.s = (char*)malloc(seq->seq.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ if (c == '\n') continue; /* skip empty lines */ \ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* error: no quality string */ \ while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT2(SCOPE, type_t, __read) \ KSTREAM_INIT(type_t, __read, 16384) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(SCOPE, type_t) \ __KSEQ_READ(SCOPE) #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) #define KSEQ_DECLARE(type_t) \ __KS_TYPE(type_t) \ __KSEQ_TYPE(type_t) \ extern kseq_t *kseq_init(type_t fd); \ void kseq_destroy(kseq_t *ks); \ int kseq_read(kseq_t *seq); #endif pysam-0.7.7/samtools/sample.h0000664000076400007650000000061412162637166016013 0ustar andreasandreas#ifndef BAM_SAMPLE_H #define BAM_SAMPLE_H #include "kstring.h" typedef struct { int n, m; char **smpl; void *rg2smid, *sm2id; } bam_sample_t; bam_sample_t *bam_smpl_init(void); int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt); int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str); void bam_smpl_destroy(bam_sample_t *sm); #endif pysam-0.7.7/samtools/knetfile.c.pysam.c0000664000076400007650000004371012162637166017703 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008 by Genome Research Ltd (GRL). 2010 by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Probably I will not do socket programming in the next few years and therefore I decide to heavily annotate this file, for Linux and Windows as well. -ac */ #include #include #include #include #include #include #include #include #ifndef _WIN32 #include #include #include #endif #include "knetfile.h" /* In winsock.h, the type of a socket is SOCKET, which is: "typedef * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed * integer -1. In knetfile.c, I use "int" for socket type * throughout. This should be improved to avoid confusion. * * In Linux/Mac, recv() and read() do almost the same thing. You can see * in the header file that netread() is simply an alias of read(). In * Windows, however, they are different and using recv() is mandatory. */ /* This function tests if the file handler is ready for reading (or * writing if is_read==0). */ static int socket_wait(int fd, int is_read) { fd_set fds, *fdr = 0, *fdw = 0; struct timeval tv; int ret; tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out FD_ZERO(&fds); FD_SET(fd, &fds); if (is_read) fdr = &fds; else fdw = &fds; ret = select(fd+1, fdr, fdw, 0, &tv); #ifndef _WIN32 if (ret == -1) perror("select"); #else if (ret == 0) fprintf(pysamerr, "select time-out\n"); else if (ret == SOCKET_ERROR) fprintf(pysamerr, "select: %d\n", WSAGetLastError()); #endif return ret; } #ifndef _WIN32 /* This function does not work with Windows due to the lack of * getaddrinfo() in winsock. It is addapted from an example in "Beej's * Guide to Network Programming" (http://beej.us/guide/bgnet/). */ static int socket_connect(const char *host, const char *port) { #define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0) int on = 1, fd; struct linger lng = { 0, 0 }; struct addrinfo hints, *res = 0; memset(&hints, 0, sizeof(struct addrinfo)); hints.ai_family = AF_UNSPEC; hints.ai_socktype = SOCK_STREAM; /* In Unix/Mac, getaddrinfo() is the most convenient way to get * server information. */ if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo"); if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket"); /* The following two setsockopt() are used by ftplib * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they * necessary. */ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt"); if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect"); freeaddrinfo(res); return fd; } #else /* MinGW's printf has problem with "%lld" */ char *int64tostr(char *buf, int64_t x) { int cnt; int i = 0; do { buf[i++] = '0' + x % 10; x /= 10; } while (x); buf[i] = 0; for (cnt = i, i = 0; i < cnt/2; ++i) { int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c; } return buf; } int64_t strtoint64(const char *buf) { int64_t x; for (x = 0; *buf != '\0'; ++buf) x = x * 10 + ((int64_t) *buf - 48); return x; } /* In windows, the first thing is to establish the TCP connection. */ int knet_win32_init() { WSADATA wsaData; return WSAStartup(MAKEWORD(2, 2), &wsaData); } void knet_win32_destroy() { WSACleanup(); } /* A slightly modfied version of the following function also works on * Mac (and presummably Linux). However, this function is not stable on * my Mac. It sometimes works fine but sometimes does not. Therefore for * non-Windows OS, I do not use this one. */ static SOCKET socket_connect(const char *host, const char *port) { #define __err_connect(func) \ do { \ fprintf(pysamerr, "%s: %d\n", func, WSAGetLastError()); \ return -1; \ } while (0) int on = 1; SOCKET fd; struct linger lng = { 0, 0 }; struct sockaddr_in server; struct hostent *hp = 0; // open socket if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket"); if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt"); if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt"); // get host info if (isalpha(host[0])) hp = gethostbyname(host); else { struct in_addr addr; addr.s_addr = inet_addr(host); hp = gethostbyaddr((char*)&addr, 4, AF_INET); } if (hp == 0) __err_connect("gethost"); // connect server.sin_addr.s_addr = *((unsigned long*)hp->h_addr); server.sin_family= AF_INET; server.sin_port = htons(atoi(port)); if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect"); // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!) return fd; } #endif static off_t my_netread(int fd, void *buf, off_t len) { off_t rest = len, curr, l = 0; /* recv() and read() may not read the required length of data with * one call. They have to be called repeatedly. */ while (rest) { if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading curr = netread(fd, buf + l, rest); /* According to the glibc manual, section 13.2, a zero returned * value indicates end-of-file (EOF), which should mean that * read() will not return zero if EOF has not been met but data * are not immediately available. */ if (curr == 0) break; l += curr; rest -= curr; } return l; } /************************* * FTP specific routines * *************************/ static int kftp_get_response(knetFile *ftp) { #ifndef _WIN32 unsigned char c; #else char c; #endif int n = 0; char *p; if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0; while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O //fputc(c, pysamerr); if (n >= ftp->max_response) { ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256; ftp->response = realloc(ftp->response, ftp->max_response); } ftp->response[n++] = c; if (c == '\n') { if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) && ftp->response[3] != '-') break; n = 0; continue; } } if (n < 2) return -1; ftp->response[n-2] = 0; return strtol(ftp->response, &p, 0); } static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get) { if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); return is_get? kftp_get_response(ftp) : 0; } static int kftp_pasv_prep(knetFile *ftp) { char *p; int v[6]; kftp_send_cmd(ftp, "PASV\r\n", 1); for (p = ftp->response; *p && *p != '('; ++p); if (*p != '(') return -1; ++p; sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]); memcpy(ftp->pasv_ip, v, 4 * sizeof(int)); ftp->pasv_port = (v[4]<<8&0xff00) + v[5]; return 0; } static int kftp_pasv_connect(knetFile *ftp) { char host[80], port[10]; if (ftp->pasv_port == 0) { fprintf(pysamerr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n"); return -1; } sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]); sprintf(port, "%d", ftp->pasv_port); ftp->fd = socket_connect(host, port); if (ftp->fd == -1) return -1; return 0; } int kftp_connect(knetFile *ftp) { ftp->ctrl_fd = socket_connect(ftp->host, ftp->port); if (ftp->ctrl_fd == -1) return -1; kftp_get_response(ftp); kftp_send_cmd(ftp, "USER anonymous\r\n", 1); kftp_send_cmd(ftp, "PASS kftp@\r\n", 1); kftp_send_cmd(ftp, "TYPE I\r\n", 1); return 0; } int kftp_reconnect(knetFile *ftp) { if (ftp->ctrl_fd != -1) { netclose(ftp->ctrl_fd); ftp->ctrl_fd = -1; } netclose(ftp->fd); ftp->fd = -1; return kftp_connect(ftp); } // initialize ->type, ->host, ->retr and ->size knetFile *kftp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p; int l; if (strstr(fn, "ftp://") != fn) return 0; for (p = (char*)fn + 6; *p && *p != '/'; ++p); if (*p != '/') return 0; l = p - fn - 6; fp = calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_FTP; fp->fd = -1; /* the Linux/Mac version of socket_connect() also recognizes a port * like "ftp", but the Windows version does not. */ fp->port = strdup("21"); fp->host = calloc(l + 1, 1); if (strchr(mode, 'c')) fp->no_reconnect = 1; strncpy(fp->host, fn + 6, l); fp->retr = calloc(strlen(p) + 8, 1); sprintf(fp->retr, "RETR %s\r\n", p); fp->size_cmd = calloc(strlen(p) + 8, 1); sprintf(fp->size_cmd, "SIZE %s\r\n", p); fp->seek_offset = 0; return fp; } // place ->fd at offset off int kftp_connect_file(knetFile *fp) { int ret; long long file_size; if (fp->fd != -1) { netclose(fp->fd); if (fp->no_reconnect) kftp_get_response(fp); } kftp_pasv_prep(fp); kftp_send_cmd(fp, fp->size_cmd, 1); #ifndef _WIN32 if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) { fprintf(pysamerr,"[kftp_connect_file] %s\n", fp->response); return -1; } #else const char *p = fp->response; while (*p != ' ') ++p; while (*p < '0' || *p > '9') ++p; file_size = strtoint64(p); #endif fp->file_size = file_size; if (fp->offset>=0) { char tmp[32]; #ifndef _WIN32 sprintf(tmp, "REST %lld\r\n", (long long)fp->offset); #else strcpy(tmp, "REST "); int64tostr(tmp + 5, fp->offset); strcat(tmp, "\r\n"); #endif kftp_send_cmd(fp, tmp, 1); } kftp_send_cmd(fp, fp->retr, 0); kftp_pasv_connect(fp); ret = kftp_get_response(fp); if (ret != 150) { fprintf(pysamerr, "[kftp_connect_file] %s\n", fp->response); netclose(fp->fd); fp->fd = -1; return -1; } fp->is_ready = 1; return 0; } /************************** * HTTP specific routines * **************************/ knetFile *khttp_parse_url(const char *fn, const char *mode) { knetFile *fp; char *p, *proxy, *q; int l; if (strstr(fn, "http://") != fn) return 0; // set ->http_host for (p = (char*)fn + 7; *p && *p != '/'; ++p); l = p - fn - 7; fp = calloc(1, sizeof(knetFile)); fp->http_host = calloc(l + 1, 1); strncpy(fp->http_host, fn + 7, l); fp->http_host[l] = 0; for (q = fp->http_host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; // get http_proxy proxy = getenv("http_proxy"); // set ->host, ->port and ->path if (proxy == 0) { fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name. fp->port = strdup(*q? q : "80"); fp->path = strdup(*p? p : "/"); } else { fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy); for (q = fp->host; *q && *q != ':'; ++q); if (*q == ':') *q++ = 0; fp->port = strdup(*q? q : "80"); fp->path = strdup(fn); } fp->type = KNF_TYPE_HTTP; fp->ctrl_fd = fp->fd = -1; fp->seek_offset = 0; return fp; } int khttp_connect_file(knetFile *fp) { int ret, l = 0; char *buf, *p; if (fp->fd != -1) netclose(fp->fd); fp->fd = socket_connect(fp->host, fp->port); buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough. l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host); l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset); l += sprintf(buf + l, "\r\n"); netwrite(fp->fd, buf, l); l = 0; while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency if (buf[l] == '\n' && l >= 3) if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break; ++l; } buf[l] = 0; if (l < 14) { // prematured header netclose(fp->fd); fp->fd = -1; return -1; } ret = strtol(buf + 8, &p, 0); // HTTP return code if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file off_t rest = fp->offset; while (rest) { off_t l = rest < 0x10000? rest : 0x10000; rest -= my_netread(fp->fd, buf, l); } } else if (ret != 206 && ret != 200) { free(buf); fprintf(pysamerr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret); netclose(fp->fd); fp->fd = -1; return -1; } free(buf); fp->is_ready = 1; return 0; } /******************** * Generic routines * ********************/ knetFile *knet_open(const char *fn, const char *mode) { knetFile *fp = 0; if (mode[0] != 'r') { fprintf(pysamerr, "[kftp_open] only mode \"r\" is supported.\n"); return 0; } if (strstr(fn, "ftp://") == fn) { fp = kftp_parse_url(fn, mode); if (fp == 0) return 0; if (kftp_connect(fp) == -1) { knet_close(fp); return 0; } kftp_connect_file(fp); } else if (strstr(fn, "http://") == fn) { fp = khttp_parse_url(fn, mode); if (fp == 0) return 0; khttp_connect_file(fp); } else { // local file #ifdef _WIN32 /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may * be undefined on some systems, although it is defined on my * Mac and the Linux I have tested on. */ int fd = open(fn, O_RDONLY | O_BINARY); #else int fd = open(fn, O_RDONLY); #endif if (fd == -1) { perror("open"); return 0; } fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; fp->ctrl_fd = -1; } if (fp && fp->fd == -1) { knet_close(fp); return 0; } return fp; } knetFile *knet_dopen(int fd, const char *mode) { knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile)); fp->type = KNF_TYPE_LOCAL; fp->fd = fd; return fp; } off_t knet_read(knetFile *fp, void *buf, off_t len) { off_t l = 0; if (fp->fd == -1) return 0; if (fp->type == KNF_TYPE_FTP) { if (fp->is_ready == 0) { if (!fp->no_reconnect) kftp_reconnect(fp); kftp_connect_file(fp); } } else if (fp->type == KNF_TYPE_HTTP) { if (fp->is_ready == 0) khttp_connect_file(fp); } if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX off_t rest = len, curr; while (rest) { do { curr = read(fp->fd, buf + l, rest); } while (curr < 0 && EINTR == errno); if (curr < 0) return -1; if (curr == 0) break; l += curr; rest -= curr; } } else l = my_netread(fp->fd, buf, len); fp->offset += l; return l; } off_t knet_seek(knetFile *fp, int64_t off, int whence) { if (whence == SEEK_SET && off == fp->offset) return 0; if (fp->type == KNF_TYPE_LOCAL) { /* Be aware that lseek() returns the offset after seeking, * while fseek() returns zero on success. */ off_t offset = lseek(fp->fd, off, whence); if (offset == -1) { // Be silent, it is OK for knet_seek to fail when the file is streamed // fprintf(pysamerr,"[knet_seek] %s\n", strerror(errno)); return -1; } fp->offset = offset; return 0; } else if (fp->type == KNF_TYPE_FTP) { if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; else if ( whence==SEEK_END) fp->offset = fp->file_size+off; fp->is_ready = 0; return 0; } else if (fp->type == KNF_TYPE_HTTP) { if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future? fprintf(pysamerr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n"); errno = ESPIPE; return -1; } if (whence==SEEK_CUR) fp->offset += off; else if (whence==SEEK_SET) fp->offset = off; fp->is_ready = 0; return 0; } errno = EINVAL; fprintf(pysamerr,"[knet_seek] %s\n", strerror(errno)); return -1; } int knet_close(knetFile *fp) { if (fp == 0) return 0; if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific if (fp->fd != -1) { /* On Linux/Mac, netclose() is an alias of close(), but on * Windows, it is an alias of closesocket(). */ if (fp->type == KNF_TYPE_LOCAL) close(fp->fd); else netclose(fp->fd); } free(fp->host); free(fp->port); free(fp->response); free(fp->retr); // FTP specific free(fp->path); free(fp->http_host); // HTTP specific free(fp); return 0; } #ifdef KNETFILE_MAIN int main(void) { char *buf; knetFile *fp; int type = 4, l; #ifdef _WIN32 knet_win32_init(); #endif buf = calloc(0x100000, 1); if (type == 0) { fp = knet_open("knetfile.c", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 1) { // NCBI FTP, large file fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); knet_seek(fp, 2500000000ll, SEEK_SET); l = knet_read(fp, buf, 255); } else if (type == 2) { fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 3) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r"); knet_seek(fp, 1000, SEEK_SET); } else if (type == 4) { fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r"); knet_read(fp, buf, 10000); knet_seek(fp, 20000, SEEK_SET); knet_seek(fp, 10000, SEEK_SET); l = knet_read(fp, buf+10000, 10000000) + 10000; } if (type != 4 && type != 1) { knet_read(fp, buf, 255); buf[255] = 0; printf("%s\n", buf); } else write(fileno(stdout), buf, l); knet_close(fp); free(buf); return 0; } #endif pysam-0.7.7/samtools/sam_view.c.pysam.c0000664000076400007650000003520312162637166017712 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include "sam_header.h" #include "sam.h" #include "faidx.h" #include "kstring.h" #include "khash.h" KHASH_SET_INIT_STR(rg) // When counting records instead of printing them, // data passed to the bam_fetch callback is encapsulated in this struct. typedef struct { bam_header_t *header; int64_t *count; // int does overflow for very big BAMs } count_func_data_t; typedef khash_t(rg) *rghash_t; // FIXME: we'd better use no global variables... static rghash_t g_rghash = 0; static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0, g_min_qlen = 0; static uint32_t g_subsam_seed = 0; static double g_subsam_frac = -1.; static char *g_library, *g_rg; static void *g_bed; void *bed_read(const char *fn); void bed_destroy(void *_h); int bed_overlap(const void *_h, const char *chr, int beg, int end); static int process_aln(const bam_header_t *h, bam1_t *b) { if (g_qual_scale > 1) { int i; uint8_t *qual = bam1_qual(b); for (i = 0; i < b->core.l_qseq; ++i) { int c = qual[i] * g_qual_scale; qual[i] = c < 93? c : 93; } } if (g_min_qlen > 0) { int k, qlen = 0; uint32_t *cigar = bam1_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP) qlen += bam_cigar_oplen(cigar[k]); if (qlen < g_min_qlen) return 1; } if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off)) return 1; if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)))) return 1; if (g_subsam_frac > 0.) { uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + g_subsam_seed; if ((double)(k&0xffffff) / 0x1000000 >= g_subsam_frac) return 1; } if (g_rg || g_rghash) { uint8_t *s = bam_aux_get(b, "RG"); if (s) { if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1; if (g_rghash) { khint_t k = kh_get(rg, g_rghash, (char*)(s + 1)); return (k != kh_end(g_rghash))? 0 : 1; } } } if (g_library) { const char *p = bam_get_library((bam_header_t*)h, b); return (p && strcmp(p, g_library) == 0)? 0 : 1; } return 0; } static char *drop_rg(char *hdtxt, rghash_t h, int *len) { char *p = hdtxt, *q, *r, *s; kstring_t str; memset(&str, 0, sizeof(kstring_t)); while (1) { int toprint = 0; q = strchr(p, '\n'); if (q == 0) q = p + strlen(p); if (q - p < 3) break; // the line is too short; then stop if (strncmp(p, "@RG\t", 4) == 0) { int c; khint_t k; if ((r = strstr(p, "\tID:")) != 0) { r += 4; for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s); c = *s; *s = '\0'; k = kh_get(rg, h, r); *s = c; if (k != kh_end(h)) toprint = 1; } } else toprint = 1; if (toprint) { kputsn(p, q - p, &str); kputc('\n', &str); } p = q + 1; } *len = str.l; return str.s; } // callback function for bam_fetch() that prints nonskipped records static int view_func(const bam1_t *b, void *data) { if (!process_aln(((samfile_t*)data)->header, (bam1_t*)b)) samwrite((samfile_t*)data, b); return 0; } // callback function for bam_fetch() that counts nonskipped records static int count_func(const bam1_t *b, void *data) { if (!process_aln(((count_func_data_t*)data)->header, (bam1_t*)b)) { (*((count_func_data_t*)data)->count)++; } return 0; } static int usage(int is_long_help); int main_samview(int argc, char *argv[]) { int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0; int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0; int64_t count = 0; samfile_t *in = 0, *out = 0; char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:m:")) >= 0) { switch (c) { case 's': if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) { srand(g_subsam_seed); g_subsam_seed = rand(); } g_subsam_frac = strtod(q, &q); break; case 'm': g_min_qlen = atoi(optarg); break; case 'c': is_count = 1; break; case 'S': is_bamin = 0; break; case 'b': is_bamout = 1; break; case 't': fn_list = strdup(optarg); is_bamin = 0; break; case 'h': is_header = 1; break; case 'H': is_header_only = 1; break; case 'o': fn_out = strdup(optarg); break; case 'f': g_flag_on = strtol(optarg, 0, 0); break; case 'F': g_flag_off = strtol(optarg, 0, 0); break; case 'q': g_min_mapQ = atoi(optarg); break; case 'u': compress_level = 0; break; case '1': compress_level = 1; break; case 'l': g_library = strdup(optarg); break; case 'L': g_bed = bed_read(optarg); break; case 'r': g_rg = strdup(optarg); break; case 'R': fn_rg = strdup(optarg); break; case 'x': of_type = BAM_OFHEX; break; case 'X': of_type = BAM_OFSTR; break; case '?': is_long_help = 1; break; case 'T': fn_ref = strdup(optarg); is_bamin = 0; break; case 'B': bam_no_B = 1; break; case 'Q': g_qual_scale = atoi(optarg); break; case '@': n_threads = strtol(optarg, 0, 0); break; default: return usage(is_long_help); } } if (compress_level >= 0) is_bamout = 1; if (is_header_only) is_header = 1; if (is_bamout) strcat(out_mode, "b"); else { if (of_type == BAM_OFHEX) strcat(out_mode, "x"); else if (of_type == BAM_OFSTR) strcat(out_mode, "X"); } if (is_bamin) strcat(in_mode, "b"); if (is_header) strcat(out_mode, "h"); if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); } if (argc == optind) return usage(is_long_help); // potential memory leak... // read the list of read groups if (fn_rg) { FILE *fp_rg; char buf[1024]; int ret; g_rghash = kh_init(rg); fp_rg = fopen(fn_rg, "r"); while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me... kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates... fclose(fp_rg); } // generate the fn_list if necessary if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref); // open file handlers if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) { fprintf(pysamerr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]); ret = 1; goto view_end; } if (in->header == 0) { fprintf(pysamerr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]); ret = 1; goto view_end; } if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for... char *tmp; int l; tmp = drop_rg(in->header->text, g_rghash, &l); free(in->header->text); in->header->text = tmp; in->header->l_text = l; } if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) { fprintf(pysamerr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output"); ret = 1; goto view_end; } if (n_threads > 1) samthreads(out, n_threads, 256); if (is_header_only) goto view_end; // no need to print alignments if (argc == optind + 1) { // convert/print the entire file bam1_t *b = bam_init1(); int r; while ((r = samread(in, b)) >= 0) { // read one alignment from `in' if (!process_aln(in->header, b)) { if (!is_count) samwrite(out, b); // write the alignment to `out' count++; } } if (r < -1) { fprintf(pysamerr, "[main_samview] truncated file.\n"); ret = 1; } bam_destroy1(b); } else { // retrieve alignments in specified regions int i; bam_index_t *idx = 0; if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index if (idx == 0) { // index is unavailable fprintf(pysamerr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n"); ret = 1; goto view_end; } for (i = optind + 1; i < argc; ++i) { int tid, beg, end, result; bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200' if (tid < 0) { // reference name is not found fprintf(pysamerr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]); continue; } // fetch alignments if (is_count) { count_func_data_t count_data = { in->header, &count }; result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func); } else result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); if (result < 0) { fprintf(pysamerr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]); ret = 1; break; } } bam_index_destroy(idx); // destroy the BAM index } view_end: if (is_count && ret == 0) printf("%" PRId64 "\n", count); // close files, free and return free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg); if (g_bed) bed_destroy(g_bed); if (g_rghash) { khint_t k; for (k = 0; k < kh_end(g_rghash); ++k) if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k)); kh_destroy(rg, g_rghash); } samclose(in); if (!is_count) samclose(out); return ret; } static int usage(int is_long_help) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools view [options] | [region1 [...]]\n\n"); fprintf(pysamerr, "Options: -b output BAM\n"); fprintf(pysamerr, " -h print header for the SAM output\n"); fprintf(pysamerr, " -H print header only (no alignments)\n"); fprintf(pysamerr, " -S input is SAM\n"); fprintf(pysamerr, " -u uncompressed BAM output (force -b)\n"); fprintf(pysamerr, " -1 fast compression (force -b)\n"); fprintf(pysamerr, " -x output FLAG in HEX (samtools-C specific)\n"); fprintf(pysamerr, " -X output FLAG in string (samtools-C specific)\n"); fprintf(pysamerr, " -c print only the count of matching records\n"); fprintf(pysamerr, " -B collapse the backward CIGAR operation\n"); fprintf(pysamerr, " -@ INT number of BAM compression threads [0]\n"); fprintf(pysamerr, " -L FILE output alignments overlapping the input BED FILE [null]\n"); fprintf(pysamerr, " -t FILE list of reference names and lengths (force -S) [null]\n"); fprintf(pysamerr, " -T FILE reference sequence file (force -S) [null]\n"); fprintf(pysamerr, " -o FILE output file name [stdout]\n"); fprintf(pysamerr, " -R FILE list of read groups to be outputted [null]\n"); fprintf(pysamerr, " -f INT required flag, 0 for unset [0]\n"); fprintf(pysamerr, " -F INT filtering flag, 0 for unset [0]\n"); fprintf(pysamerr, " -q INT minimum mapping quality [0]\n"); fprintf(pysamerr, " -l STR only output reads in library STR [null]\n"); fprintf(pysamerr, " -r STR only output reads in read group STR [null]\n"); fprintf(pysamerr, " -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n"); fprintf(pysamerr, " -? longer help\n"); fprintf(pysamerr, "\n"); if (is_long_help) fprintf(pysamerr, "Notes:\n\ \n\ 1. By default, this command assumes the file on the command line is in\n\ the BAM format and it prints the alignments in SAM. If `-t' is\n\ applied, the input file is assumed to be in the SAM format. The\n\ file supplied with `-t' is SPACE/TAB delimited with the first two\n\ fields of each line consisting of the reference name and the\n\ corresponding sequence length. The `.fai' file generated by `faidx'\n\ can be used here. This file may be empty if reads are unaligned.\n\ \n\ 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\ \n\ 3. BAM->SAM conversion: `samtools view in.bam'.\n\ \n\ 4. A region should be presented in one of the following formats:\n\ `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\ specified, the input alignment file must be an indexed BAM file.\n\ \n\ 5. Option `-u' is preferred over `-b' when the output is piped to\n\ another samtools command.\n\ \n\ 6. In a string FLAG, each character represents one bit with\n\ p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\ U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\ 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\ f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\ `-X' are samtools-C specific. Picard and older samtools do not\n\ support HEX or string flags.\n\ \n"); return 1; } int main_import(int argc, char *argv[]) { int argc2, ret; char **argv2; if (argc != 4) { fprintf(pysamerr, "Usage: bamtk import \n"); return 1; } argc2 = 6; argv2 = calloc(6, sizeof(char*)); argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2]; ret = main_samview(argc2, argv2); free(argv2); return ret; } int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 }; int main_bam2fq(int argc, char *argv[]) { bamFile fp; bam_header_t *h; bam1_t *b; int8_t *buf; int max_buf, c, no12 = 0; while ((c = getopt(argc, argv, "n")) > 0) if (c == 'n') no12 = 1; if (argc == 1) { fprintf(pysamerr, "Usage: samtools bam2fq \n"); return 1; } fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r"); if (fp == 0) return 1; h = bam_header_read(fp); b = bam_init1(); buf = 0; max_buf = 0; while (bam_read1(fp, b) >= 0) { int i, qlen = b->core.l_qseq; uint8_t *seq; putchar('@'); fputs(bam1_qname(b), stdout); if (no12) putchar('\n'); else { if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1"); else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2"); else putchar('\n'); } if (max_buf < qlen + 1) { max_buf = qlen + 1; kroundup32(max_buf); buf = realloc(buf, max_buf); } buf[qlen] = 0; seq = bam1_seq(b); for (i = 0; i < qlen; ++i) buf[i] = bam1_seqi(seq, i); if (b->core.flag & 16) { // reverse complement for (i = 0; i < qlen>>1; ++i) { int8_t t = seq_comp_table[buf[qlen - 1 - i]]; buf[qlen - 1 - i] = seq_comp_table[buf[i]]; buf[i] = t; } if (qlen&1) buf[i] = seq_comp_table[buf[i]]; } for (i = 0; i < qlen; ++i) buf[i] = bam_nt16_rev_table[buf[i]]; puts((char*)buf); puts("+"); seq = bam1_qual(b); for (i = 0; i < qlen; ++i) buf[i] = 33 + seq[i]; if (b->core.flag & 16) { // reverse for (i = 0; i < qlen>>1; ++i) { int8_t t = buf[qlen - 1 - i]; buf[qlen - 1 - i] = buf[i]; buf[i] = t; } } puts((char*)buf); } free(buf); bam_destroy1(b); bam_header_destroy(h); bam_close(fp); return 0; } pysam-0.7.7/samtools/pysam.h0000664000076400007650000000012212162637166015655 0ustar andreasandreas#ifndef PYSAM_H #define PYSAM_H #include "stdio.h" extern FILE * pysamerr; #endif pysam-0.7.7/samtools/bgzf.h0000664000076400007650000001426612162637166015472 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011, 2012 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* The BGZF library was originally written by Bob Handsaker from the Broad * Institute. It was later improved by the SAMtools developers. */ #ifndef __BGZF_H #define __BGZF_H #include #include #include #include #define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE #define BGZF_MAX_BLOCK_SIZE 0x10000 #define BGZF_ERR_ZLIB 1 #define BGZF_ERR_HEADER 2 #define BGZF_ERR_IO 4 #define BGZF_ERR_MISUSE 8 typedef struct { int errcode:16, is_write:2, compress_level:14; int cache_size; int block_length, block_offset; int64_t block_address; void *uncompressed_block, *compressed_block; void *cache; // a pointer to a hash table void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading void *mt; // only used for multi-threading } BGZF; #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifdef __cplusplus extern "C" { #endif /****************** * Basic routines * ******************/ /** * Open an existing file descriptor for reading or writing. * * @param fd file descriptor * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored. * @return BGZF file handler; 0 on error */ BGZF* bgzf_dopen(int fd, const char *mode); #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility /** * Open the specified file for reading or writing. */ BGZF* bgzf_open(const char* path, const char *mode); /** * Close the BGZF and free all associated resources. * * @param fp BGZF file handler * @return 0 on success and -1 on error */ int bgzf_close(BGZF *fp); /** * Read up to _length_ bytes from the file storing into _data_. * * @param fp BGZF file handler * @param data data array to read into * @param length size of data to read * @return number of bytes actually read; 0 on end-of-file and -1 on error */ ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length); /** * Write _length_ bytes from _data_ to the file. * * @param fp BGZF file handler * @param data data array to write * @param length size of data to write * @return number of bytes actually written; -1 on error */ ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length); /** * Write the data in the buffer to the file. */ int bgzf_flush(BGZF *fp); /** * Return a virtual file pointer to the current location in the file. * No interpetation of the value should be made, other than a subsequent * call to bgzf_seek can be used to position the file at the same point. * Return value is non-negative on success. */ #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF)) /** * Set the file to read from the location specified by _pos_. * * @param fp BGZF file handler * @param pos virtual file offset returned by bgzf_tell() * @param whence must be SEEK_SET * @return 0 on success and -1 on error */ int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence); /** * Check if the BGZF end-of-file (EOF) marker is present * * @param fp BGZF file handler opened for reading * @return 1 if EOF is present; 0 if not or on I/O error */ int bgzf_check_EOF(BGZF *fp); /** * Check if a file is in the BGZF format * * @param fn file name * @return 1 if _fn_ is BGZF; 0 if not or on I/O error */ int bgzf_is_bgzf(const char *fn); /********************* * Advanced routines * *********************/ /** * Set the cache size. Only effective when compiled with -DBGZF_CACHE. * * @param fp BGZF file handler * @param size size of cache in bytes; 0 to disable caching (default) */ void bgzf_set_cache_size(BGZF *fp, int size); /** * Flush the file if the remaining buffer size is smaller than _size_ */ int bgzf_flush_try(BGZF *fp, ssize_t size); /** * Read one byte from a BGZF file. It is faster than bgzf_read() * @param fp BGZF file handler * @return byte read; -1 on end-of-file or error */ int bgzf_getc(BGZF *fp); /** * Read one line from a BGZF file. It is faster than bgzf_getc() * * @param fp BGZF file handler * @param delim delimitor * @param str string to write to; must be initialized * @return length of the string; 0 on end-of-file; negative on error */ int bgzf_getline(BGZF *fp, int delim, kstring_t *str); /** * Read the next BGZF block. */ int bgzf_read_block(BGZF *fp); /** * Enable multi-threading (only effective on writing) * * @param fp BGZF file handler; must be opened for writing * @param n_threads #threads used for writing * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended */ int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bam_tview.h0000664000076400007650000000353012162637166016507 0ustar andreasandreas#ifndef BAM_TVIEW_H #define BAM_TVIEW_H #include #include #include #include #include #include #include "bam.h" #include "faidx.h" #include "bam2bcf.h" #include "sam_header.h" #include "khash.h" KHASH_MAP_INIT_STR(kh_rg, const char *) typedef struct AbstractTview { int mrow, mcol; bam_index_t *idx; bam_lplbuf_t *lplbuf; bam_header_t *header; bamFile fp; int curr_tid, left_pos; faidx_t *fai; bcf_callaux_t *bca; int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name; char *ref; khash_t(kh_rg) *rg_hash; /* callbacks */ void (*my_destroy)(struct AbstractTview* ); void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...); void (*my_mvaddch)(struct AbstractTview*,int,int,int); void (*my_attron)(struct AbstractTview*,int); void (*my_attroff)(struct AbstractTview*,int); void (*my_clear)(struct AbstractTview*); int (*my_colorpair)(struct AbstractTview*,int); int (*my_drawaln)(struct AbstractTview*,int,int); int (*my_loop)(struct AbstractTview*); int (*my_underline)(struct AbstractTview*); } tview_t; char bam_aux_getCEi(bam1_t *b, int i); char bam_aux_getCSi(bam1_t *b, int i); char bam_aux_getCQi(bam1_t *b, int i); #define TV_MIN_ALNROW 2 #define TV_MAX_GOTO 40 #define TV_LOW_MAPQ 10 #define TV_COLOR_MAPQ 0 #define TV_COLOR_BASEQ 1 #define TV_COLOR_NUCL 2 #define TV_COLOR_COL 3 #define TV_COLOR_COLQ 4 #define TV_BASE_NUCL 0 #define TV_BASE_COLOR_SPACE 1 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data); int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples); void base_tv_destroy(tview_t*); int base_draw_aln(tview_t *tv, int tid, int pos); typedef struct Tixel { int ch; int attributes; }tixel_t; #endif pysam-0.7.7/samtools/bam2bcf_indel.c.pysam.c0000664000076400007650000004373112162637166020554 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bam.h" #include "bam2bcf.h" #include "kaln.h" #include "kprobaln.h" #include "khash.h" KHASH_SET_INIT_STR(rg) #include "ksort.h" KSORT_INIT_GENERIC(uint32_t) #define MINUS_CONST 0x10000000 #define INDEL_WINDOW_SIZE 50 void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list) { const char *s, *p, *q, *r, *t; khash_t(rg) *hash; if (list == 0 || hdtext == 0) return _hash; if (_hash == 0) _hash = kh_init(rg); hash = (khash_t(rg)*)_hash; if ((s = strstr(hdtext, "@RG\t")) == 0) return hash; do { t = strstr(s + 4, "@RG\t"); // the next @RG if ((p = strstr(s, "\tID:")) != 0) p += 4; if ((q = strstr(s, "\tPL:")) != 0) q += 4; if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present int lp, lq; char *x; for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; x = calloc((lp > lq? lp : lq) + 1, 1); for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r; if (strstr(list, x)) { // insert ID to the hash table khint_t k; int ret; for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r; x[r-p] = 0; k = kh_get(rg, hash, x); if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret); else free(x); } else free(x); } s = t; } while (s); return hash; } void bcf_call_del_rghash(void *_hash) { khint_t k; khash_t(rg) *hash = (khash_t(rg)*)_hash; if (hash == 0) return; for (k = kh_begin(hash); k < kh_end(hash); ++k) if (kh_exist(hash, k)) free((char*)kh_key(hash, k)); kh_destroy(rg, hash); } static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos) { int k, x = c->pos, y = 0, last_y = 0; *_tpos = c->pos; for (k = 0; k < c->n_cigar; ++k) { int op = cigar[k] & BAM_CIGAR_MASK; int l = cigar[k] >> BAM_CIGAR_SHIFT; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (c->pos > tpos) return y; if (x + l > tpos) { *_tpos = tpos; return y + (tpos - x); } x += l; y += l; last_y = y; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; else if (op == BAM_CDEL || op == BAM_CREF_SKIP) { if (x + l > tpos) { *_tpos = is_left? x : x + l; return y; } x += l; } } *_tpos = x; return last_y; } // FIXME: check if the inserted sequence is consistent with the homopolymer run // l is the relative gap length and l_run is the length of the homopolymer on the reference static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run) { int q, qh; q = bca->openQ + bca->extQ * (abs(l) - 1); qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000; return q < qh? q : qh; } static inline int est_indelreg(int pos, const char *ref, int l, char *ins4) { int i, j, max = 0, max_i = pos, score = 0; l = abs(l); for (i = pos + 1, j = 0; ref[i]; ++i, ++j) { if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1; else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1; if (score < 0) break; if (max < score) max = score, max_i = i; } return max_i - pos; } /* * @n: number of samples */ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref, const void *rghash) { int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2; int N, K, l_run, ref_type, n_alt; char *inscns = 0, *ref2, *query, **ref_sample; khash_t(rg) *hash = (khash_t(rg)*)rghash; if (ref == 0 || bca == 0) return -1; // mark filtered reads if (rghash) { N = 0; for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; const uint8_t *rg = bam_aux_get(p->b, "RG"); p->aux = 1; // filtered by default if (rg) { khint_t k = kh_get(rg, hash, (const char*)(rg + 1)); if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered } } } if (N == 0) return -1; // no reads left } // determine if there is a gap for (s = N = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) if (plp[s][i].indel != 0) break; if (i < n_plp[s]) break; } if (s == n) return -1; // there is no indel at this position. for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads { // find out how many types of indels are present bca->max_support = bca->max_frac = 0; int m, n_alt = 0, n_tot = 0, indel_support_ok = 0; uint32_t *aux; aux = calloc(N + 1, 4); m = max_rd_len = 0; aux[m++] = MINUS_CONST; // zero indel is always a type for (s = 0; s < n; ++s) { int na = 0, nt = 0; for (i = 0; i < n_plp[s]; ++i) { const bam_pileup1_t *p = plp[s] + i; if (rghash == 0 || p->aux == 0) { ++nt; if (p->indel != 0) { ++na; aux[m++] = MINUS_CONST + p->indel; } } j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b)); if (j > max_rd_len) max_rd_len = j; } float frac = (float)na/nt; if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac ) indel_support_ok = 1; if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac; n_alt += na; n_tot += nt; } // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases), // check the number of N's in the sequence and skip places where half or more reference bases are Ns. int nN=0; for (i=pos; i-posi ) { free(aux); return -1; } ks_introsort(uint32_t, m, aux); // squeeze out identical types for (i = 1, n_types = 1; i < m; ++i) if (aux[i] != aux[i-1]) ++n_types; // Taking totals makes it hard to call rare indels if ( !bca->per_sample_flt ) indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1; if ( n_types == 1 || !indel_support_ok ) { // then skip free(aux); return -1; } if (n_types >= 64) { free(aux); if (bam_verbose >= 2) fprintf(pysamerr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1); return -1; } types = (int*)calloc(n_types, sizeof(int)); t = 0; types[t++] = aux[0] - MINUS_CONST; for (i = 1; i < m; ++i) if (aux[i] != aux[i-1]) types[t++] = aux[i] - MINUS_CONST; free(aux); for (t = 0; t < n_types; ++t) if (types[t] == 0) break; ref_type = t; // the index of the reference type (0) } { // calculate left and right boundary left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0; right = pos + INDEL_WINDOW_SIZE; if (types[0] < 0) right -= types[0]; // in case the alignments stand out the reference for (i = pos; i < right; ++i) if (ref[i] == 0) break; right = i; } /* The following block fixes a long-existing flaw in the INDEL * calling model: the interference of nearby SNPs. However, it also * reduces the power because sometimes, substitutions caused by * indels are not distinguishable from true mutations. Multiple * sequence realignment helps to increase the power. * * Masks mismatches present in at least 70% of the reads with 'N'. */ { // construct per-sample consensus int L = right - left + 1, max_i, max2_i; uint32_t *cns, max, max2; char *ref0, *r; ref_sample = calloc(n, sizeof(void*)); cns = calloc(L, 4); ref0 = calloc(L, 1); for (i = 0; i < right - left; ++i) ref0[i] = bam_nt16_table[(int)ref[i+left]]; for (s = 0; s < n; ++s) { r = ref_sample[s] = calloc(L, 1); memset(cns, 0, sizeof(int) * L); // collect ref and non-ref counts for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; bam1_t *b = p->b; uint32_t *cigar = bam1_cigar(b); uint8_t *seq = bam1_seq(b); int x = b->core.pos, y = 0; for (k = 0; k < b->core.n_cigar; ++k) { int op = cigar[k]&0xf; int j, l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) if (x + j >= left && x + j < right) cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000; x += l; y += l; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; } } // determine the consensus for (i = 0; i < right - left; ++i) r[i] = ref0[i]; max = max2 = 0; max_i = max2_i = -1; for (i = 0; i < right - left; ++i) { if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i; else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i; } if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1; if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1; if (max_i >= 0) r[max_i] = 15; if (max2_i >= 0) r[max2_i] = 15; //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], pysamerr); fputc('\n', pysamerr); } free(ref0); free(cns); } { // the length of the homopolymer run around the current position int c = bam_nt16_table[(int)ref[pos + 1]]; if (c == 15) l_run = 1; else { for (i = pos + 2; ref[i]; ++i) if (bam_nt16_table[(int)ref[i]] != c) break; l_run = i; for (i = pos; i >= 0; --i) if (bam_nt16_table[(int)ref[i]] != c) break; l_run -= i + 1; } } // construct the consensus sequence max_ins = types[n_types - 1]; // max_ins is at least 0 if (max_ins > 0) { int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int)); // count the number of occurrences of each base at each position for each type of insertion for (t = 0; t < n_types; ++t) { if (types[t] > 0) { for (s = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; if (p->indel == types[t]) { uint8_t *seq = bam1_seq(p->b); for (k = 1; k <= p->indel; ++k) { int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)]; assert(c<5); ++inscns_aux[(t*max_ins+(k-1))*5 + c]; } } } } } } // use the majority rule to construct the consensus inscns = calloc(n_types * max_ins, 1); for (t = 0; t < n_types; ++t) { for (j = 0; j < types[t]; ++j) { int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5]; for (k = 0; k < 5; ++k) if (ia[k] > max) max = ia[k], max_k = k; inscns[t*max_ins + j] = max? max_k : 4; if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's } } free(inscns_aux); } // compute the likelihood given each type of indel for each read max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]); ref2 = calloc(max_ref2, 1); query = calloc(right - left + max_rd_len + max_ins + 2, 1); score1 = calloc(N * n_types, sizeof(int)); score2 = calloc(N * n_types, sizeof(int)); bca->indelreg = 0; for (t = 0; t < n_types; ++t) { int l, ir; kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 }; apf1.bw = apf2.bw = abs(types[t]) + 3; // compute indelreg if (types[t] == 0) ir = 0; else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]); else ir = est_indelreg(pos, ref, -types[t], 0); if (ir > bca->indelreg) bca->indelreg = ir; // fprintf(pysamerr, "%d, %d, %d\n", pos, types[t], ir); // realignment for (s = K = 0; s < n; ++s) { // write ref2 for (k = 0, j = left; j <= pos; ++j) ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]]; if (types[t] <= 0) j += -types[t]; else for (l = 0; l < types[t]; ++l) ref2[k++] = inscns[t*max_ins + l]; for (; j < right && ref[j]; ++j) ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]]; for (; k < max_ref2; ++k) ref2[k] = 4; if (j < right) right = j; // align each read to ref2 for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; int qbeg, qend, tbeg, tend, sc, kk; uint8_t *seq = bam1_seq(p->b); uint32_t *cigar = bam1_cigar(p->b); if (p->b->core.flag&4) continue; // unmapped reads // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway. for (kk = 0; kk < p->b->core.n_cigar; ++kk) if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break; if (kk < p->b->core.n_cigar) continue; // FIXME: the following skips soft clips, but using them may be more sensitive. // determine the start and end of sequences for alignment qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg); qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend); if (types[t] < 0) { int l = -types[t]; tbeg = tbeg - l > left? tbeg - l : left; } // write the query sequence for (l = qbeg; l < qend; ++l) query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)]; { // do realignment; this is the bottleneck const uint8_t *qual = bam1_qual(p->b), *bq; uint8_t *qq; qq = calloc(qend - qbeg, 1); bq = (uint8_t*)bam_aux_get(p->b, "ZQ"); if (bq) ++bq; // skip type for (l = qbeg; l < qend; ++l) { qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l]; if (qq[l - qbeg] > 30) qq[l - qbeg] = 30; if (qq[l - qbeg] < 7) qq[l - qbeg] = 7; } sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]), (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0); l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below if (l > 255) l = 255; score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l; if (sc > 5) { sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]), (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0); l = (int)(100. * sc / (qend - qbeg) + .499); if (l > 255) l = 255; score2[K*n_types + t] = sc<<8 | l; } free(qq); } /* for (l = 0; l < tend - tbeg + abs(types[t]); ++l) fputc("ACGTN"[(int)ref2[tbeg-left+l]], pysamerr); fputc('\n', pysamerr); for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], pysamerr); fputc('\n', pysamerr); fprintf(pysamerr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc); */ } } } free(ref2); free(query); { // compute indelQ int *sc, tmp, *sumq; sc = alloca(n_types * sizeof(int)); sumq = alloca(n_types * sizeof(int)); memset(sumq, 0, sizeof(int) * n_types); for (s = K = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i, ++K) { bam_pileup1_t *p = plp[s] + i; int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; /* errmod_cal() assumes that if the call is wrong, the * likelihoods of other events are equal. This is about * right for substitutions, but is not desired for * indels. To reuse errmod_cal(), I have to make * compromise for multi-allelic indels. */ if ((sc[0]&0x3f) == ref_type) { indelQ1 = (sc[1]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run); } else { for (t = 0; t < n_types; ++t) // look for the reference type if ((sc[t]&0x3f) == ref_type) break; indelQ1 = (sc[t]>>14) - (sc[0]>>14); seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run); } tmp = sc[0]>>6 & 0xff; indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ sct = &score2[K*n_types]; for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sc[j] < sc[j-1]; --j) tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp; if ((sc[0]&0x3f) == ref_type) { indelQ2 = (sc[1]>>14) - (sc[0]>>14); } else { for (t = 0; t < n_types; ++t) // look for the reference type if ((sc[t]&0x3f) == ref_type) break; indelQ2 = (sc[t]>>14) - (sc[0]>>14); } tmp = sc[0]>>6 & 0xff; indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499); // pick the smaller between indelQ1 and indelQ2 indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2; if (indelQ > 255) indelQ = 255; if (seqQ > 255) seqQ = 255; p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ; // fprintf(pysamerr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ); } } // determine bca->indel_types[] and bca->inscns bca->maxins = max_ins; bca->inscns = realloc(bca->inscns, bca->maxins * 4); for (t = 0; t < n_types; ++t) sumq[t] = sumq[t]<<6 | t; for (t = 1; t < n_types; ++t) // insertion sort for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j) tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp; for (t = 0; t < n_types; ++t) // look for the reference type if ((sumq[t]&0x3f) == ref_type) break; if (t) { // then move the reference type to the first tmp = sumq[t]; for (; t > 0; --t) sumq[t] = sumq[t-1]; sumq[0] = tmp; } for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL; for (t = 0; t < 4 && t < n_types; ++t) { bca->indel_types[t] = types[sumq[t]&0x3f]; memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins); } // update p->aux for (s = n_alt = 0; s < n; ++s) { for (i = 0; i < n_plp[s]; ++i) { bam_pileup1_t *p = plp[s] + i; int x = types[p->aux>>16&0x3f]; for (j = 0; j < 4; ++j) if (x == bca->indel_types[j]) break; p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff)); if ((p->aux>>16&0x3f) > 0) ++n_alt; // fprintf(pysamerr, "X pos=%d read=%d:%d name=%s call=%d type=%d q=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, bca->indel_types[p->aux>>16&63], p->aux&0xff, p->aux>>8&0xff); } } } free(score1); free(score2); // free for (i = 0; i < n; ++i) free(ref_sample[i]); free(ref_sample); free(types); free(inscns); return n_alt > 0? 0 : -1; } pysam-0.7.7/samtools/razf.c.pysam.c0000664000076400007650000005747112162637166017055 0ustar andreasandreas#include "pysam.h" /* * RAZF : Random Access compressed(Z) File * Version: 1.0 * Release Date: 2008-10-27 * * Copyright 2008, Jue Ruan , Heng Li * * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF * SUCH DAMAGE. */ #ifndef _NO_RAZF #include #include #include #include #include #include "razf.h" #if ZLIB_VERNUM < 0x1221 struct _gz_header_s { int text; uLong time; int xflags; int os; Bytef *extra; uInt extra_len; uInt extra_max; Bytef *name; uInt name_max; Bytef *comment; uInt comm_max; int hcrc; int done; }; #warning "zlib < 1.2.2.1; RAZF writing is disabled." #endif #define DEF_MEM_LEVEL 8 static inline uint32_t byte_swap_4(uint32_t v){ v = ((v & 0x0000FFFFU) << 16) | (v >> 16); return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); } static inline uint64_t byte_swap_8(uint64_t v){ v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); } static inline int is_big_endian(){ int x = 0x01; char *c = (char*)&x; return (c[0] != 0x01); } #ifndef _RZ_READONLY static void add_zindex(RAZF *rz, int64_t in, int64_t out){ if(rz->index->size == rz->index->cap){ rz->index->cap = rz->index->cap * 1.5 + 2; rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap); rz->index->bin_offsets = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1)); } if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out; rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE]; rz->index->size ++; } static void save_zindex(RAZF *rz, int fd){ int32_t i, v32; int is_be; is_be = is_big_endian(); if(is_be) write(fd, &rz->index->size, sizeof(int)); else { v32 = byte_swap_4((uint32_t)rz->index->size); write(fd, &v32, sizeof(uint32_t)); } v32 = rz->index->size / RZ_BIN_SIZE + 1; if(!is_be){ for(i=0;iindex->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]); for(i=0;iindex->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]); } write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); } #endif #ifdef _USE_KNETFILE static void load_zindex(RAZF *rz, knetFile *fp){ #else static void load_zindex(RAZF *rz, int fd){ #endif int32_t i, v32; int is_be; if(!rz->load_index) return; if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex)); is_be = is_big_endian(); #ifdef _USE_KNETFILE knet_read(fp, &rz->index->size, sizeof(int)); #else read(fd, &rz->index->size, sizeof(int)); #endif if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size); rz->index->cap = rz->index->size; v32 = rz->index->size / RZ_BIN_SIZE + 1; rz->index->bin_offsets = malloc(sizeof(int64_t) * v32); #ifdef _USE_KNETFILE knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32); #else read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); #endif rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size); #ifdef _USE_KNETFILE knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size); #else read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size); #endif if(!is_be){ for(i=0;iindex->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]); for(i=0;iindex->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]); } } #ifdef _RZ_READONLY static RAZF* razf_open_w(int fd) { fprintf(pysamerr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n"); return 0; } #else static RAZF* razf_open_w(int fd){ RAZF *rz; #ifdef _WIN32 setmode(fd, O_BINARY); #endif rz = calloc(1, sizeof(RAZF)); rz->mode = 'w'; #ifdef _USE_KNETFILE rz->x.fpw = fd; #else rz->filedes = fd; #endif rz->stream = calloc(sizeof(z_stream), 1); rz->inbuf = malloc(RZ_BUFFER_SIZE); rz->outbuf = malloc(RZ_BUFFER_SIZE); rz->index = calloc(sizeof(ZBlockIndex), 1); deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY); rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; rz->header = calloc(sizeof(gz_header), 1); rz->header->os = 0x03; //Unix rz->header->text = 0; rz->header->time = 0; rz->header->extra = malloc(7); strncpy((char*)rz->header->extra, "RAZF", 4); rz->header->extra[4] = 1; // obsolete field // block size = RZ_BLOCK_SIZE, Big-Endian rz->header->extra[5] = RZ_BLOCK_SIZE >> 8; rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF; rz->header->extra_len = 7; rz->header->name = rz->header->comment = 0; rz->header->hcrc = 0; deflateSetHeader(rz->stream, rz->header); rz->block_pos = rz->block_off = 0; return rz; } static void _razf_write(RAZF* rz, const void *data, int size){ int tout; rz->stream->avail_in = size; rz->stream->next_in = (void*)data; while(1){ tout = rz->stream->avail_out; deflate(rz->stream, Z_NO_FLUSH); rz->out += tout - rz->stream->avail_out; if(rz->stream->avail_out) break; #ifdef _USE_KNETFILE write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #else write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #endif rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; if(rz->stream->avail_in == 0) break; }; rz->in += size - rz->stream->avail_in; rz->block_off += size - rz->stream->avail_in; } static void razf_flush(RAZF *rz){ uint32_t tout; if(rz->buf_len){ _razf_write(rz, rz->inbuf, rz->buf_len); rz->buf_off = rz->buf_len = 0; } if(rz->stream->avail_out){ #ifdef _USE_KNETFILE write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #else write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #endif rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; } while(1){ tout = rz->stream->avail_out; deflate(rz->stream, Z_FULL_FLUSH); rz->out += tout - rz->stream->avail_out; if(rz->stream->avail_out == 0){ #ifdef _USE_KNETFILE write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #else write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #endif rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; } else break; } rz->block_pos = rz->out; rz->block_off = 0; } static void razf_end_flush(RAZF *rz){ uint32_t tout; if(rz->buf_len){ _razf_write(rz, rz->inbuf, rz->buf_len); rz->buf_off = rz->buf_len = 0; } while(1){ tout = rz->stream->avail_out; deflate(rz->stream, Z_FINISH); rz->out += tout - rz->stream->avail_out; if(rz->stream->avail_out < RZ_BUFFER_SIZE){ #ifdef _USE_KNETFILE write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #else write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); #endif rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; } else break; } } static void _razf_buffered_write(RAZF *rz, const void *data, int size){ int i, n; while(1){ if(rz->buf_len == RZ_BUFFER_SIZE){ _razf_write(rz, rz->inbuf, rz->buf_len); rz->buf_len = 0; } if(size + rz->buf_len < RZ_BUFFER_SIZE){ for(i=0;iinbuf + rz->buf_len)[i] = ((char*)data)[i]; rz->buf_len += size; return; } else { n = RZ_BUFFER_SIZE - rz->buf_len; for(i=0;iinbuf + rz->buf_len)[i] = ((char*)data)[i]; size -= n; data += n; rz->buf_len += n; } } } int razf_write(RAZF* rz, const void *data, int size){ int ori_size, n; int64_t next_block; ori_size = size; next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE; while(rz->in + rz->buf_len + size >= next_block){ n = next_block - rz->in - rz->buf_len; _razf_buffered_write(rz, data, n); data += n; size -= n; razf_flush(rz); add_zindex(rz, rz->in, rz->out); next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE; } _razf_buffered_write(rz, data, size); return ori_size; } #endif /* gzip flag byte */ #define ASCII_FLAG 0x01 /* bit 0 set: file probably ascii text */ #define HEAD_CRC 0x02 /* bit 1 set: header CRC present */ #define EXTRA_FIELD 0x04 /* bit 2 set: extra field present */ #define ORIG_NAME 0x08 /* bit 3 set: original file name present */ #define COMMENT 0x10 /* bit 4 set: file comment present */ #define RESERVED 0xE0 /* bits 5..7: reserved */ static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){ int method, flags, n, len; if(size < 2) return 0; if(data[0] != 0x1f || data[1] != 0x8b) return 0; if(size < 4) return 0; method = data[2]; flags = data[3]; if(method != Z_DEFLATED || (flags & RESERVED)) return 0; n = 4 + 6; // Skip 6 bytes *extra_off = n + 2; *extra_len = 0; if(flags & EXTRA_FIELD){ if(size < n + 2) return 0; len = ((int)data[n + 1] << 8) | data[n]; n += 2; *extra_off = n; while(len){ if(n >= size) return 0; n ++; len --; } *extra_len = n - (*extra_off); } if(flags & ORIG_NAME) while(n < size && data[n++]); if(flags & COMMENT) while(n < size && data[n++]); if(flags & HEAD_CRC){ if(n + 2 > size) return 0; n += 2; } return n; } #ifdef _USE_KNETFILE static RAZF* razf_open_r(knetFile *fp, int _load_index){ #else static RAZF* razf_open_r(int fd, int _load_index){ #endif RAZF *rz; int ext_off, ext_len; int n, is_be, ret; int64_t end; unsigned char c[] = "RAZF"; rz = calloc(1, sizeof(RAZF)); rz->mode = 'r'; #ifdef _USE_KNETFILE rz->x.fpr = fp; #else #ifdef _WIN32 setmode(fd, O_BINARY); #endif rz->filedes = fd; #endif rz->stream = calloc(sizeof(z_stream), 1); rz->inbuf = malloc(RZ_BUFFER_SIZE); rz->outbuf = malloc(RZ_BUFFER_SIZE); rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL; #ifdef _USE_KNETFILE n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE); #else n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE); #endif ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len); if(ret == 0){ PLAIN_FILE: rz->in = n; rz->file_type = FILE_TYPE_PLAIN; memcpy(rz->outbuf, rz->inbuf, n); rz->buf_len = n; free(rz->stream); rz->stream = NULL; return rz; } rz->header_size = ret; ret = inflateInit2(rz->stream, -WINDOW_BITS); if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;} rz->stream->avail_in = n - rz->header_size; rz->stream->next_in = rz->inbuf + rz->header_size; rz->stream->avail_out = RZ_BUFFER_SIZE; rz->stream->next_out = rz->outbuf; rz->file_type = FILE_TYPE_GZ; rz->in = rz->header_size; rz->block_pos = rz->header_size; rz->next_block_pos = rz->header_size; rz->block_off = 0; if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz; if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){ fprintf(pysamerr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file. in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__); return rz; } rz->load_index = _load_index; rz->file_type = FILE_TYPE_RZ; #ifdef _USE_KNETFILE if(knet_seek(fp, -16, SEEK_END) == -1){ #else if(lseek(fd, -16, SEEK_END) == -1){ #endif UNSEEKABLE: rz->seekable = 0; rz->index = NULL; rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL; } else { is_be = is_big_endian(); rz->seekable = 1; #ifdef _USE_KNETFILE knet_read(fp, &end, sizeof(int64_t)); #else read(fd, &end, sizeof(int64_t)); #endif if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end); else rz->src_end = end; #ifdef _USE_KNETFILE knet_read(fp, &end, sizeof(int64_t)); #else read(fd, &end, sizeof(int64_t)); #endif if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end); else rz->end = end; if(n > rz->end){ rz->stream->avail_in -= n - rz->end; n = rz->end; } if(rz->end > rz->src_end){ #ifdef _USE_KNETFILE knet_seek(fp, rz->in, SEEK_SET); #else lseek(fd, rz->in, SEEK_SET); #endif goto UNSEEKABLE; } #ifdef _USE_KNETFILE knet_seek(fp, rz->end, SEEK_SET); if(knet_tell(fp) != rz->end){ knet_seek(fp, rz->in, SEEK_SET); #else if(lseek(fd, rz->end, SEEK_SET) != rz->end){ lseek(fd, rz->in, SEEK_SET); #endif goto UNSEEKABLE; } #ifdef _USE_KNETFILE load_zindex(rz, fp); knet_seek(fp, n, SEEK_SET); #else load_zindex(rz, fd); lseek(fd, n, SEEK_SET); #endif } return rz; } #ifdef _USE_KNETFILE RAZF* razf_dopen(int fd, const char *mode){ if (strstr(mode, "r")) fprintf(pysamerr,"[razf_dopen] implement me\n"); else if(strstr(mode, "w")) return razf_open_w(fd); return NULL; } RAZF* razf_dopen2(int fd, const char *mode) { fprintf(pysamerr,"[razf_dopen2] implement me\n"); return NULL; } #else RAZF* razf_dopen(int fd, const char *mode){ if(strstr(mode, "r")) return razf_open_r(fd, 1); else if(strstr(mode, "w")) return razf_open_w(fd); else return NULL; } RAZF* razf_dopen2(int fd, const char *mode) { if(strstr(mode, "r")) return razf_open_r(fd, 0); else if(strstr(mode, "w")) return razf_open_w(fd); else return NULL; } #endif static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){ int fd; RAZF *rz; if(strstr(mode, "r")){ #ifdef _USE_KNETFILE knetFile *fd = knet_open(filename, "r"); if (fd == 0) { fprintf(pysamerr, "[_razf_open] fail to open %s\n", filename); return NULL; } #else #ifdef _WIN32 fd = open(filename, O_RDONLY | O_BINARY); #else fd = open(filename, O_RDONLY); #endif #endif if(fd < 0) return NULL; rz = razf_open_r(fd, _load_index); } else if(strstr(mode, "w")){ #ifdef _WIN32 fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666); #else fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666); #endif if(fd < 0) return NULL; rz = razf_open_w(fd); } else return NULL; return rz; } RAZF* razf_open(const char *filename, const char *mode){ return _razf_open(filename, mode, 1); } RAZF* razf_open2(const char *filename, const char *mode){ return _razf_open(filename, mode, 0); } int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){ int64_t n; if(rz->mode != 'r' && rz->mode != 'R') return 0; switch(rz->file_type){ case FILE_TYPE_PLAIN: if(rz->end == 0x7fffffffffffffffLL){ #ifdef _USE_KNETFILE if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0; n = knet_tell(rz->x.fpr); knet_seek(rz->x.fpr, 0, SEEK_END); rz->end = knet_tell(rz->x.fpr); knet_seek(rz->x.fpr, n, SEEK_SET); #else if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0; rz->end = lseek(rz->filedes, 0, SEEK_END); lseek(rz->filedes, n, SEEK_SET); #endif } *u_size = *c_size = rz->end; return 1; case FILE_TYPE_GZ: return 0; case FILE_TYPE_RZ: if(rz->src_end == rz->end) return 0; *u_size = rz->src_end; *c_size = rz->end; return 1; default: return 0; } } static int _razf_read(RAZF* rz, void *data, int size){ int ret, tin; if(rz->z_eof || rz->z_err) return 0; if (rz->file_type == FILE_TYPE_PLAIN) { #ifdef _USE_KNETFILE ret = knet_read(rz->x.fpr, data, size); #else ret = read(rz->filedes, data, size); #endif if (ret == 0) rz->z_eof = 1; return ret; } rz->stream->avail_out = size; rz->stream->next_out = data; while(rz->stream->avail_out){ if(rz->stream->avail_in == 0){ if(rz->in >= rz->end){ rz->z_eof = 1; break; } if(rz->end - rz->in < RZ_BUFFER_SIZE){ #ifdef _USE_KNETFILE rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in); #else rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in); #endif } else { #ifdef _USE_KNETFILE rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE); #else rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE); #endif } if(rz->stream->avail_in == 0){ rz->z_eof = 1; break; } rz->stream->next_in = rz->inbuf; } tin = rz->stream->avail_in; ret = inflate(rz->stream, Z_BLOCK); rz->in += tin - rz->stream->avail_in; if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){ fprintf(pysamerr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__); rz->z_err = 1; break; } if(ret == Z_STREAM_END){ rz->z_eof = 1; break; } if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){ rz->buf_flush = 1; rz->next_block_pos = rz->in; break; } } return size - rz->stream->avail_out; } int razf_read(RAZF *rz, void *data, int size){ int ori_size, i; ori_size = size; while(size > 0){ if(rz->buf_len){ if(size < rz->buf_len){ for(i=0;ioutbuf + rz->buf_off)[i]; rz->buf_off += size; rz->buf_len -= size; data += size; rz->block_off += size; size = 0; break; } else { for(i=0;ibuf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i]; data += rz->buf_len; size -= rz->buf_len; rz->block_off += rz->buf_len; rz->buf_off = 0; rz->buf_len = 0; if(rz->buf_flush){ rz->block_pos = rz->next_block_pos; rz->block_off = 0; rz->buf_flush = 0; } } } else if(rz->buf_flush){ rz->block_pos = rz->next_block_pos; rz->block_off = 0; rz->buf_flush = 0; } if(rz->buf_flush) continue; rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE); if(rz->z_eof && rz->buf_len == 0) break; } rz->out += ori_size - size; return ori_size - size; } int razf_skip(RAZF* rz, int size){ int ori_size; ori_size = size; while(size > 0){ if(rz->buf_len){ if(size < rz->buf_len){ rz->buf_off += size; rz->buf_len -= size; rz->block_off += size; size = 0; break; } else { size -= rz->buf_len; rz->buf_off = 0; rz->buf_len = 0; rz->block_off += rz->buf_len; if(rz->buf_flush){ rz->block_pos = rz->next_block_pos; rz->block_off = 0; rz->buf_flush = 0; } } } else if(rz->buf_flush){ rz->block_pos = rz->next_block_pos; rz->block_off = 0; rz->buf_flush = 0; } if(rz->buf_flush) continue; rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE); if(rz->z_eof || rz->z_err) break; } rz->out += ori_size - size; return ori_size - size; } static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){ #ifdef _USE_KNETFILE knet_seek(rz->x.fpr, in, SEEK_SET); #else lseek(rz->filedes, in, SEEK_SET); #endif rz->in = in; rz->out = out; rz->block_pos = in; rz->next_block_pos = in; rz->block_off = 0; rz->buf_flush = 0; rz->z_eof = rz->z_err = 0; inflateReset(rz->stream); rz->stream->avail_in = 0; rz->buf_off = rz->buf_len = 0; } int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){ int64_t pos; rz->z_eof = 0; if(rz->file_type == FILE_TYPE_PLAIN){ rz->buf_off = rz->buf_len = 0; pos = block_start + block_offset; #ifdef _USE_KNETFILE knet_seek(rz->x.fpr, pos, SEEK_SET); pos = knet_tell(rz->x.fpr); #else pos = lseek(rz->filedes, pos, SEEK_SET); #endif rz->out = rz->in = pos; return pos; } if(block_start == rz->block_pos && block_offset >= rz->block_off) { block_offset -= rz->block_off; goto SKIP; // Needn't reset inflate } if(block_start == 0) block_start = rz->header_size; // Automaticly revist wrong block_start _razf_reset_read(rz, block_start, 0); SKIP: if(block_offset) razf_skip(rz, block_offset); return rz->block_off; } int64_t razf_seek(RAZF* rz, int64_t pos, int where){ int64_t idx; int64_t seek_pos, new_out; rz->z_eof = 0; if (where == SEEK_CUR) pos += rz->out; else if (where == SEEK_END) pos += rz->src_end; if(rz->file_type == FILE_TYPE_PLAIN){ #ifdef _USE_KNETFILE knet_seek(rz->x.fpr, pos, SEEK_SET); seek_pos = knet_tell(rz->x.fpr); #else seek_pos = lseek(rz->filedes, pos, SEEK_SET); #endif rz->buf_off = rz->buf_len = 0; rz->out = rz->in = seek_pos; return seek_pos; } else if(rz->file_type == FILE_TYPE_GZ){ if(pos >= rz->out) goto SKIP; return rz->out; } if(pos == rz->out) return pos; if(pos > rz->src_end) return rz->out; if(!rz->seekable || !rz->load_index){ if(pos >= rz->out) goto SKIP; } idx = pos / RZ_BLOCK_SIZE - 1; seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]); new_out = (idx + 1) * RZ_BLOCK_SIZE; if(pos > rz->out && new_out <= rz->out) goto SKIP; _razf_reset_read(rz, seek_pos, new_out); SKIP: razf_skip(rz, (int)(pos - rz->out)); return rz->out; } uint64_t razf_tell2(RAZF *rz) { /* if (rz->load_index) { int64_t idx, seek_pos; idx = rz->out / RZ_BLOCK_SIZE - 1; seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]); if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off) fprintf(pysamerr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n", (long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off); } */ return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff); } int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where) { if (where != SEEK_SET) return -1; return razf_jump(rz, voffset>>16, voffset&0xffff); } void razf_close(RAZF *rz){ if(rz->mode == 'w'){ #ifndef _RZ_READONLY razf_end_flush(rz); deflateEnd(rz->stream); #ifdef _USE_KNETFILE save_zindex(rz, rz->x.fpw); if(is_big_endian()){ write(rz->x.fpw, &rz->in, sizeof(int64_t)); write(rz->x.fpw, &rz->out, sizeof(int64_t)); } else { uint64_t v64 = byte_swap_8((uint64_t)rz->in); write(rz->x.fpw, &v64, sizeof(int64_t)); v64 = byte_swap_8((uint64_t)rz->out); write(rz->x.fpw, &v64, sizeof(int64_t)); } #else save_zindex(rz, rz->filedes); if(is_big_endian()){ write(rz->filedes, &rz->in, sizeof(int64_t)); write(rz->filedes, &rz->out, sizeof(int64_t)); } else { uint64_t v64 = byte_swap_8((uint64_t)rz->in); write(rz->filedes, &v64, sizeof(int64_t)); v64 = byte_swap_8((uint64_t)rz->out); write(rz->filedes, &v64, sizeof(int64_t)); } #endif #endif } else if(rz->mode == 'r'){ if(rz->stream) inflateEnd(rz->stream); } if(rz->inbuf) free(rz->inbuf); if(rz->outbuf) free(rz->outbuf); if(rz->header){ free(rz->header->extra); free(rz->header->name); free(rz->header->comment); free(rz->header); } if(rz->index){ free(rz->index->bin_offsets); free(rz->index->cell_offsets); free(rz->index); } free(rz->stream); #ifdef _USE_KNETFILE if (rz->mode == 'r') knet_close(rz->x.fpr); if (rz->mode == 'w') close(rz->x.fpw); #else close(rz->filedes); #endif free(rz); } #endif pysam-0.7.7/samtools/sam.h0000664000076400007650000000520012162637166015306 0ustar andreasandreas#ifndef BAM_SAM_H #define BAM_SAM_H #include "bam.h" /*! @header This file provides higher level of I/O routines and unifies the APIs for SAM and BAM formats. These APIs are more convenient and recommended. @copyright Genome Research Ltd. */ /*! @typedef @abstract SAM/BAM file handler @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format @field bam BAM file handler; valid if (type&1) == 1 @field tamr SAM file handler for reading; valid if type == 2 @field tamw SAM file handler for writing; valid if type == 0 @field header header struct */ typedef struct { int type; union { tamFile tamr; bamFile bam; FILE *tamw; } x; bam_header_t *header; } samfile_t; #ifdef __cplusplus extern "C" { #endif /*! @abstract Open a SAM/BAM file @param fn SAM/BAM file name; "-" is recognized as stdin (for reading) or stdout (for writing). @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading, 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output, 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for string flag. If 'b' present, it must immediately follow 'r' or 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX", "rb", "wb" and "wbu" exclusively. @param aux auxiliary data; if mode[0]=='w', aux points to bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM are absent, aux points the file name of the list of the reference; aux is not used otherwise. If @SQ header lines are present in SAM, aux is not used, either. @return SAM/BAM file handler */ samfile_t *samopen(const char *fn, const char *mode, const void *aux); /*! @abstract Close a SAM/BAM handler @param fp file handler to be closed */ void samclose(samfile_t *fp); /*! @abstract Read one alignment @param fp file handler @param b alignment @return bytes read */ int samread(samfile_t *fp, bam1_t *b); /*! @abstract Write one alignment @param fp file handler @param b alignment @return bytes written */ int samwrite(samfile_t *fp, const bam1_t *b); /*! @abstract Get the pileup for a whole alignment file @param fp file handler @param mask mask transferred to bam_plbuf_set_mask() @param func user defined function called in the pileup process #param data user provided data for func() */ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data); char *samfaipath(const char *fn_ref); int samthreads(samfile_t *fp, int n_threads, int n_sub_blks); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bam_plcmd.c.pysam.c0000664000076400007650000005343312162637166020023 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include #include #include "sam.h" #include "faidx.h" #include "kstring.h" #include "sam_header.h" static inline int printw(int c, FILE *fp) { char buf[16]; int l, x; if (c == 0) return fputc('0', fp); for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0'; if (c < 0) buf[l++] = '-'; buf[l] = 0; for (x = 0; x < l/2; ++x) { int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y; } fputs(buf, fp); return 0; } static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref) { int j; if (p->is_head) { putchar('^'); putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33); } if (!p->is_del) { int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; if (ref) { int rb = pos < ref_len? ref[pos] : 'N'; if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.'; else c = bam1_strand(p->b)? tolower(c) : toupper(c); } else { if (c == '=') c = bam1_strand(p->b)? ',' : '.'; else c = bam1_strand(p->b)? tolower(c) : toupper(c); } putchar(c); } else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*'); if (p->indel > 0) { putchar('+'); printw(p->indel, stdout); for (j = 1; j <= p->indel; ++j) { int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)]; putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); } } else if (p->indel < 0) { printw(p->indel, stdout); for (j = 1; j <= -p->indel; ++j) { int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N'; putchar(bam1_strand(p->b)? tolower(c) : toupper(c)); } } if (p->is_tail) putchar('$'); } #include #include "bam2bcf.h" #include "sample.h" #define MPLP_GLF 0x10 #define MPLP_NO_COMP 0x20 #define MPLP_NO_ORPHAN 0x40 #define MPLP_REALN 0x80 #define MPLP_NO_INDEL 0x400 #define MPLP_REDO_BAQ 0x800 #define MPLP_ILLUMINA13 0x1000 #define MPLP_IGNORE_RG 0x2000 #define MPLP_PRINT_POS 0x4000 #define MPLP_PRINT_MAPQ 0x8000 #define MPLP_PER_SAMPLE 0x10000 void *bed_read(const char *fn); void bed_destroy(void *_h); int bed_overlap(const void *_h, const char *chr, int beg, int end); typedef struct { int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag; int rflag_require, rflag_filter; int openQ, extQ, tandemQ, min_support; // for indels double min_frac; // for indels char *reg, *pl_list, *fai_fname; faidx_t *fai; void *bed, *rghash; } mplp_conf_t; typedef struct { bamFile fp; bam_iter_t iter; bam_header_t *h; int ref_id; char *ref; const mplp_conf_t *conf; } mplp_aux_t; typedef struct { int n; int *n_plp, *m_plp; bam_pileup1_t **plp; } mplp_pileup_t; static int mplp_func(void *data, bam1_t *b) { extern int bam_realn(bam1_t *b, const char *ref); extern int bam_prob_realn_core(bam1_t *b, const char *ref, int); extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres); mplp_aux_t *ma = (mplp_aux_t*)data; int ret, skip = 0; do { int has_ref; ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b); if (ret < 0) break; if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads skip = 1; continue; } if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; } if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; } if (ma->conf->bed) { // test overlap skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))); if (skip) continue; } if (ma->conf->rghash) { // exclude read groups uint8_t *rg = bam_aux_get(b, "RG"); skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0); if (skip) continue; } if (ma->conf->flag & MPLP_ILLUMINA13) { int i; uint8_t *qual = bam1_qual(b); for (i = 0; i < b->core.l_qseq; ++i) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres); if (q < 0) skip = 1; else if (b->core.qual > q) b->core.qual = q; } else if (b->core.qual < ma->conf->min_mq) skip = 1; else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1; } while (skip); return ret; } static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf, int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg) { int i, j; memset(m->n_plp, 0, m->n * sizeof(int)); for (i = 0; i < n; ++i) { for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; uint8_t *q; int id = -1; q = ignore_rg? 0 : bam_aux_get(p->b, "RG"); if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf); if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf); if (id < 0 || id >= m->n) { assert(q); // otherwise a bug fprintf(pysamerr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]); exit(1); } if (m->n_plp[id] == m->m_plp[id]) { m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8; m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]); } m->plp[id][m->n_plp[id]++] = *p; } } } static int mpileup(mplp_conf_t *conf, int n, char **fn) { extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list); extern void bcf_call_del_rghash(void *rghash); mplp_aux_t **data; int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth; const bam_pileup1_t **plp; bam_mplp_t iter; bam_header_t *h = 0; char *ref; void *rghash = 0; bcf_callaux_t *bca = 0; bcf_callret1_t *bcr = 0; bcf_call_t bc; bcf_t *bp = 0; bcf_hdr_t *bh = 0; bam_sample_t *sm = 0; kstring_t buf; mplp_pileup_t gplp; memset(&gplp, 0, sizeof(mplp_pileup_t)); memset(&buf, 0, sizeof(kstring_t)); memset(&bc, 0, sizeof(bcf_call_t)); data = calloc(n, sizeof(void*)); plp = calloc(n, sizeof(void*)); n_plp = calloc(n, sizeof(int*)); sm = bam_smpl_init(); // read the header and initialize data for (i = 0; i < n; ++i) { bam_header_t *h_tmp; data[i] = calloc(1, sizeof(mplp_aux_t)); data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r"); if ( !data[i]->fp ) { fprintf(pysamerr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno)); exit(1); } data[i]->conf = conf; h_tmp = bam_header_read(data[i]->fp); if ( !h_tmp ) { fprintf(pysamerr,"[%s] fail to read the header of %s\n", __func__, fn[i]); exit(1); } data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text); rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list); if (conf->reg) { int beg, end; bam_index_t *idx; idx = bam_index_load(fn[i]); if (idx == 0) { fprintf(pysamerr, "[%s] fail to load index for %s\n", __func__, fn[i]); exit(1); } if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) { fprintf(pysamerr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]); exit(1); } if (i == 0) tid0 = tid, beg0 = beg, end0 = end; data[i]->iter = bam_iter_query(idx, tid, beg, end); bam_index_destroy(idx); } if (i == 0) h = h_tmp; else { // FIXME: to check consistency bam_header_destroy(h_tmp); } } gplp.n = sm->n; gplp.n_plp = calloc(sm->n, sizeof(int)); gplp.m_plp = calloc(sm->n, sizeof(int)); gplp.plp = calloc(sm->n, sizeof(void*)); fprintf(pysamerr, "[%s] %d samples in %d input files\n", __func__, sm->n, n); // write the VCF header if (conf->flag & MPLP_GLF) { kstring_t s; bh = calloc(1, sizeof(bcf_hdr_t)); s.l = s.m = 0; s.s = 0; bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w"); for (i = 0; i < h->n_targets; ++i) { kputs(h->target_name[i], &s); kputc('\0', &s); } bh->l_nm = s.l; bh->name = malloc(s.l); memcpy(bh->name, s.s, s.l); s.l = 0; for (i = 0; i < sm->n; ++i) { kputs(sm->smpl[i], &s); kputc('\0', &s); } bh->l_smpl = s.l; bh->sname = malloc(s.l); memcpy(bh->sname, s.s, s.l); s.l = 0; ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION); if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname); h->dict = sam_header_parse2(h->text); int nseq; const char *tags[] = {"SN","LN","UR","M5",NULL}; char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq); for (i=0; i\n", &s); } if (tbl) free(tbl); bh->txt = s.s; bh->l_txt = 1 + s.l; bcf_hdr_sync(bh); bcf_hdr_write(bp, bh); bca = bcf_call_init(-1., conf->min_baseQ); bcr = calloc(sm->n, sizeof(bcf_callret1_t)); bca->rghash = rghash; bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ; bca->min_frac = conf->min_frac; bca->min_support = conf->min_support; bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE; } if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; } else ref_tid = -1, ref = 0; iter = bam_mplp_init(n, mplp_func, (void**)data); max_depth = conf->max_depth; if (max_depth * sm->n > 1<<20) fprintf(pysamerr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__); if (max_depth * sm->n < 8000) { max_depth = 8000 / sm->n; fprintf(pysamerr, "<%s> Set max per-file depth to %d\n", __func__, max_depth); } max_indel_depth = conf->max_indel_depth * sm->n; bam_mplp_set_maxcnt(iter, max_depth); while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) { if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue; if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; ref_tid = tid; } if (conf->flag & MPLP_GLF) { int total_depth, _ref0, ref16; bcf1_t *b = calloc(1, sizeof(bcf1_t)); for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i]; group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG); _ref0 = (ref && pos < ref_len)? ref[pos] : 'N'; ref16 = bam_nt16_table[_ref0]; for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i); bcf_call_combine(gplp.n, bcr, bca, ref16, &bc); bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0); bcf_write(bp, bh, b); bcf_destroy(b); // call indels if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) { for (i = 0; i < gplp.n; ++i) bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i); if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) { b = calloc(1, sizeof(bcf1_t)); bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref); bcf_write(bp, bh, b); bcf_destroy(b); } } } else { printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N'); for (i = 0; i < n; ++i) { int j, cnt; for (j = cnt = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt; } printf("\t%d\t", cnt); if (n_plp[i] == 0) { printf("*\t*"); // FIXME: printf() is very slow... if (conf->flag & MPLP_PRINT_POS) printf("\t*"); } else { for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) pileup_seq(plp[i] + j, pos, ref_len, ref); } putchar('\t'); for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; int c = bam1_qual(p->b)[p->qpos]; if (c >= conf->min_baseQ) { c = c + 33 < 126? c + 33 : 126; putchar(c); } } if (conf->flag & MPLP_PRINT_MAPQ) { putchar('\t'); for (j = 0; j < n_plp[i]; ++j) { int c = plp[i][j].b->core.qual + 33; if (c > 126) c = 126; putchar(c); } } if (conf->flag & MPLP_PRINT_POS) { putchar('\t'); for (j = 0; j < n_plp[i]; ++j) { if (j > 0) putchar(','); printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow... } } } } putchar('\n'); } } bcf_close(bp); bam_smpl_destroy(sm); free(buf.s); for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]); free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp); bcf_call_del_rghash(rghash); bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr); bam_mplp_destroy(iter); bam_header_destroy(h); for (i = 0; i < n; ++i) { bam_close(data[i]->fp); if (data[i]->iter) bam_iter_destroy(data[i]->iter); free(data[i]); } free(data); free(plp); free(ref); free(n_plp); return 0; } #define MAX_PATH_LEN 1024 int read_file_list(const char *file_list,int *n,char **argv[]) { char buf[MAX_PATH_LEN]; int len, nfiles = 0; char **files = NULL; struct stat sb; *n = 0; *argv = NULL; FILE *fh = fopen(file_list,"r"); if ( !fh ) { fprintf(pysamerr,"%s: %s\n", file_list,strerror(errno)); return 1; } files = calloc(nfiles,sizeof(char*)); nfiles = 0; while ( fgets(buf,MAX_PATH_LEN,fh) ) { // allow empty lines and trailing spaces len = strlen(buf); while ( len>0 && isspace(buf[len-1]) ) len--; if ( !len ) continue; // check sanity of the file list buf[len] = 0; if (stat(buf, &sb) != 0) { // no such file, check if it is safe to print its name int i, safe_to_print = 1; for (i=0; i= 0) { switch (c) { case 1 : mplp.rflag_require = strtol(optarg,0,0); break; case 2 : mplp.rflag_filter = strtol(optarg,0,0); break; case 'f': mplp.fai = fai_load(optarg); if (mplp.fai == 0) return 1; mplp.fai_fname = optarg; break; case 'd': mplp.max_depth = atoi(optarg); break; case 'r': mplp.reg = strdup(optarg); break; case 'l': mplp.bed = bed_read(optarg); break; case 'P': mplp.pl_list = strdup(optarg); break; case 'p': mplp.flag |= MPLP_PER_SAMPLE; break; case 'g': mplp.flag |= MPLP_GLF; break; case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break; case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break; case 'B': mplp.flag &= ~MPLP_REALN; break; case 'D': mplp.fmt_flag |= B2B_FMT_DP; break; case 'S': mplp.fmt_flag |= B2B_FMT_SP; break; case 'V': mplp.fmt_flag |= B2B_FMT_DV; break; case 'I': mplp.flag |= MPLP_NO_INDEL; break; case 'E': mplp.flag |= MPLP_REDO_BAQ; break; case '6': mplp.flag |= MPLP_ILLUMINA13; break; case 'R': mplp.flag |= MPLP_IGNORE_RG; break; case 's': mplp.flag |= MPLP_PRINT_MAPQ; break; case 'O': mplp.flag |= MPLP_PRINT_POS; break; case 'C': mplp.capQ_thres = atoi(optarg); break; case 'M': mplp.max_mq = atoi(optarg); break; case 'q': mplp.min_mq = atoi(optarg); break; case 'Q': mplp.min_baseQ = atoi(optarg); break; case 'b': file_list = optarg; break; case 'o': mplp.openQ = atoi(optarg); break; case 'e': mplp.extQ = atoi(optarg); break; case 'h': mplp.tandemQ = atoi(optarg); break; case 'A': use_orphan = 1; break; case 'F': mplp.min_frac = atof(optarg); break; case 'm': mplp.min_support = atoi(optarg); break; case 'L': mplp.max_indel_depth = atoi(optarg); break; case 'G': { FILE *fp_rg; char buf[1024]; mplp.rghash = bcf_str2id_init(); if ((fp_rg = fopen(optarg, "r")) == 0) fprintf(pysamerr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg); while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me... bcf_str2id_add(mplp.rghash, strdup(buf)); fclose(fp_rg); } break; } } if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN; if (argc == 1) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n"); fprintf(pysamerr, "Input options:\n\n"); fprintf(pysamerr, " -6 assume the quality is in the Illumina-1.3+ encoding\n"); fprintf(pysamerr, " -A count anomalous read pairs\n"); fprintf(pysamerr, " -B disable BAQ computation\n"); fprintf(pysamerr, " -b FILE list of input BAM filenames, one per line [null]\n"); fprintf(pysamerr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n"); fprintf(pysamerr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth); fprintf(pysamerr, " -E recalculate extended BAQ on the fly thus ignoring existing BQs\n"); fprintf(pysamerr, " -f FILE faidx indexed reference sequence file [null]\n"); fprintf(pysamerr, " -G FILE exclude read groups listed in FILE [null]\n"); fprintf(pysamerr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n"); fprintf(pysamerr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq); fprintf(pysamerr, " -r STR region in which pileup is generated [null]\n"); fprintf(pysamerr, " -R ignore RG tags\n"); fprintf(pysamerr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq); fprintf(pysamerr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ); fprintf(pysamerr, " --rf INT required flags: skip reads with mask bits unset []\n"); fprintf(pysamerr, " --ff INT filter flags: skip reads with mask bits set []\n"); fprintf(pysamerr, "\nOutput options:\n\n"); fprintf(pysamerr, " -D output per-sample DP in BCF (require -g/-u)\n"); fprintf(pysamerr, " -g generate BCF output (genotype likelihoods)\n"); fprintf(pysamerr, " -O output base positions on reads (disabled by -g/-u)\n"); fprintf(pysamerr, " -s output mapping quality (disabled by -g/-u)\n"); fprintf(pysamerr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n"); fprintf(pysamerr, " -u generate uncompress BCF output\n"); fprintf(pysamerr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n"); fprintf(pysamerr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ); fprintf(pysamerr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac); fprintf(pysamerr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ); fprintf(pysamerr, " -I do not perform indel calling\n"); fprintf(pysamerr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth); fprintf(pysamerr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support); fprintf(pysamerr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ); fprintf(pysamerr, " -p apply -m and -F per-sample to increase sensitivity\n"); fprintf(pysamerr, " -P STR comma separated list of platforms for indels [all]\n"); fprintf(pysamerr, "\n"); fprintf(pysamerr, "Notes: Assuming diploid individuals.\n\n"); return 1; } bam_no_B = 1; if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) return 1; mpileup(&mplp,nfiles,fn); for (c=0; c #include #include #include "bam.h" #include "ksort.h" #define TV_GAP 2 typedef struct __freenode_t { uint32_t level:28, cnt:4; struct __freenode_t *next; } freenode_t, *freenode_p; #define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level)) KSORT_INIT(node, freenode_p, freenode_lt) /* Memory pool, similar to the one in bam_pileup.c */ typedef struct { int cnt, n, max; freenode_t **buf; } mempool_t; static mempool_t *mp_init() { return (mempool_t*)calloc(1, sizeof(mempool_t)); } static void mp_destroy(mempool_t *mp) { int k; for (k = 0; k < mp->n; ++k) free(mp->buf[k]); free(mp->buf); free(mp); } static inline freenode_t *mp_alloc(mempool_t *mp) { ++mp->cnt; if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t)); else return mp->buf[--mp->n]; } static inline void mp_free(mempool_t *mp, freenode_t *p) { --mp->cnt; p->next = 0; p->cnt = TV_GAP; if (mp->n == mp->max) { mp->max = mp->max? mp->max<<1 : 256; mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max); } mp->buf[mp->n++] = p; } /* core part */ struct __bam_lplbuf_t { int max, n_cur, n_pre; int max_level, *cur_level, *pre_level; mempool_t *mp; freenode_t **aux, *head, *tail; int n_nodes, m_aux; bam_pileup_f func; void *user_data; bam_plbuf_t *plbuf; }; void bam_lplbuf_reset(bam_lplbuf_t *buf) { freenode_t *p, *q; bam_plbuf_reset(buf->plbuf); for (p = buf->head; p->next;) { q = p->next; mp_free(buf->mp, p); p = q; } buf->head = buf->tail; buf->max_level = 0; buf->n_cur = buf->n_pre = 0; buf->n_nodes = 0; } static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data) { bam_lplbuf_t *tv = (bam_lplbuf_t*)data; freenode_t *p; int i, l, max_level; // allocate memory if necessary if (tv->max < n) { // enlarge tv->max = n; kroundup32(tv->max); tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max); tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max); } tv->n_cur = n; // update cnt for (p = tv->head; p->next; p = p->next) if (p->cnt > 0) --p->cnt; // calculate cur_level[] max_level = 0; for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) { if (tv->head->next && tv->head->cnt == 0) { // then take a free slot freenode_t *p = tv->head->next; tv->cur_level[i] = tv->head->level; mp_free(tv->mp, tv->head); tv->head = p; --tv->n_nodes; } else tv->cur_level[i] = ++tv->max_level; } else { tv->cur_level[i] = tv->pre_level[l++]; if (p->is_tail) { // then return a free slot tv->tail->level = tv->cur_level[i]; tv->tail->next = mp_alloc(tv->mp); tv->tail = tv->tail->next; ++tv->n_nodes; } } if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i]; ((bam_pileup1_t*)p)->level = tv->cur_level[i]; } assert(l == tv->n_pre); tv->func(tid, pos, n, pl, tv->user_data); // sort the linked list if (tv->n_nodes) { freenode_t *q; if (tv->n_nodes + 1 > tv->m_aux) { // enlarge tv->m_aux = tv->n_nodes + 1; kroundup32(tv->m_aux); tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux); } for (p = tv->head, i = l = 0; p->next;) { if (p->level > max_level) { // then discard this entry q = p->next; mp_free(tv->mp, p); p = q; } else { tv->aux[i++] = p; p = p->next; } } tv->aux[i] = tv->tail; // add a proper tail for the loop below tv->n_nodes = i; if (tv->n_nodes) { ks_introsort(node, tv->n_nodes, tv->aux); for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1]; tv->head = tv->aux[0]; } else tv->head = tv->tail; } // clean up tv->max_level = max_level; memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4); // squeeze out terminated levels for (i = l = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (!p->is_tail) tv->pre_level[l++] = tv->pre_level[i]; } tv->n_pre = l; /* fprintf(pysamerr, "%d\t", pos+1); for (i = 0; i < n; ++i) { const bam_pileup1_t *p = pl + i; if (p->is_head) fprintf(pysamerr, "^"); if (p->is_tail) fprintf(pysamerr, "$"); fprintf(pysamerr, "%d,", p->level); } fprintf(pysamerr, "\n"); */ return 0; } bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data) { bam_lplbuf_t *tv; tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t)); tv->mp = mp_init(); tv->head = tv->tail = mp_alloc(tv->mp); tv->func = func; tv->user_data = data; tv->plbuf = bam_plbuf_init(tview_func, tv); return (bam_lplbuf_t*)tv; } void bam_lplbuf_destroy(bam_lplbuf_t *tv) { freenode_t *p, *q; free(tv->cur_level); free(tv->pre_level); bam_plbuf_destroy(tv->plbuf); free(tv->aux); for (p = tv->head; p->next;) { q = p->next; mp_free(tv->mp, p); p = q; } mp_free(tv->mp, p); assert(tv->mp->cnt == 0); mp_destroy(tv->mp); free(tv); } int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv) { return bam_plbuf_push(b, tv->plbuf); } pysam-0.7.7/samtools/padding.c.pysam.c0000664000076400007650000004153612162637166017514 0ustar andreasandreas#include "pysam.h" #include #include #include #include "kstring.h" #include "sam_header.h" #include "sam.h" #include "bam.h" #include "faidx.h" bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/ static void replace_cigar(bam1_t *b, int n, uint32_t *cigar) { if (n != b->core.n_cigar) { int o = b->core.l_qname + b->core.n_cigar * 4; if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) { b->m_data = b->data_len + (n - b->core.n_cigar) * 4; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o); memcpy(b->data + b->core.l_qname, cigar, n * 4); b->data_len += (n - b->core.n_cigar) * 4; b->core.n_cigar = n; } else memcpy(b->data + b->core.l_qname, cigar, n * 4); } #define write_cigar(_c, _n, _m, _v) do { \ if (_n == _m) { \ _m = _m? _m<<1 : 4; \ _c = (uint32_t*)realloc(_c, _m * 4); \ } \ _c[_n++] = (_v); \ } while (0) static void unpad_seq(bam1_t *b, kstring_t *s) { int k, j, i; int length; uint32_t *cigar = bam1_cigar(b); uint8_t *seq = bam1_seq(b); // b->core.l_qseq gives length of the SEQ entry (including soft clips, S) // We need the padded length after alignment from the CIGAR (excluding // soft clips S, but including pads from CIGAR D operations) length = 0; for (k = 0; k < b->core.n_cigar; ++k) { int op, ol; op= bam_cigar_op(cigar[k]); ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL) length += ol; } ks_resize(s, length); for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) { int op, ol; op = bam_cigar_op(cigar[k]); ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j); } else if (op == BAM_CSOFT_CLIP) { j += ol; } else if (op == BAM_CHARD_CLIP) { /* do nothing */ } else if (op == BAM_CDEL) { for (i = 0; i < ol; ++i) s->s[s->l++] = 0; } else { fprintf(pysamerr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b)); assert(-1); } } assert(length == s->l); } int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq) { char base; char *fai_ref = 0; int fai_ref_len = 0, k; fai_ref = fai_fetch(fai, ref_name, &fai_ref_len); if (fai_ref_len != ref_len) { fprintf(pysamerr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len); free(fai_ref); return -1; } ks_resize(seq, ref_len); seq->l = 0; for (k = 0; k < ref_len; ++k) { base = fai_ref[k]; if (base == '-' || base == '*') { // Map gaps to null to match unpad_seq function seq->s[seq->l++] = 0; } else { int i = bam_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(pysamerr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name); free(fai_ref); return -1; } seq->s[seq->l++] = i; } } assert(ref_len == seq->l); free(fai_ref); return 0; } int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len) { char base; char *fai_ref = 0; int fai_ref_len = 0, k; int bases=0, gaps=0; fai_ref = fai_fetch(fai, ref_name, &fai_ref_len); if (fai_ref_len != padded_len) { fprintf(pysamerr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len); free(fai_ref); return -1; } for (k = 0; k < padded_len; ++k) { //fprintf(pysamerr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref)); base = fai_ref[k]; if (base == '-' || base == '*') { gaps += 1; } else { int i = bam_nt16_table[(int)base]; if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16 fprintf(pysamerr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name); free(fai_ref); return -1; } bases += 1; } } free(fai_ref); assert (padded_len == bases + gaps); return bases; } inline int * update_posmap(int *posmap, kstring_t ref) { int i, k; posmap = realloc(posmap, ref.m * sizeof(int)); for (i = k = 0; i < ref.l; ++i) { posmap[i] = k; if (ref.s[i]) ++k; } return posmap; } int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai) { bam_header_t *h = 0; bam1_t *b = 0; kstring_t r, q; int r_tid = -1; uint32_t *cigar2 = 0; int ret = 0, n2 = 0, m2 = 0, *posmap = 0; b = bam_init1(); r.l = r.m = q.l = q.m = 0; r.s = q.s = 0; int read_ret; h = in->header; while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in' uint32_t *cigar = bam1_cigar(b); n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) { // fprintf(pysamerr, "[depad] Found embedded reference '%s'\n", bam1_qname(b)); r_tid = b->core.tid; unpad_seq(b, &r); if (h->target_len[r_tid] != r.l) { fprintf(pysamerr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l); return -1; } if (fai) { // Check the embedded reference matches the FASTA file if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) { fprintf(pysamerr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]); return -1; } assert(r.l == q.l); int i; for (i = 0; i < r.l; ++i) { if (r.s[i] != q.s[i]) { // Show gaps as ASCII 45 fprintf(pysamerr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n", h->target_name[b->core.tid], i+1, r.s[i] ? bam_nt16_rev_table[(int)r.s[i]] : 45, q.s[i] ? bam_nt16_rev_table[(int)q.s[i]] : 45); return -1; } } } write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH)); replace_cigar(b, n2, cigar2); posmap = update_posmap(posmap, r); } else if (b->core.n_cigar > 0) { int i, k, op; if (b->core.tid < 0) { fprintf(pysamerr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b)); return -1; } else if (b->core.tid == r_tid) { ; // good case, reference available //fprintf(pysamerr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b)); } else if (fai) { if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) { fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]); return -1; } posmap = update_posmap(posmap, r); r_tid = b->core.tid; // fprintf(pysamerr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]); } else { fprintf(pysamerr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]); return -1; } unpad_seq(b, &q); if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) { write_cigar(cigar2, n2, m2, cigar[0]); if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[1]); } } /* Determine CIGAR operator for each base in the aligned read */ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD); /* Include any pads if starts with an insert */ if (q.s[0] == BAM_CINS) { for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k); if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD)); } /* Count consecutive CIGAR operators to turn into a CIGAR string */ for (i = k = 1, op = q.s[0]; i < q.l; ++i) { if (op != q.s[i]) { write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); op = q.s[i]; k = 1; } else ++k; } write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op)); if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) { if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) { write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]); } write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]); } /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */ int pre_op, post_op; for (i = 2; i < n2; ++i) if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) { pre_op = bam_cigar_op(cigar2[i-2]); post_op = bam_cigar_op(cigar2[i]); /* Note don't need to check for X/= as code above will use M only */ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) { /* This is a redundant P operator */ cigar2[i-1] = 0; // i.e. 0M /* If had same operator either side, combine them in post_op */ if (pre_op == post_op) { /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op); cigar2[i-2] = 0; // i.e. 0M } } } /* Remove the zero'd operators (0M) */ for (i = k = 0; i < n2; ++i) if (cigar2[i]) cigar2[k++] = cigar2[i]; n2 = k; replace_cigar(b, n2, cigar2); b->core.pos = posmap[b->core.pos]; if (b->core.mtid < 0 || b->core.mpos < 0) { /* Nice case, no mate to worry about*/ // fprintf(pysamerr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b)); /* TODO - Warning if FLAG says mate should be mapped? */ /* Clean up funny input where mate position is given but mate reference is missing: */ b->core.mtid = -1; b->core.mpos = -1; } else if (b->core.mtid == b->core.tid) { /* Nice case, same reference */ // fprintf(pysamerr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b)); b->core.mpos = posmap[b->core.mpos]; } else { /* Nasty case, Must load alternative posmap */ // fprintf(pysamerr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]); if (!fai) { fprintf(pysamerr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]); return -1; } /* Temporarily load the other reference sequence */ if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) { fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]); return -1; } posmap = update_posmap(posmap, r); b->core.mpos = posmap[b->core.mpos]; /* Restore the reference and posmap*/ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) { fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]); return -1; } posmap = update_posmap(posmap, r); } } samwrite(out, b); } if (read_ret < -1) { fprintf(pysamerr, "[depad] truncated file.\n"); ret = 1; } free(r.s); free(q.s); free(posmap); bam_destroy1(b); return ret; } bam_header_t * fix_header(bam_header_t *old, faidx_t *fai) { int i = 0, unpadded_len = 0; bam_header_t *header = 0 ; header = bam_header_dup(old); for (i = 0; i < old->n_targets; ++i) { unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]); if (unpadded_len < 0) { fprintf(pysamerr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]); } else { header->target_len[i] = unpadded_len; //fprintf(pysamerr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]); } } /* Duplicating the header allocated new buffer for header string */ /* After modifying the @SQ lines it will only get smaller, since */ /* the LN entries will be the same or shorter, and we'll remove */ /* any MD entries (MD5 checksums). */ assert(strlen(old->text) == strlen(header->text)); assert (0==strcmp(old->text, header->text)); const char *text; text = old->text; header->text[0] = '\0'; /* Resuse the allocated buffer */ char * newtext = header->text; char * end=NULL; while (text[0]=='@') { end = strchr(text, '\n'); assert(end != 0); if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') { /* TODO - edit the @SQ line here to remove MD and fix LN. */ /* For now just remove the @SQ line, and samtools will */ /* automatically generate a minimal replacement with LN. */ /* However, that discards any other tags like AS, SP, UR. */ //fprintf(pysamerr, "[depad] Removing @SQ line\n"); } else { /* Copy this line to the new header */ strncat(newtext, text, end - text + 1); } text = end + 1; } assert (text[0]=='\0'); /* Check we didn't overflow the buffer */ assert (strlen(header->text) <= strlen(old->text)); if (strlen(header->text) < header->l_text) { //fprintf(pysamerr, "[depad] Reallocating header buffer\n"); assert (newtext == header->text); newtext = malloc(strlen(header->text) + 1); strcpy(newtext, header->text); free(header->text); header->text = newtext; header->l_text = strlen(newtext); } //fprintf(pysamerr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text); return header; } static int usage(int is_long_help); int main_pad2unpad(int argc, char *argv[]) { samfile_t *in = 0, *out = 0; bam_header_t *h = 0; faidx_t *fai = 0; int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0; char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0; int ret=0; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) { switch (c) { case 'S': is_bamin = 0; break; case 's': assert(compress_level == -1); is_bamout = 0; break; case 'o': fn_out = strdup(optarg); break; case 'u': assert(is_bamout == 1); compress_level = 0; break; case '1': assert(is_bamout == 1); compress_level = 1; break; case 'T': fn_ref = strdup(optarg); break; case '?': is_long_help = 1; break; default: return usage(is_long_help); } } if (argc == optind) return usage(is_long_help); if (is_bamin) strcat(in_mode, "b"); if (is_bamout) strcat(out_mode, "b"); strcat(out_mode, "h"); if (compress_level >= 0) { char tmp[2]; tmp[0] = compress_level + '0'; tmp[1] = '\0'; strcat(out_mode, tmp); } // Load FASTA reference (also needed for SAM -> BAM if missing header) if (fn_ref) { fn_list = samfaipath(fn_ref); fai = fai_load(fn_ref); } // open file handlers if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) { fprintf(pysamerr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]); ret = 1; goto depad_end; } if (in->header == 0) { fprintf(pysamerr, "[depad] failed to read the header from \"%s\".\n", argv[optind]); ret = 1; goto depad_end; } if (in->header->text == 0 || in->header->l_text == 0) { fprintf(pysamerr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]); assert (0 == in->header->l_text); assert (0 == in->header->text); } if (fn_ref) { h = fix_header(in->header, fai); } else { fprintf(pysamerr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n"); h = in->header; } if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) { fprintf(pysamerr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output"); ret = 1; goto depad_end; } // Do the depad ret = bam_pad2unpad(in, out, fai); depad_end: // close files, free and return if (fai) fai_destroy(fai); if (h != in->header) bam_header_destroy(h); samclose(in); samclose(out); free(fn_list); free(fn_out); return ret; } static int usage(int is_long_help) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools depad \n\n"); fprintf(pysamerr, "Options: -s output is SAM (default is BAM)\n"); fprintf(pysamerr, " -S input is SAM (default is BAM)\n"); fprintf(pysamerr, " -u uncompressed BAM output (can't use with -s)\n"); fprintf(pysamerr, " -1 fast compression BAM output (can't use with -s)\n"); fprintf(pysamerr, " -T FILE reference sequence file [null]\n"); fprintf(pysamerr, " -o FILE output file name [stdout]\n"); fprintf(pysamerr, " -? longer help\n"); fprintf(pysamerr, "\n"); if (is_long_help) fprintf(pysamerr, "Notes:\n\ \n\ 1. Requires embedded reference sequences (before the reads for that reference),\n\ with the future aim to also support a FASTA padded reference sequence file.\n\ \n\ 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\ \n"); return 1; } pysam-0.7.7/samtools/knetfile.h0000664000076400007650000000311312162637166016330 0ustar andreasandreas#ifndef KNETFILE_H #define KNETFILE_H #include #include #ifndef _WIN32 #define netread(fd, ptr, len) read(fd, ptr, len) #define netwrite(fd, ptr, len) write(fd, ptr, len) #define netclose(fd) close(fd) #else #include #define netread(fd, ptr, len) recv(fd, ptr, len, 0) #define netwrite(fd, ptr, len) send(fd, ptr, len, 0) #define netclose(fd) closesocket(fd) #endif // FIXME: currently I/O is unbuffered #define KNF_TYPE_LOCAL 1 #define KNF_TYPE_FTP 2 #define KNF_TYPE_HTTP 3 typedef struct knetFile_s { int type, fd; int64_t offset; char *host, *port; // the following are for FTP only int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready; char *response, *retr, *size_cmd; int64_t seek_offset; // for lazy seek int64_t file_size; // the following are for HTTP only char *path, *http_host; } knetFile; #define knet_tell(fp) ((fp)->offset) #define knet_fileno(fp) ((fp)->fd) #ifdef __cplusplus extern "C" { #endif #ifdef _WIN32 int knet_win32_init(); void knet_win32_destroy(); #endif knetFile *knet_open(const char *fn, const char *mode); /* This only works with local files. */ knetFile *knet_dopen(int fd, const char *mode); /* If ->is_ready==0, this routine updates ->fd; otherwise, it simply reads from ->fd. */ off_t knet_read(knetFile *fp, void *buf, off_t len); /* This routine only sets ->offset and ->is_ready=0. It does not communicate with the FTP server. */ off_t knet_seek(knetFile *fp, int64_t off, int whence); int knet_close(knetFile *fp); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bam_cat.c.pysam.c0000664000076400007650000001331512162637166017466 0ustar andreasandreas#include "pysam.h" /* bam_cat -- efficiently concatenates bam files bam_cat can be used to concatenate BAM files. Under special circumstances, it can be used as an alternative to 'samtools merge' to concatenate multiple sorted files into a single sorted file. For this to work each file must be sorted, and the sorted files must be given as command line arguments in order such that the final read in file i is less than or equal to the first read in file i+1. This code is derived from the bam_reheader function in samtools 0.1.8 and modified to perform concatenation by Chris Saunders on behalf of Illumina. ########## License: The MIT License Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd. Modified SAMtools work copyright (c) 2010 Illumina, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* makefile: """ CC=gcc CFLAGS+=-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I$(SAMTOOLS_DIR) LDFLAGS+=-L$(SAMTOOLS_DIR) LDLIBS+=-lbam -lz all:bam_cat """ */ #include #include #include #include "knetfile.h" #include "bgzf.h" #include "bam.h" #define BUF_SIZE 0x10000 #define GZIPID1 31 #define GZIPID2 139 #define BGZF_EMPTY_BLOCK_SIZE 28 int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam) { BGZF *fp; FILE* fp_file; uint8_t *buf; uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE]; const int es=BGZF_EMPTY_BLOCK_SIZE; int i; fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w"); if (fp == 0) { fprintf(pysamerr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outbam); return 1; } if (h) bam_header_write(fp, h); buf = (uint8_t*) malloc(BUF_SIZE); for(i = 0; i < nfn; ++i){ BGZF *in; bam_header_t *old; int len,j; in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(fileno(stdin), "r"); if (in == 0) { fprintf(pysamerr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]); return -1; } if (in->is_write) return -1; old = bam_header_read(in); if (h == 0 && i == 0) bam_header_write(fp, old); if (in->block_offset < in->block_length) { bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset); bgzf_flush(fp); } j=0; #ifdef _USE_KNETFILE fp_file = fp->fp; while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) { #else fp_file = fp->fp; while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) { #endif if(len= 0) { switch (c) { case 'h': { tamFile fph = sam_open(optarg); if (fph == 0) { fprintf(pysamerr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]); return 1; } h = sam_header_read(fph); sam_close(fph); break; } case 'o': outfn = strdup(optarg); break; } } if (argc - optind < 2) { fprintf(pysamerr, "Usage: samtools cat [-h header.sam] [-o out.bam] [...]\n"); return 1; } ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-"); free(outfn); return ret; } pysam-0.7.7/samtools/bam2bcf.c.pysam.c0000664000076400007650000003475612162637166017410 0ustar andreasandreas#include "pysam.h" #include #include #include #include "bam.h" #include "kstring.h" #include "bam2bcf.h" #include "errmod.h" #include "bcftools/bcf.h" extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CALL_ETA 0.03f #define CALL_MAX 256 #define CALL_DEFTHETA 0.83f #define DEF_MAPQ 20 #define CAP_DIST 25 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ) { bcf_callaux_t *bca; if (theta <= 0.) theta = CALL_DEFTHETA; bca = calloc(1, sizeof(bcf_callaux_t)); bca->capQ = 60; bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100; bca->min_baseQ = min_baseQ; bca->e = errmod_init(1. - theta); bca->min_frac = 0.002; bca->min_support = 1; bca->per_sample_flt = 0; bca->npos = 100; bca->ref_pos = calloc(bca->npos, sizeof(int)); bca->alt_pos = calloc(bca->npos, sizeof(int)); return bca; } static int get_position(const bam_pileup1_t *p, int *len) { int icig, n_tot_bases = 0, iread = 0, edist = p->qpos + 1; for (icig=0; icigb->core.n_cigar; icig++) { // Conversion from uint32_t to MIDNSHP // 0123456 // MIDNSHP int cig = bam1_cigar(p->b)[icig] & BAM_CIGAR_MASK; int ncig = bam1_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT; if ( cig==0 ) { n_tot_bases += ncig; iread += ncig; } else if ( cig==1 ) { n_tot_bases += ncig; iread += ncig; } else if ( cig==4 ) { iread += ncig; if ( iread<=p->qpos ) edist -= ncig; } } *len = n_tot_bases; return edist; } void bcf_call_destroy(bcf_callaux_t *bca) { if (bca == 0) return; errmod_destroy(bca->e); if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; } free(bca->bases); free(bca->inscns); free(bca); } /* ref_base is the 4-bit representation of the reference base. It is * negative if we are looking at an indel. */ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r) { int i, n, ref4, is_indel, ori_depth = 0; memset(r, 0, sizeof(bcf_callret1_t)); if (ref_base >= 0) { ref4 = bam_nt16_nt4_table[ref_base]; is_indel = 0; } else ref4 = 4, is_indel = 1; if (_n == 0) return -1; // enlarge the bases array if necessary if (bca->max_bases < _n) { bca->max_bases = _n; kroundup32(bca->max_bases); bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases); } // fill the bases array for (i = n = r->n_supp = 0; i < _n; ++i) { const bam_pileup1_t *p = pl + i; int q, b, mapQ, baseQ, is_diff, min_dist, seqQ; // set base if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; ++ori_depth; baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality seqQ = is_indel? (p->aux>>8&0xff) : 99; if (q < bca->min_baseQ) continue; if (q > seqQ) q = seqQ; mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255 mapQ = mapQ < bca->capQ? mapQ : bca->capQ; if (q > mapQ) q = mapQ; if (q > 63) q = 63; if (q < 4) q = 4; if (!is_indel) { b = bam1_seqi(bam1_seq(p->b), p->qpos); // base b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base is_diff = (ref4 < 4 && b == ref4)? 0 : 1; } else { b = p->aux>>16&0x3f; is_diff = (b != 0); } if (is_diff) ++r->n_supp; bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b; // collect annotations if (b < 4) r->qsum[b] += q; ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)]; min_dist = p->b->core.l_qseq - 1 - p->qpos; if (min_dist > p->qpos) min_dist = p->qpos; if (min_dist > CAP_DIST) min_dist = CAP_DIST; r->anno[1<<2|is_diff<<1|0] += baseQ; r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ; r->anno[2<<2|is_diff<<1|0] += mapQ; r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ; r->anno[3<<2|is_diff<<1|0] += min_dist; r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist; // collect read positions for ReadPosBias int len, pos = get_position(p, &len); int epos = (double)pos/(len+1) * bca->npos; if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base ) bca->ref_pos[epos]++; else bca->alt_pos[epos]++; } r->depth = n; r->ori_depth = ori_depth; // glfgen errmod_cal(bca->e, n, 5, bca->bases, r->p); return r->depth; } double mann_whitney_1947(int n, int m, int U) { if (U<0) return 0; if (n==0||m==0) return U==0 ? 1 : 0; return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U); } void calc_ReadPosBias(bcf_callaux_t *bca, bcf_call_t *call) { int i, nref = 0, nalt = 0; unsigned long int U = 0; for (i=0; inpos; i++) { nref += bca->ref_pos[i]; nalt += bca->alt_pos[i]; U += nref*bca->alt_pos[i]; bca->ref_pos[i] = 0; bca->alt_pos[i] = 0; } #if 0 //todo double var = 0, avg = (double)(nref+nalt)/bca->npos; for (i=0; inpos; i++) { double ediff = bca->ref_pos[i] + bca->alt_pos[i] - avg; var += ediff*ediff; bca->ref_pos[i] = 0; bca->alt_pos[i] = 0; } call->read_pos.avg = avg; call->read_pos.var = sqrt(var/bca->npos); call->read_pos.dp = nref+nalt; #endif if ( !nref || !nalt ) { call->read_pos_bias = -1; return; } if ( nref>=8 || nalt>=8 ) { // normal approximation double mean = ((double)nref*nalt+1.0)/2.0; double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0; double z = (U-mean)/sqrt(var2); call->read_pos_bias = z; //fprintf(pysamerr,"nref=%d nalt=%d U=%ld mean=%e var=%e zval=%e\n", nref,nalt,U,mean,sqrt(var2),call->read_pos_bias); } else { double p = mann_whitney_1947(nalt,nref,U); // biased form claimed by GATK to behave better empirically // double var2 = (1.0+1.0/(nref+nalt+1.0))*(double)nref*nalt*(nref+nalt+1.0)/12.0; double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0; double z; if ( p >= 1./sqrt(var2*2*M_PI) ) z = 0; // equal to mean else { if ( U >= nref*nalt/2. ) z = sqrt(-2*log(sqrt(var2*2*M_PI)*p)); else z = -sqrt(-2*log(sqrt(var2*2*M_PI)*p)); } call->read_pos_bias = z; //fprintf(pysamerr,"nref=%d nalt=%d U=%ld p=%e var2=%e zval=%e\n", nref,nalt,U, p,var2,call->read_pos_bias); } } float mean_diff_to_prob(float mdiff, int dp, int readlen) { if ( dp==2 ) { if ( mdiff==0 ) return (2.0*readlen + 4.0*(readlen-1.0))/((float)readlen*readlen); else return 8.0*(readlen - 4.0*mdiff)/((float)readlen*readlen); } // This is crude empirical approximation and is not very accurate for // shorter read lengths (<100bp). There certainly is a room for // improvement. const float mv[24][2] = { {0,0}, {0,0}, {0,0}, { 9.108, 4.934}, { 9.999, 3.991}, {10.273, 3.485}, {10.579, 3.160}, {10.828, 2.889}, {11.014, 2.703}, {11.028, 2.546}, {11.244, 2.391}, {11.231, 2.320}, {11.323, 2.138}, {11.403, 2.123}, {11.394, 1.994}, {11.451, 1.928}, {11.445, 1.862}, {11.516, 1.815}, {11.560, 1.761}, {11.544, 1.728}, {11.605, 1.674}, {11.592, 1.652}, {11.674, 1.613}, {11.641, 1.570} }; float m, v; if ( dp>=24 ) { m = readlen/8.; if (dp>100) dp = 100; v = 1.476/(0.182*pow(dp,0.514)); v = v*(readlen/100.); } else { m = mv[dp][0]; v = mv[dp][1]; m = m*readlen/100.; v = v*readlen/100.; v *= 1.2; // allow more variability } return 1.0/(v*sqrt(2*M_PI)) * exp(-0.5*((mdiff-m)/v)*((mdiff-m)/v)); } void calc_vdb(bcf_callaux_t *bca, bcf_call_t *call) { int i, dp = 0; float mean_pos = 0, mean_diff = 0; for (i=0; inpos; i++) { if ( !bca->alt_pos[i] ) continue; dp += bca->alt_pos[i]; int j = inpos/2 ? i : bca->npos - i; mean_pos += bca->alt_pos[i]*j; } if ( dp<2 ) { call->vdb = -1; return; } mean_pos /= dp; for (i=0; inpos; i++) { if ( !bca->alt_pos[i] ) continue; int j = inpos/2 ? i : bca->npos - i; mean_diff += bca->alt_pos[i] * fabs(j - mean_pos); } mean_diff /= dp; call->vdb = mean_diff_to_prob(mean_diff, dp, bca->npos); } /** * bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles * @n: number of samples * @calls: each sample's calls * @bca: auxiliary data structure for holding temporary values * @ref_base: the reference base * @call: filled with the annotations */ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call) { int ref4, i, j, qsum[4]; int64_t tmp; if (ref_base >= 0) { call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base]; if (ref4 > 4) ref4 = 4; } else call->ori_ref = -1, ref4 = 0; // calculate qsum memset(qsum, 0, 4 * sizeof(int)); for (i = 0; i < n; ++i) for (j = 0; j < 4; ++j) qsum[j] += calls[i].qsum[j]; int qsum_tot=0; for (j=0; j<4; j++) { qsum_tot += qsum[j]; call->qsum[j] = 0; } for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j; // find the top 2 alleles for (i = 1; i < 4; ++i) // insertion sort for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j) tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp; // set the reference allele and alternative allele(s) for (i = 0; i < 5; ++i) call->a[i] = -1; call->unseen = -1; call->a[0] = ref4; for (i = 3, j = 1; i >= 0; --i) { if ((qsum[i]&3) != ref4) { if (qsum[i]>>2 != 0) { if ( j<4 ) call->qsum[j] = (float)(qsum[i]>>2)/qsum_tot; // ref N can make j>=4 call->a[j++] = qsum[i]&3; } else break; } else call->qsum[0] = (float)(qsum[i]>>2)/qsum_tot; } if (ref_base >= 0) { // for SNPs, find the "unseen" base if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0) call->unseen = j, call->a[j++] = qsum[i]&3; call->n_alleles = j; } else { call->n_alleles = j; if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything } // set the PL array if (call->n < n) { call->n = n; call->PL = realloc(call->PL, 15 * n); } { int x, g[15], z; double sum_min = 0.; x = call->n_alleles * (call->n_alleles + 1) / 2; // get the possible genotypes for (i = z = 0; i < call->n_alleles; ++i) for (j = 0; j <= i; ++j) g[z++] = call->a[j] * 5 + call->a[i]; for (i = 0; i < n; ++i) { uint8_t *PL = call->PL + x * i; const bcf_callret1_t *r = calls + i; float min = 1e37; for (j = 0; j < x; ++j) if (min > r->p[g[j]]) min = r->p[g[j]]; sum_min += min; for (j = 0; j < x; ++j) { int y; y = (int)(r->p[g[j]] - min + .499); if (y > 255) y = 255; PL[j] = y; } } // if (ref_base < 0) fprintf(pysamerr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen); call->shift = (int)(sum_min + .499); } // combine annotations memset(call->anno, 0, 16 * sizeof(int)); for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) { call->depth += calls[i].depth; call->ori_depth += calls[i].ori_depth; for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j]; } calc_vdb(bca, call); calc_ReadPosBias(bca, call); return 0; } int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref) { extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two); kstring_t s; int i, j; b->n_smpl = bc->n; b->tid = tid; b->pos = pos; b->qual = 0; s.s = b->str; s.m = b->m_str; s.l = 0; kputc('\0', &s); if (bc->ori_ref < 0) { // an indel // write REF kputc(ref[pos], &s); for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s); kputc('\0', &s); // write ALT kputc(ref[pos], &s); for (i = 1; i < 4; ++i) { if (bc->a[i] < 0) break; if (i > 1) { kputc(',', &s); kputc(ref[pos], &s); } if (bca->indel_types[bc->a[i]] < 0) { // deletion for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s); } else { // insertion; cannot be a reference unless a bug char *inscns = &bca->inscns[bc->a[i] * bca->maxins]; for (j = 0; j < bca->indel_types[bc->a[i]]; ++j) kputc("ACGTN"[(int)inscns[j]], &s); for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s); } } kputc('\0', &s); } else { // a SNP kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s); for (i = 1; i < 5; ++i) { if (bc->a[i] < 0) break; if (i > 1) kputc(',', &s); kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s); } kputc('\0', &s); } kputc('\0', &s); // INFO if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IS=%d,%f;", bca->max_support, bca->max_frac); kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s); for (i = 0; i < 16; ++i) { if (i) kputc(',', &s); kputw(bc->anno[i], &s); } //ksprintf(&s,";RPS=%d,%f,%f", bc->read_pos.dp,bc->read_pos.avg,bc->read_pos.var); ksprintf(&s,";QS=%f,%f,%f,%f", bc->qsum[0],bc->qsum[1],bc->qsum[2],bc->qsum[3]); if (bc->vdb != -1) ksprintf(&s, ";VDB=%e", bc->vdb); if (bc->read_pos_bias != -1 ) ksprintf(&s, ";RPB=%e", bc->read_pos_bias); kputc('\0', &s); // FMT kputs("PL", &s); if (bcr && fmt_flag) { if (fmt_flag & B2B_FMT_DP) kputs(":DP", &s); if (fmt_flag & B2B_FMT_DV) kputs(":DV", &s); if (fmt_flag & B2B_FMT_SP) kputs(":SP", &s); } kputc('\0', &s); b->m_str = s.m; b->str = s.s; b->l_str = s.l; bcf_sync(b); memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n); if (bcr && fmt_flag) { uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0; uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0; int32_t *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0; for (i = 0; i < bc->n; ++i) { bcf_callret1_t *p = bcr + i; if (dp) dp[i] = p->depth < 0xffff? p->depth : 0xffff; if (dv) dv[i] = p->n_supp < 0xffff? p->n_supp : 0xffff; if (sp) { if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2 || p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2) { sp[i] = 0; } else { double left, right, two; int x; kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two); x = (int)(-4.343 * log(two) + .499); if (x > 255) x = 255; sp[i] = x; } } } } return 0; } pysam-0.7.7/samtools/bam_tview_curses.c.pysam.c0000664000076400007650000001733512162637166021447 0ustar andreasandreas#include "pysam.h" #undef _HAVE_CURSES #if _CURSES_LIB == 0 #elif _CURSES_LIB == 1 #include #ifndef NCURSES_VERSION #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled" #else #define _HAVE_CURSES #endif #elif _CURSES_LIB == 2 #include #define _HAVE_CURSES #else #warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled" #endif #include "bam_tview.h" #ifdef _HAVE_CURSES typedef struct CursesTview { tview_t view; WINDOW *wgoto, *whelp; } curses_tview_t; #define FROM_TV(ptr) ((curses_tview_t*)ptr) static void curses_destroy(tview_t* base) { curses_tview_t* tv=(curses_tview_t*)base; delwin(tv->wgoto); delwin(tv->whelp); endwin(); base_tv_destroy(base); free(tv); } /* void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...); void (*my_)(struct AbstractTview*,int,int,int); void (*my_attron)(struct AbstractTview*,int); void (*my_attroff)(struct AbstractTview*,int); void (*my_clear)(struct AbstractTview*); int (*my_colorpair)(struct AbstractTview*,int); */ static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...) { unsigned int size=tv->mcol+2; char* str=malloc(size); if(str==0) exit(EXIT_FAILURE); va_list argptr; va_start(argptr, fmt); vsnprintf(str,size, fmt, argptr); va_end(argptr); mvprintw(y,x,str); free(str); } static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch) { mvaddch(y,x,ch); } static void curses_attron(struct AbstractTview* tv,int flag) { attron(flag); } static void curses_attroff(struct AbstractTview* tv,int flag) { attroff(flag); } static void curses_clear(struct AbstractTview* tv) { clear(); } static int curses_colorpair(struct AbstractTview* tv,int flag) { return COLOR_PAIR(flag); } static int curses_drawaln(struct AbstractTview* tv, int tid, int pos) { return base_draw_aln(tv, tid, pos); } static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos) { char str[256], *p; int i, l = 0; tview_t *base=(tview_t*)tv; wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+'); mvwprintw(tv->wgoto, 1, 2, "Goto: "); for (;;) { int c = wgetch(tv->wgoto); wrefresh(tv->wgoto); if (c == KEY_BACKSPACE || c == '\010' || c == '\177') { if(l > 0) --l; } else if (c == KEY_ENTER || c == '\012' || c == '\015') { int _tid = -1, _beg, _end; if (str[0] == '=') { _beg = strtol(str+1, &p, 10) - 1; if (_beg > 0) { *pos = _beg; return; } } else { bam_parse_region(base->header, str, &_tid, &_beg, &_end); if (_tid >= 0) { *tid = _tid; *pos = _beg; return; } } } else if (isgraph(c)) { if (l < TV_MAX_GOTO) str[l++] = c; } else if (c == '\027') l = 0; else if (c == '\033') return; str[l] = '\0'; for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' '); mvwprintw(tv->wgoto, 1, 8, "%s", str); } } static void tv_win_help(curses_tview_t *tv) { int r = 1; tview_t* base=(tview_t*)base; WINDOW *win = tv->whelp; wborder(win, '|', '|', '-', '-', '+', '+', '+', '+'); mvwprintw(win, r++, 2, " -=- Help -=- "); r++; mvwprintw(win, r++, 2, "? This window"); mvwprintw(win, r++, 2, "Arrows Small scroll movement"); mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement"); mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement"); mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left"); mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right"); mvwprintw(win, r++, 2, "space Scroll one screen"); mvwprintw(win, r++, 2, "backspace Scroll back one screen"); mvwprintw(win, r++, 2, "g Go to specific location"); mvwprintw(win, r++, 2, "m Color for mapping qual"); mvwprintw(win, r++, 2, "n Color for nucleotide"); mvwprintw(win, r++, 2, "b Color for base quality"); mvwprintw(win, r++, 2, "c Color for cs color"); mvwprintw(win, r++, 2, "z Color for cs qual"); mvwprintw(win, r++, 2, ". Toggle on/off dot view"); mvwprintw(win, r++, 2, "s Toggle on/off ref skip"); mvwprintw(win, r++, 2, "r Toggle on/off rd name"); mvwprintw(win, r++, 2, "N Turn on nt view"); mvwprintw(win, r++, 2, "C Turn on cs view"); mvwprintw(win, r++, 2, "i Toggle on/off ins"); mvwprintw(win, r++, 2, "q Exit"); r++; mvwprintw(win, r++, 2, "Underline: Secondary or orphan"); mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19"); mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30"); wrefresh(win); wgetch(win); } static int curses_underline(tview_t* tv) { return A_UNDERLINE; } static int curses_loop(tview_t* tv) { int tid, pos; curses_tview_t *CTV=(curses_tview_t *)tv; tid = tv->curr_tid; pos = tv->left_pos; while (1) { int c = getch(); switch (c) { case '?': tv_win_help(CTV); break; case '\033': case 'q': goto end_loop; case '/': case 'g': tv_win_goto(CTV, &tid, &pos); break; case 'm': tv->color_for = TV_COLOR_MAPQ; break; case 'b': tv->color_for = TV_COLOR_BASEQ; break; case 'n': tv->color_for = TV_COLOR_NUCL; break; case 'c': tv->color_for = TV_COLOR_COL; break; case 'z': tv->color_for = TV_COLOR_COLQ; break; case 's': tv->no_skip = !tv->no_skip; break; case 'r': tv->show_name = !tv->show_name; break; case KEY_LEFT: case 'h': --pos; break; case KEY_RIGHT: case 'l': ++pos; break; case KEY_SLEFT: case 'H': pos -= 20; break; case KEY_SRIGHT: case 'L': pos += 20; break; case '.': tv->is_dot = !tv->is_dot; break; case 'N': tv->base_for = TV_BASE_NUCL; break; case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break; case 'i': tv->ins = !tv->ins; break; case '\010': pos -= 1000; break; case '\014': pos += 1000; break; case ' ': pos += tv->mcol; break; case KEY_UP: case 'j': --tv->row_shift; break; case KEY_DOWN: case 'k': ++tv->row_shift; break; case KEY_BACKSPACE: case '\177': pos -= tv->mcol; break; case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break; default: continue; } if (pos < 0) pos = 0; if (tv->row_shift < 0) tv->row_shift = 0; tv->my_drawaln(tv, tid, pos); } end_loop: return 0; } tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples) { curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t)); tview_t* base=(tview_t*)tv; if(tv==0) { fprintf(pysamerr,"Calloc failed\n"); return 0; } base_tv_init(base,fn,fn_fa,samples); /* initialize callbacks */ #define SET_CALLBACK(fun) base->my_##fun=curses_##fun; SET_CALLBACK(destroy); SET_CALLBACK(mvprintw); SET_CALLBACK(mvaddch); SET_CALLBACK(attron); SET_CALLBACK(attroff); SET_CALLBACK(clear); SET_CALLBACK(colorpair); SET_CALLBACK(drawaln); SET_CALLBACK(loop); SET_CALLBACK(underline); #undef SET_CALLBACK initscr(); keypad(stdscr, TRUE); clear(); noecho(); cbreak(); getmaxyx(stdscr, base->mrow, base->mcol); tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5); tv->whelp = newwin(29, 40, 5, 5); start_color(); init_pair(1, COLOR_BLUE, COLOR_BLACK); init_pair(2, COLOR_GREEN, COLOR_BLACK); init_pair(3, COLOR_YELLOW, COLOR_BLACK); init_pair(4, COLOR_WHITE, COLOR_BLACK); init_pair(5, COLOR_GREEN, COLOR_BLACK); init_pair(6, COLOR_CYAN, COLOR_BLACK); init_pair(7, COLOR_YELLOW, COLOR_BLACK); init_pair(8, COLOR_RED, COLOR_BLACK); init_pair(9, COLOR_BLUE, COLOR_BLACK); return base; } #else // #ifdef _HAVE_CURSES #include #warning "No curses library is available; tview with curses is disabled." extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples); tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples) { return text_tv_init(fn,fn_fa,samples); } #endif // #ifdef _HAVE_CURSES pysam-0.7.7/samtools/faidx.h0000664000076400007650000000616412162637166015633 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ #ifndef FAIDX_H #define FAIDX_H /*! @header Index FASTA files and extract subsequence. @copyright The Wellcome Trust Sanger Institute. */ struct __faidx_t; typedef struct __faidx_t faidx_t; #ifdef __cplusplus extern "C" { #endif /*! @abstract Build index for a FASTA or razip compressed FASTA file. @param fn FASTA file name @return 0 on success; or -1 on failure @discussion File "fn.fai" will be generated. */ int fai_build(const char *fn); /*! @abstract Distroy a faidx_t struct. @param fai Pointer to the struct to be destroyed */ void fai_destroy(faidx_t *fai); /*! @abstract Load index from "fn.fai". @param fn File name of the FASTA file */ faidx_t *fai_load(const char *fn); /*! @abstract Fetch the sequence in a region. @param fai Pointer to the faidx_t struct @param reg Region in the format "chr2:20,000-30,000" @param len Length of the region @return Pointer to the sequence; null on failure @discussion The returned sequence is allocated by malloc family and should be destroyed by end users by calling free() on it. */ char *fai_fetch(const faidx_t *fai, const char *reg, int *len); /*! @abstract Fetch the number of sequences. @param fai Pointer to the faidx_t struct @return The number of sequences */ int faidx_fetch_nseq(const faidx_t *fai); /*! @abstract Fetch the sequence in a region. @param fai Pointer to the faidx_t struct @param c_name Region name @param p_beg_i Beginning position number (zero-based) @param p_end_i End position number (zero-based) @param len Length of the region @return Pointer to the sequence; null on failure @discussion The returned sequence is allocated by malloc family and should be destroyed by end users by calling free() on it. */ char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len); #ifdef __cplusplus } #endif #endif pysam-0.7.7/samtools/bgzf.c.pysam.c0000664000076400007650000005123312162637166017031 0ustar andreasandreas#include "pysam.h" /* The MIT License Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology 2011 Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include "bgzf.h" #ifdef _USE_KNETFILE #include "knetfile.h" typedef knetFile *_bgzf_file_t; #define _bgzf_open(fn, mode) knet_open(fn, mode) #define _bgzf_dopen(fp, mode) knet_dopen(fp, mode) #define _bgzf_close(fp) knet_close(fp) #define _bgzf_fileno(fp) ((fp)->fd) #define _bgzf_tell(fp) knet_tell(fp) #define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence) #define _bgzf_read(fp, buf, len) knet_read(fp, buf, len) #define _bgzf_write(fp, buf, len) knet_write(fp, buf, len) #else // ~defined(_USE_KNETFILE) #if defined(_WIN32) || defined(_MSC_VER) #define ftello(fp) ftell(fp) #define fseeko(fp, offset, whence) fseek(fp, offset, whence) #else // ~defined(_WIN32) extern off_t ftello(FILE *stream); extern int fseeko(FILE *stream, off_t offset, int whence); #endif // ~defined(_WIN32) typedef FILE *_bgzf_file_t; #define _bgzf_open(fn, mode) fopen(fn, mode) #define _bgzf_dopen(fp, mode) fdopen(fp, mode) #define _bgzf_close(fp) fclose(fp) #define _bgzf_fileno(fp) fileno(fp) #define _bgzf_tell(fp) ftello(fp) #define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence) #define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp) #define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp) #endif // ~define(_USE_KNETFILE) #define BLOCK_HEADER_LENGTH 18 #define BLOCK_FOOTER_LENGTH 8 /* BGZF/GZIP header (speciallized from RFC 1952; little endian): +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN| +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+ */ static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0"; #ifdef BGZF_CACHE typedef struct { int size; uint8_t *block; int64_t end_offset; } cache_t; #include "khash.h" KHASH_MAP_INIT_INT64(cache, cache_t) #endif static inline void packInt16(uint8_t *buffer, uint16_t value) { buffer[0] = value; buffer[1] = value >> 8; } static inline int unpackInt16(const uint8_t *buffer) { return buffer[0] | buffer[1] << 8; } static inline void packInt32(uint8_t *buffer, uint32_t value) { buffer[0] = value; buffer[1] = value >> 8; buffer[2] = value >> 16; buffer[3] = value >> 24; } static BGZF *bgzf_read_init() { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->is_write = 0; fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); #ifdef BGZF_CACHE fp->cache = kh_init(cache); #endif return fp; } static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level { BGZF *fp; fp = calloc(1, sizeof(BGZF)); fp->is_write = 1; fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE); fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE); fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1 if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION; return fp; } // get the compress level from the mode string static int mode2level(const char *__restrict mode) { int i, compress_level = -1; for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; if (mode[i]) compress_level = (int)mode[i] - '0'; if (strchr(mode, 'u')) compress_level = 0; return compress_level; } BGZF *bgzf_open(const char *path, const char *mode) { BGZF *fp = 0; assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_open(path, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fopen(path, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } BGZF *bgzf_dopen(int fd, const char *mode) { BGZF *fp = 0; assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE); if (strchr(mode, 'r') || strchr(mode, 'R')) { _bgzf_file_t fpr; if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0; fp = bgzf_read_init(); fp->fp = fpr; } else if (strchr(mode, 'w') || strchr(mode, 'W')) { FILE *fpw; if ((fpw = fdopen(fd, "w")) == 0) return 0; fp = bgzf_write_init(mode2level(mode)); fp->fp = fpw; } return fp; } static int bgzf_compress(void *_dst, int *dlen, void *src, int slen, int level) { uint32_t crc; z_stream zs; uint8_t *dst = (uint8_t*)_dst; // compress the body zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = src; zs.avail_in = slen; zs.next_out = dst + BLOCK_HEADER_LENGTH; zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH; if (deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY) != Z_OK) return -1; // -15 to disable zlib header/footer if (deflate(&zs, Z_FINISH) != Z_STREAM_END) return -1; if (deflateEnd(&zs) != Z_OK) return -1; *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH; // write the header memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes // write the footer crc = crc32(crc32(0L, NULL, 0L), src, slen); packInt32((uint8_t*)&dst[*dlen - 8], crc); packInt32((uint8_t*)&dst[*dlen - 4], slen); return 0; } // Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length. static int deflate_block(BGZF *fp, int block_length) { int comp_size = BGZF_MAX_BLOCK_SIZE; if (bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level) != 0) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } fp->block_offset = 0; return comp_size; } // Inflate the block in fp->compressed_block into fp->uncompressed_block static int inflate_block(BGZF* fp, int block_length) { z_stream zs; zs.zalloc = NULL; zs.zfree = NULL; zs.next_in = fp->compressed_block + 18; zs.avail_in = block_length - 16; zs.next_out = fp->uncompressed_block; zs.avail_out = BGZF_MAX_BLOCK_SIZE; if (inflateInit2(&zs, -15) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflate(&zs, Z_FINISH) != Z_STREAM_END) { inflateEnd(&zs); fp->errcode |= BGZF_ERR_ZLIB; return -1; } if (inflateEnd(&zs) != Z_OK) { fp->errcode |= BGZF_ERR_ZLIB; return -1; } return zs.total_out; } static int check_header(const uint8_t *header) { return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0 && unpackInt16((uint8_t*)&header[10]) == 6 && header[12] == 'B' && header[13] == 'C' && unpackInt16((uint8_t*)&header[14]) == 2); } #ifdef BGZF_CACHE static void free_cache(BGZF *fp) { khint_t k; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (fp->is_write) return; for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) free(kh_val(h, k).block); kh_destroy(cache, h); } static int load_block_from_cache(BGZF *fp, int64_t block_address) { khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; k = kh_get(cache, h, block_address); if (k == kh_end(h)) return 0; p = &kh_val(h, k); if (fp->block_length != 0) fp->block_offset = 0; fp->block_address = block_address; fp->block_length = p->size; memcpy(fp->uncompressed_block, p->block, BGZF_MAX_BLOCK_SIZE); _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET); return p->size; } static void cache_block(BGZF *fp, int size) { int ret; khint_t k; cache_t *p; khash_t(cache) *h = (khash_t(cache)*)fp->cache; if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return; if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > fp->cache_size) { /* A better way would be to remove the oldest block in the * cache, but here we remove a random one for simplicity. This * should not have a big impact on performance. */ for (k = kh_begin(h); k < kh_end(h); ++k) if (kh_exist(h, k)) break; if (k < kh_end(h)) { free(kh_val(h, k).block); kh_del(cache, h, k); } } k = kh_put(cache, h, fp->block_address, &ret); if (ret == 0) return; // if this happens, a bug! p = &kh_val(h, k); p->size = fp->block_length; p->end_offset = fp->block_address + size; p->block = malloc(BGZF_MAX_BLOCK_SIZE); memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE); } #else static void free_cache(BGZF *fp) {} static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;} static void cache_block(BGZF *fp, int size) {} #endif int bgzf_read_block(BGZF *fp) { uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block; int count, size = 0, block_length, remaining; int64_t block_address; block_address = _bgzf_tell((_bgzf_file_t)fp->fp); if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0; count = _bgzf_read(fp->fp, header, sizeof(header)); if (count == 0) { // no data read fp->block_length = 0; return 0; } if (count != sizeof(header) || !check_header(header)) { fp->errcode |= BGZF_ERR_HEADER; return -1; } size = count; block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1" compressed_block = (uint8_t*)fp->compressed_block; memcpy(compressed_block, header, BLOCK_HEADER_LENGTH); remaining = block_length - BLOCK_HEADER_LENGTH; count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining); if (count != remaining) { fp->errcode |= BGZF_ERR_IO; return -1; } size += count; if ((count = inflate_block(fp, block_length)) < 0) return -1; if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek. fp->block_address = block_address; fp->block_length = count; cache_block(fp, size); return 0; } ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length) { ssize_t bytes_read = 0; uint8_t *output = data; if (length <= 0) return 0; assert(fp->is_write == 0); while (bytes_read < length) { int copy_length, available = fp->block_length - fp->block_offset; uint8_t *buffer; if (available <= 0) { if (bgzf_read_block(fp) != 0) return -1; available = fp->block_length - fp->block_offset; if (available <= 0) break; } copy_length = length - bytes_read < available? length - bytes_read : available; buffer = fp->uncompressed_block; memcpy(output, buffer + fp->block_offset, copy_length); fp->block_offset += copy_length; output += copy_length; bytes_read += copy_length; } if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = fp->block_length = 0; } return bytes_read; } /***** BEGIN: multi-threading *****/ typedef struct { BGZF *fp; struct mtaux_t *mt; void *buf; int i, errcode, toproc; } worker_t; typedef struct mtaux_t { int n_threads, n_blks, curr, done; volatile int proc_cnt; void **blk; int *len; worker_t *w; pthread_t *tid; pthread_mutex_t lock; pthread_cond_t cv; } mtaux_t; static int worker_aux(worker_t *w) { int i, tmp, stop = 0; // wait for condition: to process or all done pthread_mutex_lock(&w->mt->lock); while (!w->toproc && !w->mt->done) pthread_cond_wait(&w->mt->cv, &w->mt->lock); if (w->mt->done) stop = 1; w->toproc = 0; pthread_mutex_unlock(&w->mt->lock); if (stop) return 1; // to quit the thread w->errcode = 0; for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) { int clen = BGZF_MAX_BLOCK_SIZE; if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->fp->compress_level) != 0) w->errcode |= BGZF_ERR_ZLIB; memcpy(w->mt->blk[i], w->buf, clen); w->mt->len[i] = clen; } tmp = __sync_fetch_and_add(&w->mt->proc_cnt, 1); return 0; } static void *mt_worker(void *data) { while (worker_aux(data) == 0); return 0; } int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks) { int i; mtaux_t *mt; pthread_attr_t attr; if (!fp->is_write || fp->mt || n_threads <= 1) return -1; mt = calloc(1, sizeof(mtaux_t)); mt->n_threads = n_threads; mt->n_blks = n_threads * n_sub_blks; mt->len = calloc(mt->n_blks, sizeof(int)); mt->blk = calloc(mt->n_blks, sizeof(void*)); for (i = 0; i < mt->n_blks; ++i) mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE); mt->tid = calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master mt->w = calloc(mt->n_threads, sizeof(worker_t)); for (i = 0; i < mt->n_threads; ++i) { mt->w[i].i = i; mt->w[i].mt = mt; mt->w[i].fp = fp; mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE); } pthread_attr_init(&attr); pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE); pthread_mutex_init(&mt->lock, 0); pthread_cond_init(&mt->cv, 0); for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]); fp->mt = mt; return 0; } static void mt_destroy(mtaux_t *mt) { int i; // signal all workers to quit pthread_mutex_lock(&mt->lock); mt->done = 1; mt->proc_cnt = 0; pthread_cond_broadcast(&mt->cv); pthread_mutex_unlock(&mt->lock); for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread // free other data allocated on heap for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]); for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf); free(mt->blk); free(mt->len); free(mt->w); free(mt->tid); pthread_cond_destroy(&mt->cv); pthread_mutex_destroy(&mt->lock); free(mt); } static void mt_queue(BGZF *fp) { mtaux_t *mt = (mtaux_t*)fp->mt; assert(mt->curr < mt->n_blks); // guaranteed by the caller memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset); mt->len[mt->curr] = fp->block_offset; fp->block_offset = 0; ++mt->curr; } static int mt_flush(BGZF *fp) { int i; mtaux_t *mt = (mtaux_t*)fp->mt; if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail // signal all the workers to compress pthread_mutex_lock(&mt->lock); for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1; mt->proc_cnt = 0; pthread_cond_broadcast(&mt->cv); pthread_mutex_unlock(&mt->lock); // worker 0 is doing things here worker_aux(&mt->w[0]); // wait for all the threads to complete while (mt->proc_cnt < mt->n_threads); // dump data to disk for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode; for (i = 0; i < mt->curr; ++i) if (fwrite(mt->blk[i], 1, mt->len[i], fp->fp) != mt->len[i]) fp->errcode |= BGZF_ERR_IO; mt->curr = 0; return 0; } static int mt_lazy_flush(BGZF *fp) { mtaux_t *mt = (mtaux_t*)fp->mt; if (fp->block_offset) mt_queue(fp); if (mt->curr == mt->n_blks) return mt_flush(fp); return -1; } static ssize_t mt_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; ssize_t rest = length; while (rest) { int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest; memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; rest -= copy_length; if (fp->block_offset == BGZF_BLOCK_SIZE) mt_lazy_flush(fp); } return length - rest; } /***** END: multi-threading *****/ int bgzf_flush(BGZF *fp) { if (!fp->is_write) return 0; if (fp->mt) return mt_flush(fp); while (fp->block_offset > 0) { int block_length; block_length = deflate_block(fp, fp->block_offset); if (block_length < 0) return -1; if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) { fp->errcode |= BGZF_ERR_IO; // possibly truncated file return -1; } fp->block_address += block_length; } return 0; } int bgzf_flush_try(BGZF *fp, ssize_t size) { if (fp->block_offset + size > BGZF_BLOCK_SIZE) { if (fp->mt) return mt_lazy_flush(fp); else return bgzf_flush(fp); } return -1; } ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length) { const uint8_t *input = data; int block_length = BGZF_BLOCK_SIZE, bytes_written = 0; assert(fp->is_write); if (fp->mt) return mt_write(fp, data, length); while (bytes_written < length) { uint8_t* buffer = fp->uncompressed_block; int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written; memcpy(buffer + fp->block_offset, input, copy_length); fp->block_offset += copy_length; input += copy_length; bytes_written += copy_length; if (fp->block_offset == block_length && bgzf_flush(fp)) break; } return bytes_written; } int bgzf_close(BGZF* fp) { int ret, count, block_length; if (fp == 0) return -1; if (fp->is_write) { if (bgzf_flush(fp) != 0) return -1; fp->compress_level = -1; block_length = deflate_block(fp, 0); // write an empty block count = fwrite(fp->compressed_block, 1, block_length, fp->fp); if (fflush(fp->fp) != 0) { fp->errcode |= BGZF_ERR_IO; return -1; } if (fp->mt) mt_destroy(fp->mt); } ret = fp->is_write? fclose(fp->fp) : _bgzf_close(fp->fp); if (ret != 0) return -1; free(fp->uncompressed_block); free(fp->compressed_block); free_cache(fp); free(fp); return 0; } void bgzf_set_cache_size(BGZF *fp, int cache_size) { if (fp) fp->cache_size = cache_size; } int bgzf_check_EOF(BGZF *fp) { static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0"; uint8_t buf[28]; off_t offset; offset = _bgzf_tell((_bgzf_file_t)fp->fp); if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0; _bgzf_read(fp->fp, buf, 28); _bgzf_seek(fp->fp, offset, SEEK_SET); return (memcmp(magic, buf, 28) == 0)? 1 : 0; } int64_t bgzf_seek(BGZF* fp, int64_t pos, int where) { int block_offset; int64_t block_address; if (fp->is_write || where != SEEK_SET) { fp->errcode |= BGZF_ERR_MISUSE; return -1; } block_offset = pos & 0xFFFF; block_address = pos >> 16; if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) { fp->errcode |= BGZF_ERR_IO; return -1; } fp->block_length = 0; // indicates current block has not been loaded fp->block_address = block_address; fp->block_offset = block_offset; return 0; } int bgzf_is_bgzf(const char *fn) { uint8_t buf[16]; int n; _bgzf_file_t fp; if ((fp = _bgzf_open(fn, "r")) == 0) return 0; n = _bgzf_read(fp, buf, 16); _bgzf_close(fp); if (n != 16) return 0; return memcmp(g_magic, buf, 16) == 0? 1 : 0; } int bgzf_getc(BGZF *fp) { int c; if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) return -2; /* error */ if (fp->block_length == 0) return -1; /* end-of-file */ } c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++]; if (fp->block_offset == fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } return c; } #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif int bgzf_getline(BGZF *fp, int delim, kstring_t *str) { int l, state = 0; unsigned char *buf = (unsigned char*)fp->uncompressed_block; str->l = 0; do { if (fp->block_offset >= fp->block_length) { if (bgzf_read_block(fp) != 0) { state = -2; break; } if (fp->block_length == 0) { state = -1; break; } } for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l); if (l < fp->block_length) state = 1; l -= fp->block_offset; if (str->l + l + 1 >= str->m) { str->m = str->l + l + 2; kroundup32(str->m); str->s = (char*)realloc(str->s, str->m); } memcpy(str->s + str->l, buf + fp->block_offset, l); str->l += l; fp->block_offset += l + 1; if (fp->block_offset >= fp->block_length) { fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp); fp->block_offset = 0; fp->block_length = 0; } } while (state == 0); if (str->l == 0 && state < 0) return state; str->s[str->l] = 0; return str->l; } pysam-0.7.7/samtools/bam_md.c.pysam.c0000664000076400007650000003130012162637166017311 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "faidx.h" #include "sam.h" #include "kstring.h" #include "kaln.h" #include "kprobaln.h" #define USE_EQUAL 1 #define DROP_TAG 2 #define BIN_QUAL 4 #define UPDATE_NM 8 #define UPDATE_MD 16 #define HASH_QNM 32 char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; int bam_aux_drop_other(bam1_t *b, uint8_t *s); void bam_fillmd1_core(bam1_t *b, char *ref, int flag, int max_nm) { uint8_t *seq = bam1_seq(b); uint32_t *cigar = bam1_cigar(b); bam1_core_t *c = &b->core; int i, x, y, u = 0; kstring_t *str; int32_t old_nm_i = -1, nm = 0; str = (kstring_t*)calloc(1, sizeof(kstring_t)); for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { int j, l = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) { int z = y + j; int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; if (ref[x+j] == 0) break; // out of boundary if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f; ++u; } else { kputw(u, str); kputc(ref[x+j], str); u = 0; ++nm; } } if (j < l) break; x += l; y += l; } else if (op == BAM_CDEL) { kputw(u, str); kputc('^', str); for (j = 0; j < l; ++j) { if (ref[x+j] == 0) break; kputc(ref[x+j], str); } u = 0; if (j < l) break; x += l; nm += l; } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) { y += l; if (op == BAM_CINS) nm += l; } else if (op == BAM_CREF_SKIP) { x += l; } } kputw(u, str); // apply max_nm if (max_nm > 0 && nm >= max_nm) { for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { int j, l = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) { int z = y + j; int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; if (ref[x+j] == 0) break; // out of boundary if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match seq[z/2] |= (z&1)? 0x0f : 0xf0; bam1_qual(b)[z] = 0; } } if (j < l) break; x += l; y += l; } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l; else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; } } // update NM if (flag & UPDATE_NM) { uint8_t *old_nm = bam_aux_get(b, "NM"); if (c->flag & BAM_FUNMAP) return; if (old_nm) old_nm_i = bam_aux2i(old_nm); if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm); else if (nm != old_nm_i) { fprintf(pysamerr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm); bam_aux_del(b, old_nm); bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm); } } // update MD if (flag & UPDATE_MD) { uint8_t *old_md = bam_aux_get(b, "MD"); if (c->flag & BAM_FUNMAP) return; if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s); else { int is_diff = 0; if (strlen((char*)old_md+1) == str->l) { for (i = 0; i < str->l; ++i) if (toupper(old_md[i+1]) != toupper(str->s[i])) break; if (i < str->l) is_diff = 1; } else is_diff = 1; if (is_diff) { fprintf(pysamerr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s); bam_aux_del(b, old_md); bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s); } } } // drop all tags but RG if (flag&DROP_TAG) { uint8_t *q = bam_aux_get(b, "RG"); bam_aux_drop_other(b, q); } // reduce the resolution of base quality if (flag&BIN_QUAL) { uint8_t *qual = bam1_qual(b); for (i = 0; i < b->core.l_qseq; ++i) if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7; } free(str->s); free(str); } void bam_fillmd1(bam1_t *b, char *ref, int flag) { bam_fillmd1_core(b, ref, flag, 0); } int bam_cap_mapQ(bam1_t *b, char *ref, int thres) { uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b); uint32_t *cigar = bam1_cigar(b); bam1_core_t *c = &b->core; int i, x, y, mm, q, len, clip_l, clip_q; double t; if (thres < 0) thres = 40; // set the default mm = q = len = clip_l = clip_q = 0; for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { int j, l = cigar[i]>>4, op = cigar[i]&0xf; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) { int z = y + j; int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; if (ref[x+j] == 0) break; // out of boundary if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous ++len; if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch ++mm; q += qual[z] > 33? 33 : qual[z]; } } } if (j < l) break; x += l; y += l; len += l; } else if (op == BAM_CDEL) { for (j = 0; j < l; ++j) if (ref[x+j] == 0) break; if (j < l) break; x += l; } else if (op == BAM_CSOFT_CLIP) { for (j = 0; j < l; ++j) clip_q += qual[y+j]; clip_l += l; y += l; } else if (op == BAM_CHARD_CLIP) { clip_q += 13 * l; clip_l += l; } else if (op == BAM_CINS) y += l; else if (op == BAM_CREF_SKIP) x += l; } for (i = 0, t = 1; i < mm; ++i) t *= (double)len / (i+1); t = q - 4.343 * log(t) + clip_q / 5.; if (t > thres) return -1; if (t < 0) t = 0; t = sqrt((thres - t) / thres) * thres; // fprintf(pysamerr, "%s %lf %d\n", bam1_qname(b), t, q); return (int)(t + .499); } int bam_prob_realn_core(bam1_t *b, const char *ref, int flag) { int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1, redo_baq = flag&4; uint32_t *cigar = bam1_cigar(b); bam1_core_t *c = &b->core; kpa_par_t conf = kpa_par_def; uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b); if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing // test if BQ or ZQ is present if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; if (bq && redo_baq) { bam_aux_del(b, bq-1); bq = 0; } if (bq && zq) { // remove the ZQ tag bam_aux_del(b, zq-1); zq = 0; } if (bq || zq) { if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing if (bq && apply_baq) { // then convert BQ to ZQ for (i = 0; i < c->l_qseq; ++i) qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64); *(bq - 3) = 'Z'; } else if (zq && !apply_baq) { // then convert ZQ to BQ for (i = 0; i < c->l_qseq; ++i) qual[i] += (int)zq[i] - 64; *(zq - 3) = 'B'; } return 0; } // find the start and end of the alignment x = c->pos, y = 0, yb = ye = xb = xe = -1; for (k = 0; k < c->n_cigar; ++k) { int op, l; op = cigar[k]&0xf; l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { if (yb < 0) yb = y; if (xb < 0) xb = x; ye = y + l; xe = x + l; x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; else if (op == BAM_CDEL) x += l; else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip } // set bandwidth and the start and the end bw = 7; if (abs((xe - xb) - (ye - yb)) > bw) bw = abs((xe - xb) - (ye - yb)) + 3; conf.bw = bw; xb -= yb + bw/2; if (xb < 0) xb = 0; xe += c->l_qseq - ye + bw/2; if (xe - xb - c->l_qseq > bw) xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2; { // glocal uint8_t *s, *r, *q, *seq = bam1_seq(b), *bq; int *state; bq = calloc(c->l_qseq + 1, 1); memcpy(bq, qual, c->l_qseq); s = calloc(c->l_qseq, 1); for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)]; r = calloc(xe - xb, 1); for (i = xb; i < xe; ++i) { if (ref[i] == 0) { xe = i; break; } r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]]; } state = calloc(c->l_qseq, sizeof(int)); q = calloc(c->l_qseq, 1); kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q); if (!extend_baq) { // in this block, bq[] is capped by base quality qual[] for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { int op = cigar[k]&0xf, l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (i = y; i < y + l; ++i) { if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0; else bq[i] = bq[i] < q[i]? bq[i] : q[i]; } x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; else if (op == BAM_CDEL) x += l; } for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!) uint8_t *left, *rght; left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1); for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { int op = cigar[k]&0xf, l = cigar[k]>>4; if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (i = y; i < y + l; ++i) bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i]; for (left[y] = bq[y], i = y + 1; i < y + l; ++i) left[i] = bq[i] > left[i-1]? bq[i] : left[i-1]; for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i) rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1]; for (i = y; i < y + l; ++i) bq[i] = left[i] < rght[i]? left[i] : rght[i]; x += l; y += l; } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l; else if (op == BAM_CDEL) x += l; } for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ free(left); free(rght); } if (apply_baq) { for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq); } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq); free(bq); free(s); free(r); free(q); free(state); } return 0; } int bam_prob_realn(bam1_t *b, const char *ref) { return bam_prob_realn_core(b, ref, 1); } int bam_fillmd(int argc, char *argv[]) { int c, flt_flag, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag; samfile_t *fp, *fpout = 0; faidx_t *fai; char *ref = 0, mode_w[8], mode_r[8]; bam1_t *b; flt_flag = UPDATE_NM | UPDATE_MD; is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0; mode_w[0] = mode_r[0] = 0; strcpy(mode_r, "r"); strcpy(mode_w, "w"); while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) { switch (c) { case 'r': is_realn = 1; break; case 'e': flt_flag |= USE_EQUAL; break; case 'd': flt_flag |= DROP_TAG; break; case 'q': flt_flag |= BIN_QUAL; break; case 'h': flt_flag |= HASH_QNM; break; case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break; case 'b': is_bam_out = 1; break; case 'u': is_uncompressed = is_bam_out = 1; break; case 'S': is_sam_in = 1; break; case 'n': max_nm = atoi(optarg); break; case 'C': capQ = atoi(optarg); break; case 'A': baq_flag |= 1; break; case 'E': baq_flag |= 2; break; default: fprintf(pysamerr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1; } } if (!is_sam_in) strcat(mode_r, "b"); if (is_bam_out) strcat(mode_w, "b"); else strcat(mode_w, "h"); if (is_uncompressed) strcat(mode_w, "u"); if (optind + 1 >= argc) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools fillmd [-eubrS] \n\n"); fprintf(pysamerr, "Options: -e change identical bases to '='\n"); fprintf(pysamerr, " -u uncompressed BAM output (for piping)\n"); fprintf(pysamerr, " -b compressed BAM output\n"); fprintf(pysamerr, " -S the input is SAM with header\n"); fprintf(pysamerr, " -A modify the quality string\n"); fprintf(pysamerr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n"); fprintf(pysamerr, " -E extended BAQ for better sensitivity but lower specificity\n\n"); return 1; } fp = samopen(argv[optind], mode_r, 0); if (fp == 0) return 1; if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) { fprintf(pysamerr, "[bam_fillmd] input SAM does not have header. Abort!\n"); return 1; } fpout = samopen("-", mode_w, fp->header); fai = fai_load(argv[optind+1]); b = bam_init1(); while ((ret = samread(fp, b)) >= 0) { if (b->core.tid >= 0) { if (tid != b->core.tid) { free(ref); ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len); tid = b->core.tid; if (ref == 0) fprintf(pysamerr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n", fp->header->target_name[tid]); } if (is_realn) bam_prob_realn_core(b, ref, baq_flag); if (capQ > 10) { int q = bam_cap_mapQ(b, ref, capQ); if (b->core.qual > q) b->core.qual = q; } if (ref) bam_fillmd1_core(b, ref, flt_flag, max_nm); } samwrite(fpout, b); } bam_destroy1(b); free(ref); fai_destroy(fai); samclose(fp); samclose(fpout); return 0; } pysam-0.7.7/samtools/bedidx.c.pysam.c0000664000076400007650000000747612162637166017352 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #ifdef _WIN32 #define drand48() ((double)rand() / RAND_MAX) #endif #include "ksort.h" KSORT_INIT_GENERIC(uint64_t) #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 8192) typedef struct { int n, m; uint64_t *a; int *idx; } bed_reglist_t; #include "khash.h" KHASH_MAP_INIT_STR(reg, bed_reglist_t) #define LIDX_SHIFT 13 typedef kh_reg_t reghash_t; int *bed_index_core(int n, uint64_t *a, int *n_idx) { int i, j, m, *idx; m = *n_idx = 0; idx = 0; for (i = 0; i < n; ++i) { int beg, end; beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT; if (m < end + 1) { int oldm = m; m = end + 1; kroundup32(m); idx = realloc(idx, m * sizeof(int)); for (j = oldm; j < m; ++j) idx[j] = -1; } if (beg == end) { if (idx[beg] < 0) idx[beg] = i; } else { for (j = beg; j <= end; ++j) if (idx[j] < 0) idx[j] = i; } *n_idx = end + 1; } return idx; } void bed_index(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { bed_reglist_t *p = &kh_val(h, k); if (p->idx) free(p->idx); ks_introsort(uint64_t, p->n, p->a); p->idx = bed_index_core(p->n, p->a, &p->m); } } } int bed_overlap_core(const bed_reglist_t *p, int beg, int end) { int i, min_off; if (p->n == 0) return 0; min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT]; if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here int n = beg>>LIDX_SHIFT; if (n > p->n) n = p->n; for (i = n - 1; i >= 0; --i) if (p->idx[i] >= 0) break; min_off = i >= 0? p->idx[i] : 0; } for (i = min_off; i < p->n; ++i) { if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end) return 1; // find the overlap; return } return 0; } int bed_overlap(const void *_h, const char *chr, int beg, int end) { const reghash_t *h = (const reghash_t*)_h; khint_t k; if (!h) return 0; k = kh_get(reg, h, chr); if (k == kh_end(h)) return 0; return bed_overlap_core(&kh_val(h, k), beg, end); } void *bed_read(const char *fn) { reghash_t *h = kh_init(reg); gzFile fp; kstream_t *ks; int dret; kstring_t *str; // read the list fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); if (fp == 0) return 0; str = calloc(1, sizeof(kstring_t)); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name int beg = -1, end = -1; bed_reglist_t *p; khint_t k = kh_get(reg, h, str->s); if (k == kh_end(h)) { // absent from the hash table int ret; char *s = strdup(str->s); k = kh_put(reg, h, s, &ret); memset(&kh_val(h, k), 0, sizeof(bed_reglist_t)); } p = &kh_val(h, k); if (dret != '\n') { // if the lines has other characters if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) { beg = atoi(str->s); // begin if (dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) { end = atoi(str->s); // end if (end < beg) end = -1; } } } } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column if (beg >= 0 && end > beg) { if (p->n == p->m) { p->m = p->m? p->m<<1 : 4; p->a = realloc(p->a, p->m * 8); } p->a[p->n++] = (uint64_t)beg<<32 | end; } } ks_destroy(ks); gzclose(fp); free(str->s); free(str); bed_index(h); return h; } void bed_destroy(void *_h) { reghash_t *h = (reghash_t*)_h; khint_t k; for (k = 0; k < kh_end(h); ++k) { if (kh_exist(h, k)) { free(kh_val(h, k).a); free(kh_val(h, k).idx); free((char*)kh_key(h, k)); } } kh_destroy(reg, h); } pysam-0.7.7/samtools/bam2depth.c.pysam.c0000664000076400007650000001337412162637166017753 0ustar andreasandreas#include "pysam.h" /* This program demonstrates how to generate pileup from multiple BAMs * simutaneously, to achieve random access and to use the BED interface. * To compile this program separately, you may: * * gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz */ #include #include #include #include #include "bam.h" typedef struct { // auxiliary data structure bamFile fp; // the file handler bam_iter_t iter; // NULL if a region not specified int min_mapQ, min_len; // mapQ filter; length filter } aux_t; void *bed_read(const char *fn); // read a BED or position list file void bed_destroy(void *_h); // destroy the BED data structure int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps // This function reads a BAM alignment from one BAM file. static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup { aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b); if (!(b->core.flag&BAM_FUNMAP)) { if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP; else if (aux->min_len && bam_cigar2qlen(&b->core, bam1_cigar(b)) < aux->min_len) b->core.flag |= BAM_FUNMAP; } return ret; } int read_file_list(const char *file_list,int *n,char **argv[]); #ifdef _MAIN_BAM2DEPTH int main(int argc, char *argv[]) #else int main_depth(int argc, char *argv[]) #endif { int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles; const bam_pileup1_t **plp; char *reg = 0; // specified region void *bed = 0; // BED data structure char *file_list = NULL, **fn = NULL; bam_header_t *h = 0; // BAM header of the 1st input aux_t **data; bam_mplp_t mplp; // parse the command line while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) { switch (n) { case 'l': min_len = atoi(optarg); break; // minimum query length case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now case 'q': baseQ = atoi(optarg); break; // base quality threshold case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold case 'f': file_list = optarg; break; } } if (optind == argc && !file_list) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n"); fprintf(pysamerr, "Options:\n"); fprintf(pysamerr, " -b list of positions or regions\n"); fprintf(pysamerr, " -f list of input BAM filenames, one per line [null]\n"); fprintf(pysamerr, " -l minQLen\n"); fprintf(pysamerr, " -q base quality threshold\n"); fprintf(pysamerr, " -Q mapping quality threshold\n"); fprintf(pysamerr, " -r region\n"); fprintf(pysamerr, "\n"); return 1; } // initialize the auxiliary data structures if (file_list) { if ( read_file_list(file_list,&nfiles,&fn) ) return 1; n = nfiles; argv = fn; optind = 0; } else n = argc - optind; // the number of BAMs on the command line data = calloc(n, sizeof(void*)); // data[i] for the i-th input beg = 0; end = 1<<30; tid = -1; // set the default region for (i = 0; i < n; ++i) { bam_header_t *htmp; data[i] = calloc(1, sizeof(aux_t)); data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM data[i]->min_mapQ = mapQ; // set the mapQ filter data[i]->min_len = min_len; // set the qlen filter htmp = bam_header_read(data[i]->fp); // read the BAM header if (i == 0) { h = htmp; // keep the header of the 1st BAM if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header if (tid >= 0) { // if a region is specified and parsed successfully bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator bam_index_destroy(idx); // the index is not needed any more; phase out of the memory } } // the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position if (pos < beg || pos >= end) continue; // out of range; skip if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster for (i = 0; i < n; ++i) { // base level filters have to go here int j, m = 0; for (j = 0; j < n_plp[i]; ++j) { const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality } printf("\t%d", n_plp[i] - m); // this the depth to output } putchar('\n'); } free(n_plp); free(plp); bam_mplp_destroy(mplp); bam_header_destroy(h); for (i = 0; i < n; ++i) { bam_close(data[i]->fp); if (data[i]->iter) bam_iter_destroy(data[i]->iter); free(data[i]); } free(data); free(reg); if (bed) bed_destroy(bed); if ( file_list ) { for (i=0; i #include "sam.h" #include "khash.h" #include "klist.h" #define QUEUE_CLEAR_SIZE 0x100000 #define MAX_POS 0x7fffffff typedef struct { int endpos; uint32_t score:31, discarded:1; bam1_t *b; } elem_t, *elem_p; #define __free_elem(p) bam_destroy1((p)->data.b) KLIST_INIT(q, elem_t, __free_elem) typedef klist_t(q) queue_t; KHASH_MAP_INIT_INT(best, elem_p) typedef khash_t(best) besthash_t; typedef struct { uint64_t n_checked, n_removed; besthash_t *left, *rght; } lib_aux_t; KHASH_MAP_INIT_STR(lib, lib_aux_t) static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib) { khint_t k = kh_get(lib, aux, lib); if (k == kh_end(aux)) { int ret; char *p = strdup(lib); lib_aux_t *q; k = kh_put(lib, aux, p, &ret); q = &kh_val(aux, k); q->left = kh_init(best); q->rght = kh_init(best); q->n_checked = q->n_removed = 0; return q; } else return &kh_val(aux, k); } static inline int sum_qual(const bam1_t *b) { int i, q; uint8_t *qual = bam1_qual(b); for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i]; return q; } static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score) { elem_t *p = kl_pushp(q, queue); p->discarded = 0; p->endpos = endpos; p->score = score; if (p->b == 0) p->b = bam_init1(); bam_copy1(p->b, b); return p; } static void clear_besthash(besthash_t *h, int32_t pos) { khint_t k; for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos) kh_del(best, h, k); } static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h) { if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) { khint_t k; while (1) { elem_t *q; if (queue->head == queue->tail) break; q = &kl_val(queue->head); if (q->discarded) { q->b->data_len = 0; kl_shift(q, queue, 0); continue; } if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break; samwrite(out, q->b); q->b->data_len = 0; kl_shift(q, queue, 0); } for (k = kh_begin(h); k != kh_end(h); ++k) { if (kh_exist(h, k)) { clear_besthash(kh_val(h, k).left, pos); clear_besthash(kh_val(h, k).rght, pos); } } } } void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se) { bam1_t *b; queue_t *queue; khint_t k; int last_tid = -2; khash_t(lib) *aux; aux = kh_init(lib); b = bam_init1(); queue = kl_init(q); while (samread(in, b) >= 0) { bam1_core_t *c = &b->core; int endpos = bam_calend(c, bam1_cigar(b)); int score = sum_qual(b); if (last_tid != c->tid) { if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux); last_tid = c->tid; } else dump_alignment(out, queue, c->pos, aux); if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) { push_queue(queue, b, endpos, score); } else { const char *lib; lib_aux_t *q; besthash_t *h; uint32_t key; int ret; lib = bam_get_library(in->header, b); q = lib? get_aux(aux, lib) : get_aux(aux, "\t"); ++q->n_checked; h = (c->flag&BAM_FREVERSE)? q->rght : q->left; key = (c->flag&BAM_FREVERSE)? endpos : c->pos; k = kh_put(best, h, key, &ret); if (ret == 0) { // in the hash table elem_t *p = kh_val(h, k); ++q->n_removed; if (p->score < score) { if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue p->discarded = 1; kh_val(h, k) = push_queue(queue, b, endpos, score); } else { // replace p->score = score; p->endpos = endpos; bam_copy1(p->b, b); } } // otherwise, discard the alignment } else kh_val(h, k) = push_queue(queue, b, endpos, score); } } dump_alignment(out, queue, MAX_POS, aux); for (k = kh_begin(aux); k != kh_end(aux); ++k) { if (kh_exist(aux, k)) { lib_aux_t *q = &kh_val(aux, k); fprintf(pysamerr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed, (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k)); kh_destroy(best, q->left); kh_destroy(best, q->rght); free((char*)kh_key(aux, k)); } } kh_destroy(lib, aux); bam_destroy1(b); kl_destroy(q, queue); } pysam-0.7.7/samtools/bam_aux.c.pysam.c0000664000076400007650000001176312162637166017521 0ustar andreasandreas#include "pysam.h" #include #include "bam.h" #include "khash.h" typedef char *str_p; KHASH_MAP_INIT_STR(s, int) KHASH_MAP_INIT_STR(r2l, str_p) void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data) { int ori_len = b->data_len; b->data_len += 3 + len; b->l_aux += 3 + len; if (b->m_data < b->data_len) { b->m_data = b->data_len; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1]; b->data[ori_len + 2] = type; memcpy(b->data + ori_len + 3, data, len); } uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]) { return bam_aux_get(b, tag); } #define __skip_tag(s) do { \ int type = toupper(*(s)); \ ++(s); \ if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \ else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \ else (s) += bam_aux_type2size(type); \ } while(0) uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]) { uint8_t *s; int y = tag[0]<<8 | tag[1]; s = bam1_aux(b); while (s < b->data + b->data_len) { int x = (int)s[0]<<8 | s[1]; s += 2; if (x == y) return s; __skip_tag(s); } return 0; } // s MUST BE returned by bam_aux_get() int bam_aux_del(bam1_t *b, uint8_t *s) { uint8_t *p, *aux; aux = bam1_aux(b); p = s - 2; __skip_tag(s); memmove(p, s, b->l_aux - (s - aux)); b->data_len -= s - p; b->l_aux -= s - p; return 0; } int bam_aux_drop_other(bam1_t *b, uint8_t *s) { if (s) { uint8_t *p, *aux; aux = bam1_aux(b); p = s - 2; __skip_tag(s); memmove(aux, p, s - p); b->data_len -= b->l_aux - (s - p); b->l_aux = s - p; } else { b->data_len -= b->l_aux; b->l_aux = 0; } return 0; } void bam_init_header_hash(bam_header_t *header) { if (header->hash == 0) { int ret, i; khiter_t iter; khash_t(s) *h; header->hash = h = kh_init(s); for (i = 0; i < header->n_targets; ++i) { iter = kh_put(s, h, header->target_name[i], &ret); kh_value(h, iter) = i; } } } void bam_destroy_header_hash(bam_header_t *header) { if (header->hash) kh_destroy(s, (khash_t(s)*)header->hash); } int32_t bam_get_tid(const bam_header_t *header, const char *seq_name) { khint_t k; khash_t(s) *h = (khash_t(s)*)header->hash; k = kh_get(s, h, seq_name); return k == kh_end(h)? -1 : kh_value(h, k); } int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end) { char *s; int i, l, k, name_end; khiter_t iter; khash_t(s) *h; bam_init_header_hash(header); h = (khash_t(s)*)header->hash; *ref_id = *beg = *end = -1; name_end = l = strlen(str); s = (char*)malloc(l+1); // remove space for (i = k = 0; i < l; ++i) if (!isspace(str[i])) s[k++] = str[i]; s[k] = 0; l = k; // determine the sequence name for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end if (i >= 0) name_end = i; if (name_end < l) { // check if this is really the end int n_hyphen = 0; for (i = name_end + 1; i < l; ++i) { if (s[i] == '-') ++n_hyphen; else if (!isdigit(s[i]) && s[i] != ',') break; } if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name s[name_end] = 0; iter = kh_get(s, h, s); if (iter == kh_end(h)) { // cannot find the sequence name iter = kh_get(s, h, str); // try str as the name if (iter == kh_end(h)) { if (bam_verbose >= 2) fprintf(pysamerr, "[%s] fail to determine the sequence name.\n", __func__); free(s); return -1; } else s[name_end] = ':', name_end = l; } } else iter = kh_get(s, h, str); if (iter == kh_end(h)) { free(s); return -1; } *ref_id = kh_val(h, iter); // parse the interval if (name_end < l) { for (i = k = name_end + 1; i < l; ++i) if (s[i] != ',') s[k++] = s[i]; s[k] = 0; *beg = atoi(s + name_end + 1); for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break; *end = i < k? atoi(s + i + 1) : 1<<29; if (*beg > 0) --*beg; } else *beg = 0, *end = 1<<29; free(s); return *beg <= *end? 0 : -1; } int32_t bam_aux2i(const uint8_t *s) { int type; if (s == 0) return 0; type = *s++; if (type == 'c') return (int32_t)*(int8_t*)s; else if (type == 'C') return (int32_t)*(uint8_t*)s; else if (type == 's') return (int32_t)*(int16_t*)s; else if (type == 'S') return (int32_t)*(uint16_t*)s; else if (type == 'i' || type == 'I') return *(int32_t*)s; else return 0; } float bam_aux2f(const uint8_t *s) { int type; type = *s++; if (s == 0) return 0.0; if (type == 'f') return *(float*)s; else return 0.0; } double bam_aux2d(const uint8_t *s) { int type; type = *s++; if (s == 0) return 0.0; if (type == 'd') return *(double*)s; else return 0.0; } char bam_aux2A(const uint8_t *s) { int type; type = *s++; if (s == 0) return 0; if (type == 'A') return *(char*)s; else return 0; } char *bam_aux2Z(const uint8_t *s) { int type; type = *s++; if (s == 0) return 0; if (type == 'Z' || type == 'H') return (char*)s; else return 0; } #ifdef _WIN32 double drand48() { return (double)rand() / RAND_MAX; } #endif pysam-0.7.7/samtools/bam.c.pysam.c0000664000076400007650000003720512162637166016643 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include "bam.h" #include "bam_endian.h" #include "kstring.h" #include "sam_header.h" int bam_is_be = 0, bam_verbose = 2, bam_no_B = 0; char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0"; /************************** * CIGAR related routines * **************************/ uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar) { int k, end = c->pos; for (k = 0; k < c->n_cigar; ++k) { int op = bam_cigar_op(cigar[k]); int len = bam_cigar_oplen(cigar[k]); if (op == BAM_CBACK) { // move backward int l, u, v; if (k == c->n_cigar - 1) break; // skip trailing 'B' for (l = k - 1, u = v = 0; l >= 0; --l) { int op1 = bam_cigar_op(cigar[l]); int len1 = bam_cigar_oplen(cigar[l]); if (bam_cigar_type(op1)&1) { // consume query if (u + len1 >= len) { // stop if (bam_cigar_type(op1)&2) v += len - u; break; } else u += len1; } if (bam_cigar_type(op1)&2) v += len1; } end = l < 0? c->pos : end - v; } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]); } return end; } int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar) { uint32_t k; int32_t l = 0; for (k = 0; k < c->n_cigar; ++k) if (bam_cigar_type(bam_cigar_op(cigar[k]))&1) l += bam_cigar_oplen(cigar[k]); return l; } /******************** * BAM I/O routines * ********************/ bam_header_t *bam_header_init() { bam_is_be = bam_is_big_endian(); return (bam_header_t*)calloc(1, sizeof(bam_header_t)); } void bam_header_destroy(bam_header_t *header) { int32_t i; extern void bam_destroy_header_hash(bam_header_t *header); if (header == 0) return; if (header->target_name) { for (i = 0; i < header->n_targets; ++i) free(header->target_name[i]); free(header->target_name); free(header->target_len); } free(header->text); if (header->dict) sam_header_free(header->dict); if (header->rg2lib) sam_tbl_destroy(header->rg2lib); bam_destroy_header_hash(header); free(header); } bam_header_t *bam_header_read(bamFile fp) { bam_header_t *header; char buf[4]; int magic_len; int32_t i = 1, name_len; // check EOF i = bgzf_check_EOF(fp); if (i < 0) { // If the file is a pipe, checking the EOF marker will *always* fail // with ESPIPE. Suppress the error message in this case. if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF"); } else if (i == 0) fprintf(pysamerr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n"); // read "BAM1" magic_len = bam_read(fp, buf, 4); if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) { fprintf(pysamerr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n"); return 0; } header = bam_header_init(); // read plain text and the number of reference sequences bam_read(fp, &header->l_text, 4); if (bam_is_be) bam_swap_endian_4p(&header->l_text); header->text = (char*)calloc(header->l_text + 1, 1); bam_read(fp, header->text, header->l_text); bam_read(fp, &header->n_targets, 4); if (bam_is_be) bam_swap_endian_4p(&header->n_targets); // read reference sequence names and lengths header->target_name = (char**)calloc(header->n_targets, sizeof(char*)); header->target_len = (uint32_t*)calloc(header->n_targets, 4); for (i = 0; i != header->n_targets; ++i) { bam_read(fp, &name_len, 4); if (bam_is_be) bam_swap_endian_4p(&name_len); header->target_name[i] = (char*)calloc(name_len, 1); bam_read(fp, header->target_name[i], name_len); bam_read(fp, &header->target_len[i], 4); if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]); } return header; } int bam_header_write(bamFile fp, const bam_header_t *header) { char buf[4]; int32_t i, name_len, x; // write "BAM1" strncpy(buf, "BAM\001", 4); bam_write(fp, buf, 4); // write plain text and the number of reference sequences if (bam_is_be) { x = bam_swap_endian_4(header->l_text); bam_write(fp, &x, 4); if (header->l_text) bam_write(fp, header->text, header->l_text); x = bam_swap_endian_4(header->n_targets); bam_write(fp, &x, 4); } else { bam_write(fp, &header->l_text, 4); if (header->l_text) bam_write(fp, header->text, header->l_text); bam_write(fp, &header->n_targets, 4); } // write sequence names and lengths for (i = 0; i != header->n_targets; ++i) { char *p = header->target_name[i]; name_len = strlen(p) + 1; if (bam_is_be) { x = bam_swap_endian_4(name_len); bam_write(fp, &x, 4); } else bam_write(fp, &name_len, 4); bam_write(fp, p, name_len); if (bam_is_be) { x = bam_swap_endian_4(header->target_len[i]); bam_write(fp, &x, 4); } else bam_write(fp, &header->target_len[i], 4); } bgzf_flush(fp); return 0; } static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data) { uint8_t *s; uint32_t i, *cigar = (uint32_t*)(data + c->l_qname); s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2; for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]); while (s < data + data_len) { uint8_t type; s += 2; // skip key type = toupper(*s); ++s; // skip type if (type == 'C' || type == 'A') ++s; else if (type == 'S') { bam_swap_endian_2p(s); s += 2; } else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; } else if (type == 'D') { bam_swap_endian_8p(s); s += 8; } else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; } else if (type == 'B') { int32_t n, Bsize = bam_aux_type2size(*s); memcpy(&n, s + 1, 4); if (1 == Bsize) { } else if (2 == Bsize) { for (i = 0; i < n; i += 2) bam_swap_endian_2p(s + 5 + i); } else if (4 == Bsize) { for (i = 0; i < n; i += 4) bam_swap_endian_4p(s + 5 + i); } bam_swap_endian_4p(s+1); } } } int bam_read1(bamFile fp, bam1_t *b) { bam1_core_t *c = &b->core; int32_t block_len, ret, i; uint32_t x[8]; assert(BAM_CORE_SIZE == 32); if ((ret = bam_read(fp, &block_len, 4)) != 4) { if (ret == 0) return -1; // normal end-of-file else return -2; // truncated } if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3; if (bam_is_be) { bam_swap_endian_4p(&block_len); for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i); } c->tid = x[0]; c->pos = x[1]; c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff; c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff; c->l_qseq = x[4]; c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7]; b->data_len = block_len - BAM_CORE_SIZE; if (b->m_data < b->data_len) { b->m_data = b->data_len; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); } if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4; b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2; if (bam_is_be) swap_endian_data(c, b->data_len, b->data); if (bam_no_B) bam_remove_B(b); return 4 + block_len; } inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data) { uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y; int i; assert(BAM_CORE_SIZE == 32); x[0] = c->tid; x[1] = c->pos; x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname; x[3] = (uint32_t)c->flag<<16 | c->n_cigar; x[4] = c->l_qseq; x[5] = c->mtid; x[6] = c->mpos; x[7] = c->isize; bgzf_flush_try(fp, 4 + block_len); if (bam_is_be) { for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i); y = block_len; bam_write(fp, bam_swap_endian_4p(&y), 4); swap_endian_data(c, data_len, data); } else bam_write(fp, &block_len, 4); bam_write(fp, x, BAM_CORE_SIZE); bam_write(fp, data, data_len); if (bam_is_be) swap_endian_data(c, data_len, data); return 4 + block_len; } int bam_write1(bamFile fp, const bam1_t *b) { return bam_write1_core(fp, &b->core, b->data_len, b->data); } char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of) { uint8_t *s = bam1_seq(b), *t = bam1_qual(b); int i; const bam1_core_t *c = &b->core; kstring_t str; str.l = str.m = 0; str.s = 0; kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str); if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); } else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag); else { // BAM_OFSTR for (i = 0; i < 16; ++i) if ((c->flag & 1<tid < 0) kputsn("*\t", 2, &str); else { if (header) kputs(header->target_name[c->tid] , &str); else kputw(c->tid, &str); kputc('\t', &str); } kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str); if (c->n_cigar == 0) kputc('*', &str); else { uint32_t *cigar = bam1_cigar(b); for (i = 0; i < c->n_cigar; ++i) { kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str); kputc(bam_cigar_opchr(cigar[i]), &str); } } kputc('\t', &str); if (c->mtid < 0) kputsn("*\t", 2, &str); else if (c->mtid == c->tid) kputsn("=\t", 2, &str); else { if (header) kputs(header->target_name[c->mtid], &str); else kputw(c->mtid, &str); kputc('\t', &str); } kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str); if (c->l_qseq) { for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str); kputc('\t', &str); if (t[0] == 0xff) kputc('*', &str); else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str); } else kputsn("*\t*", 3, &str); s = bam1_aux(b); while (s < b->data + b->data_len) { uint8_t type, key[2]; key[0] = s[0]; key[1] = s[1]; s += 2; type = *s; ++s; kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str); if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; } else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; } else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; } else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; } else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; } else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; } else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; } else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; } else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; } else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; } else if (type == 'B') { uint8_t sub_type = *(s++); int32_t n; memcpy(&n, s, 4); s += 4; // no point to the start of the array kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing for (i = 0; i < n; ++i) { kputc(',', &str); if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; } else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; } else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; } else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; } else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; } else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; } else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; } } } } return str.s; } char *bam_format1(const bam_header_t *header, const bam1_t *b) { return bam_format1_core(header, b, BAM_OFDEC); } void bam_view1(const bam_header_t *header, const bam1_t *b) { char *s = bam_format1(header, b); puts(s); free(s); } int bam_validate1(const bam_header_t *header, const bam1_t *b) { char *s; if (b->core.tid < -1 || b->core.mtid < -1) return 0; if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0; if (b->data_len < b->core.l_qname) return 0; s = memchr(bam1_qname(b), '\0', b->core.l_qname); if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0; // FIXME: Other fields could also be checked, especially the auxiliary data return 1; } // FIXME: we should also check the LB tag associated with each alignment const char *bam_get_library(bam_header_t *h, const bam1_t *b) { const uint8_t *rg; if (h->dict == 0) h->dict = sam_header_parse2(h->text); if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); rg = bam_aux_get(b, "RG"); return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); } /************ * Remove B * ************/ int bam_remove_B(bam1_t *b) { int i, j, end_j, k, l, no_qual; uint32_t *cigar, *new_cigar; uint8_t *seq, *qual, *p; // test if removal is necessary if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing cigar = bam1_cigar(b); for (k = 0; k < b->core.n_cigar; ++k) if (bam_cigar_op(cigar[k]) == BAM_CBACK) break; if (k == b->core.n_cigar) return 0; // no 'B' if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed // allocate memory for the new CIGAR if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory b->m_data = b->data_len + b->core.n_cigar * 4; kroundup32(b->m_data); b->data = (uint8_t*)realloc(b->data, b->m_data); cigar = bam1_cigar(b); // after realloc, cigar may be changed } new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data // the core loop seq = bam1_seq(b); qual = bam1_qual(b); no_qual = (qual[0] == 0xff); // test whether base quality is available i = j = 0; end_j = -1; for (k = l = 0; k < b->core.n_cigar; ++k) { int op = bam_cigar_op(cigar[k]); int len = bam_cigar_oplen(cigar[k]); if (op == BAM_CBACK) { // the backward operation int t, u; if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR if (len > j) goto rmB_err; // an excessively long backward for (t = l - 1, u = 0; t >= 0; --t) { // look back int op1 = bam_cigar_op(new_cigar[t]); int len1 = bam_cigar_oplen(new_cigar[t]); if (bam_cigar_type(op1)&1) { // consume the query if (u + len1 >= len) { // stop new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT; break; } else u += len1; } } if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation l = t + 1; end_j = j; j -= len; } else { // other CIGAR operations new_cigar[l++] = cigar[k]; if (bam_cigar_type(op)&1) { // consume the query if (i != j) { // no need to copy if i == j int u, c, c0; for (u = 0; u < len; ++u) { // construct the consensus c = bam1_seqi(seq, i+u); if (j + u < end_j) { // in an overlap c0 = bam1_seqi(seq, j+u); if (c != c0) { // a mismatch; choose the better base if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u] - qual[j+u]; } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u]; } else { // not in an overlap; copy over bam1_seq_seti(seq, j+u, c); qual[j+u] = qual[i+u]; } } } i += len, j += len; } } } if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified // merge adjacent operations if possible for (k = 1; k < l; ++k) if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1])) new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf; // kill zero length operations for (k = i = 0; k < l; ++k) if (new_cigar[k] >> BAM_CIGAR_SHIFT) new_cigar[i++] = new_cigar[k]; l = i; // update b memcpy(cigar, new_cigar, l * 4); // set CIGAR p = b->data + b->core.l_qname + l * 4; memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ memmove(p, qual, j); p += j; // set QUAL memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length b->data_len = p - b->data; // update record length return 0; rmB_err: b->core.flag |= BAM_FUNMAP; return -1; } pysam-0.7.7/samtools/bam_stat.c.pysam.c0000664000076400007650000000623212162637166017672 0ustar andreasandreas#include "pysam.h" #include #include #include "bam.h" typedef struct { long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2]; long long n_sgltn[2], n_read1[2], n_read2[2]; long long n_dup[2]; long long n_diffchr[2], n_diffhigh[2]; } bam_flagstat_t; #define flagstat_loop(s, c) do { \ int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0; \ ++(s)->n_reads[w]; \ if ((c)->flag & BAM_FPAIRED) { \ ++(s)->n_pair_all[w]; \ if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w]; \ if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w]; \ if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w]; \ if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w]; \ if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \ ++(s)->n_pair_map[w]; \ if ((c)->mtid != (c)->tid) { \ ++(s)->n_diffchr[w]; \ if ((c)->qual >= 5) ++(s)->n_diffhigh[w]; \ } \ } \ } \ if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w]; \ if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w]; \ } while (0) bam_flagstat_t *bam_flagstat_core(bamFile fp) { bam_flagstat_t *s; bam1_t *b; bam1_core_t *c; int ret; s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t)); b = bam_init1(); c = &b->core; while ((ret = bam_read1(fp, b)) >= 0) flagstat_loop(s, c); bam_destroy1(b); if (ret != -1) fprintf(pysamerr, "[bam_flagstat_core] Truncated file? Continue anyway.\n"); return s; } int bam_flagstat(int argc, char *argv[]) { bamFile fp; bam_header_t *header; bam_flagstat_t *s; if (argc == optind) { fprintf(pysamerr, "Usage: samtools flagstat \n"); return 1; } fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r"); assert(fp); header = bam_header_read(fp); s = bam_flagstat_core(fp); printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]); printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]); printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0); printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]); printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]); printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]); printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0); printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]); printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0); printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]); printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]); free(s); bam_header_destroy(header); bam_close(fp); return 0; } pysam-0.7.7/samtools/phase.c.pysam.c0000664000076400007650000005057712162637166017213 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include #include "bam.h" #include "errmod.h" #include "kseq.h" KSTREAM_INIT(gzFile, gzread, 16384) #define MAX_VARS 256 #define FLIP_PENALTY 2 #define FLIP_THRES 4 #define MASK_THRES 3 #define FLAG_FIX_CHIMERA 0x1 #define FLAG_LIST_EXCL 0x4 #define FLAG_DROP_AMBI 0x8 typedef struct { // configurations, initialized in the main function int flag, k, min_baseQ, min_varLOD, max_depth; // other global variables int vpos_shift; bamFile fp; char *pre; bamFile out[3]; // alignment queue int n, m; bam1_t **b; } phaseg_t; typedef struct { int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation! int vpos, beg, end; uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1; uint32_t in:16, out:16; // in-phase and out-phase } frag_t, *frag_p; #define rseq_lt(a,b) ((a)->vpos < (b)->vpos) #include "khash.h" KHASH_SET_INIT_INT64(set64) KHASH_MAP_INIT_INT64(64, frag_t) typedef khash_t(64) nseq_t; #include "ksort.h" KSORT_INIT(rseq, frag_p, rseq_lt) static char nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; static inline uint64_t X31_hash_string(const char *s) { uint64_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } static void count1(int l, const uint8_t *seq, int *cnt) { int i, j, n_ambi; uint32_t z, x; if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases if (seq[i] == 0) ++n_ambi; if (l - n_ambi <= 1) return; // only one SNP for (x = 0; x < 1u<>j&1; ++j; } z = z<<1 | c; } ++cnt[z]; } } static int **count_all(int l, int vpos, nseq_t *hash) { khint_t k; int i, j, **cnt; uint8_t *seq; seq = calloc(l, 1); cnt = calloc(vpos, sizeof(void*)); for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<vpos >= vpos || f->single) continue; // out of region; or singleton if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right f->single = 1; continue; } for (j = 1; j < f->vlen; ++j) { for (i = 0; i < l; ++i) seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)]; count1(l, seq, cnt[f->vpos + j]); } } } free(seq); return cnt; } // phasing static int8_t *dynaprog(int l, int vpos, int **w) { int *f[2], *curr, *prev, max, i; int8_t **b, *h = 0; uint32_t x, z = 1u<<(l-1), mask = (1u<>1; y1 = xc>>1; c0 = prev[y0] + wi[x] + wi[xc]; c1 = prev[y1] + wi[x] + wi[xc]; if (c0 > c1) bi[x] = 0, curr[x] = c0; else bi[x] = 1, curr[x] = c1; } tmp = prev; prev = curr; curr = tmp; // swap } { // backtrack uint32_t max_x = 0; int which = 0; h = calloc(vpos, 1); for (x = 0, max = 0, max_x = 0; x < z; ++x) if (prev[x] > max) max = prev[x], max_x = x; for (i = vpos - 1, x = max_x; i >= 0; --i) { h[i] = which? (~x&1) : (x&1); which = b[i][x]? !which : which; x = b[i][x]? (~x&mask)>>1 : x>>1; } } // free for (i = 0; i < vpos; ++i) free(b[i]); free(f[0]); free(f[1]); free(b); return h; } // phase each fragment static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip) { khint_t k; uint64_t *pcnt; uint32_t *left, *rght, max; left = rght = 0; max = 0; pcnt = calloc(vpos, 8); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { int i, c[2]; frag_t *f = &kh_val(hash, k); if (f->vpos >= vpos) continue; // get the phase c[0] = c[1] = 0; for (i = 0; i < f->vlen; ++i) { if (f->seq[i] == 0) continue; ++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1]; } f->phase = c[0] > c[1]? 0 : 1; f->in = c[f->phase]; f->out = c[1 - f->phase]; f->phased = f->in == f->out? 0 : 1; f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0; // fix chimera f->flip = 0; if (flip && c[0] >= 3 && c[1] >= 3) { int sum[2], m, mi, md; if (f->vlen > max) { // enlarge the array max = f->vlen; kroundup32(max); left = realloc(left, max * 4); rght = realloc(rght, max * 4); } for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } left[i] = sum[1]<<16 | sum[0]; } for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts if (f->seq[i]) { int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; ++sum[c == path[f->vpos + i]? 0 : 1]; } rght[i] = sum[1]<<16 | sum[0]; } // find the best flip point for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) { int a[2]; a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY; a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY; if (a[0] > a[1]) { if (a[0] > m) m = a[0], md = 0, mi = i; } else { if (a[1] > m) m = a[1], md = 1, mi = i; } } if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip f->flip = 1; if (md == 0) { // flip the tail for (i = mi + 1; i < f->vlen; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } else { // flip the head for (i = 0; i <= mi; ++i) if (f->seq[i] == 1) f->seq[i] = 2; else if (f->seq[i] == 2) f->seq[i] = 1; } } } // update pcnt[] if (!f->single) { for (i = 0; i < f->vlen; ++i) { int c; if (f->seq[i] == 0) continue; c = f->phase? 2 - f->seq[i] : f->seq[i] - 1; if (c == path[f->vpos + i]) { if (f->phase == 0) ++pcnt[f->vpos + i]; else pcnt[f->vpos + i] += 1ull<<32; } else { if (f->phase == 0) pcnt[f->vpos + i] += 1<<16; else pcnt[f->vpos + i] += 1ull<<48; } } } } } free(left); free(rght); return pcnt; } static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n) { int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0; uint64_t *list = 0; for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int c[4], pre = score, s; c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff; s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1); if (c[3] > c[2]) s += c[3] - c[2]; if (c[1] > c[0]) s += c[1] - c[0]; score += s; if (score < 0) score = 0; if (pre == 0 && score > 0) beg = i; // change from zero to non-zero if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) { if (n == m) { m = m? m<<1 : 4; list = realloc(list, m * 8); } list[n++] = (uint64_t)beg<<32 | max_i; i = max_i; // reset i to max_i score = 0; } else if (score > max) max = score, max_i = i; if (score == 0) max = 0; } *_n = n; return list; } // trim heading and tailing ambiguous bases; mark deleted and remove sequence static int clean_seqs(int vpos, nseq_t *hash) { khint_t k; int ret = 0; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); int beg, end, i; if (f->vpos >= vpos) { ret = 1; continue; } for (i = 0; i < f->vlen; ++i) if (f->seq[i] != 0) break; beg = i; for (i = f->vlen - 1; i >= 0; --i) if (f->seq[i] != 0) break; end = i + 1; if (end - beg <= 0) kh_del(64, hash, k); else { if (beg != 0) memmove(f->seq, f->seq + beg, end - beg); f->vpos += beg; f->vlen = end - beg; f->single = f->vlen == 1? 1 : 0; } } } return ret; } static void dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash) { int i, is_flip, drop_ambi; drop_ambi = g->flag & FLAG_DROP_AMBI; is_flip = (drand48() < 0.5); for (i = 0; i < g->n; ++i) { int end, which; uint64_t key; khint_t k; bam1_t *b = g->b[i]; key = X31_hash_string(bam1_qname(b)); end = bam_calend(&b->core, bam1_cigar(b)); if (end > min_pos) break; k = kh_get(64, hash, key); if (k == kh_end(hash)) which = 3; else { frag_t *f = &kh_val(hash, k); if (f->ambig) which = drop_ambi? 2 : 3; else if (f->phased && f->flip) which = 2; else if (f->phased == 0) which = 3; else { // phased and not flipped char c = 'Y'; which = f->phase; bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c); } if (which < 2 && is_flip) which = 1 - which; // increase the randomness } if (which == 3) which = (drand48() < 0.5); bam_write1(g->out[which], b); bam_destroy1(b); g->b[i] = 0; } memmove(g->b, g->b + i, (g->n - i) * sizeof(void*)); g->n -= i; } static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash) { int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos; khint_t k; frag_t **seqs; int8_t *path, *sitemask; uint64_t *pcnt, *regmask; if (vpos == 0) return 0; i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos min_pos = i? cns[vpos]>>32 : 0x7fffffff; if (vpos == 1) { printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1); printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1, "ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1); for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos) continue; f->flip = 0; if (f->seq[0] == 0) f->phased = 0; else f->phased = 1, f->phase = f->seq[0] - 1; } } dump_aln(g, min_pos, hash); ++g->vpos_shift; return 1; } { // phase int **cnt; uint64_t *mask; printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1); sitemask = calloc(vpos, 1); cnt = count_all(g->k, vpos, hash); path = dynaprog(g->k, vpos, cnt); for (i = 0; i < vpos; ++i) free(cnt[i]); free(cnt); pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking mask = genmask(vpos, pcnt, &n_masked); regmask = calloc(n_masked, 8); for (i = 0; i < n_masked; ++i) { regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32; for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j) sitemask[j] = 1; } free(mask); if (g->flag & FLAG_FIX_CHIMERA) { free(pcnt); pcnt = fragphase(vpos, path, hash, 1); } } for (i = 0; i < n_masked; ++i) printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1); for (i = 0; i < vpos; ++i) { uint64_t x = pcnt[i]; int8_t c[2]; c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3); c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3); printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]], i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff)); } free(path); free(pcnt); free(regmask); free(sitemask); seqs = calloc(n_seqs, sizeof(void*)); for (k = 0, i = 0; k < kh_end(hash); ++k) if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single) seqs[i++] = &kh_val(hash, k); n_seqs = i; ks_introsort_rseq(n_seqs, seqs); for (i = 0; i < n_seqs; ++i) { frag_t *f = seqs[i]; printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen); for (j = 0; j < f->vlen; ++j) { uint32_t c = cns[f->vpos + j]; if (f->seq[j] == 0) putchar('N'); else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]); } printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1); } free(seqs); printf("//\n"); fflush(stdout); g->vpos_shift += vpos; dump_aln(g, min_pos, hash); return vpos; } static void update_vpos(int vpos, nseq_t *hash) { khint_t k; for (k = 0; k < kh_end(hash); ++k) { if (kh_exist(hash, k)) { frag_t *f = &kh_val(hash, k); if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it else f->vpos -= vpos; } } } static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement { return hash; } static int readaln(void *data, bam1_t *b) { phaseg_t *g = (phaseg_t*)data; int ret; ret = bam_read1(g->fp, b); if (ret < 0) return ret; if (!(b->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FQCFAIL|BAM_FDUP)) && g->pre) { if (g->n == g->m) { g->m = g->m? g->m<<1 : 16; g->b = realloc(g->b, g->m * sizeof(void*)); } g->b[g->n++] = bam_dup1(b); } return ret; } static khash_t(set64) *loadpos(const char *fn, bam_header_t *h) { gzFile fp; kstream_t *ks; int ret, dret; kstring_t *str; khash_t(set64) *hash; hash = kh_init(set64); str = calloc(1, sizeof(kstring_t)); fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); ks = ks_init(fp); while (ks_getuntil(ks, 0, str, &dret) >= 0) { int tid = bam_get_tid(h, str->s); if (tid >= 0 && dret != '\n') { if (ks_getuntil(ks, 0, str, &dret) >= 0) { uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1); kh_put(set64, hash, x, &ret); } else break; } if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); if (dret < 0) break; } ks_destroy(ks); gzclose(fp); free(str->s); free(str); return hash; } static int gl2cns(float q[16]) { int i, j, min_ij; float min, min2; min = min2 = 1e30; min_ij = -1; for (i = 0; i < 4; ++i) { for (j = i; j < 4; ++j) { if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j]; else if (q[i<<2|j] < min2) min2 = q[i<<2|j]; } } return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2; } int main_phase(int argc, char *argv[]) { extern void bam_init_header_hash(bam_header_t *header); int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0; const bam_pileup1_t *plp; bam_plp_t iter; bam_header_t *h; nseq_t *seqs; uint64_t *cns = 0; phaseg_t g; char *fn_list = 0; khash_t(set64) *set = 0; errmod_t *em; uint16_t *bases; memset(&g, 0, sizeof(phaseg_t)); g.flag = FLAG_FIX_CHIMERA; g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256; while ((c = getopt(argc, argv, "Q:eFq:k:b:l:D:A:")) >= 0) { switch (c) { case 'D': g.max_depth = atoi(optarg); break; case 'q': g.min_varLOD = atoi(optarg); break; case 'Q': g.min_baseQ = atoi(optarg); break; case 'k': g.k = atoi(optarg); break; case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break; case 'e': g.flag |= FLAG_LIST_EXCL; break; case 'A': g.flag |= FLAG_DROP_AMBI; break; case 'b': g.pre = strdup(optarg); break; case 'l': fn_list = strdup(optarg); break; } } if (argc == optind) { fprintf(pysamerr, "\n"); fprintf(pysamerr, "Usage: samtools phase [options] \n\n"); fprintf(pysamerr, "Options: -k INT block length [%d]\n", g.k); fprintf(pysamerr, " -b STR prefix of BAMs to output [null]\n"); fprintf(pysamerr, " -q INT min het phred-LOD [%d]\n", g.min_varLOD); fprintf(pysamerr, " -Q INT min base quality in het calling [%d]\n", g.min_baseQ); fprintf(pysamerr, " -D INT max read depth [%d]\n", g.max_depth); // fprintf(pysamerr, " -l FILE list of sites to phase [null]\n"); fprintf(pysamerr, " -F do not attempt to fix chimeras\n"); fprintf(pysamerr, " -A drop reads with ambiguous phase\n"); // fprintf(pysamerr, " -e do not discover SNPs (effective with -l)\n"); fprintf(pysamerr, "\n"); return 1; } g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r"); h = bam_header_read(g.fp); if (fn_list) { // read the list of sites to phase bam_init_header_hash(h); set = loadpos(fn_list, h); free(fn_list); } else g.flag &= ~FLAG_LIST_EXCL; if (g.pre) { // open BAMs to write char *s = malloc(strlen(g.pre) + 20); strcpy(s, g.pre); strcat(s, ".0.bam"); g.out[0] = bam_open(s, "w"); strcpy(s, g.pre); strcat(s, ".1.bam"); g.out[1] = bam_open(s, "w"); strcpy(s, g.pre); strcat(s, ".chimera.bam"); g.out[2] = bam_open(s, "w"); for (c = 0; c <= 2; ++c) bam_header_write(g.out[c], h); free(s); } iter = bam_plp_init(readaln, &g); g.vpos_shift = 0; seqs = kh_init(64); em = errmod_init(1. - 0.83); bases = calloc(g.max_depth, 2); printf("CC\n"); printf("CC\tDescriptions:\nCC\n"); printf("CC\t CC comments\n"); printf("CC\t PS start of a phase set\n"); printf("CC\t FL filtered region\n"); printf("CC\t M[012] markers; 0 for singletons, 1 for phased and 2 for filtered\n"); printf("CC\t EV supporting reads; SAM format\n"); printf("CC\t // end of a phase set\nCC\n"); printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n"); printf("CC\t PS chr phaseSetStart phaseSetEnd\n"); printf("CC\t FL chr filterStart filterEnd\n"); printf("CC\t M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1\n"); printf("CC\nCC\n"); fflush(stdout); while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) { int i, k, c, tmp, dophase = 1, in_set = 0; float q[16]; if (tid < 0) break; if (tid != lasttid) { // change of chromosome g.vpos_shift = 0; if (lasttid >= 0) { seqs = shrink_hash(seqs); phase(&g, h->target_name[lasttid], vpos, cns, seqs); update_vpos(0x7fffffff, seqs); } lasttid = tid; vpos = 0; } if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1; if (n > g.max_depth) continue; // do not proceed if the depth is too high // fill the bases array and check if there is a variant for (i = k = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint8_t *seq; int q, baseQ, b; if (p->is_del || p->is_refskip) continue; baseQ = bam1_qual(p->b)[p->qpos]; if (baseQ < g.min_baseQ) continue; seq = bam1_seq(p->b); b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)]; if (b > 3) continue; q = baseQ < p->b->core.qual? baseQ : p->b->core.qual; if (q < 4) q = 4; if (q > 63) q = 63; bases[k++] = q<<5 | (int)bam1_strand(p->b)<<4 | b; } if (k == 0) continue; errmod_cal(em, k, 4, bases, q); // compute genotype likelihood c = gl2cns(q); // get the consensus // tell if to proceed if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant // add the variant if (vpos == max_vpos) { max_vpos = max_vpos? max_vpos<<1 : 128; cns = realloc(cns, max_vpos * 8); } cns[vpos] = (uint64_t)pos<<32 | c; for (i = 0; i < n; ++i) { const bam_pileup1_t *p = plp + i; uint64_t key; khint_t k; uint8_t *seq = bam1_seq(p->b); frag_t *f; if (p->is_del || p->is_refskip) continue; if (p->b->core.qual == 0) continue; // get the base code c = nt16_nt4_table[(int)bam1_seqi(seq, p->qpos)]; if (c == (cns[vpos]&3)) c = 1; else if (c == (cns[vpos]>>16&3)) c = 2; else c = 0; // write to seqs key = X31_hash_string(bam1_qname(p->b)); k = kh_put(64, seqs, key, &tmp); f = &kh_val(seqs, k); if (tmp == 0) { // present in the hash table if (vpos - f->vpos + 1 < MAX_VARS) { f->vlen = vpos - f->vpos + 1; f->seq[f->vlen-1] = c; f->end = bam_calend(&p->b->core, bam1_cigar(p->b)); } dophase = 0; } else { // absent memset(f->seq, 0, MAX_VARS); f->beg = p->b->core.pos; f->end = bam_calend(&p->b->core, bam1_cigar(p->b)); f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0; } } if (dophase) { seqs = shrink_hash(seqs); phase(&g, h->target_name[tid], vpos, cns, seqs); update_vpos(vpos, seqs); cns[0] = cns[vpos]; vpos = 0; } ++vpos; } if (tid >= 0) phase(&g, h->target_name[tid], vpos, cns, seqs); bam_header_destroy(h); bam_plp_destroy(iter); bam_close(g.fp); kh_destroy(64, seqs); kh_destroy(set64, set); free(cns); errmod_destroy(em); free(bases); if (g.pre) { for (c = 0; c <= 2; ++c) bam_close(g.out[c]); free(g.pre); free(g.b); } return 0; } pysam-0.7.7/samtools/bam_endian.h0000664000076400007650000000205012162637166016603 0ustar andreasandreas#ifndef BAM_ENDIAN_H #define BAM_ENDIAN_H #include static inline int bam_is_big_endian() { long one= 1; return !(*((char *)(&one))); } static inline uint16_t bam_swap_endian_2(uint16_t v) { return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8)); } static inline void *bam_swap_endian_2p(void *x) { *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x); return x; } static inline uint32_t bam_swap_endian_4(uint32_t v) { v = ((v & 0x0000FFFFU) << 16) | (v >> 16); return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8); } static inline void *bam_swap_endian_4p(void *x) { *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x); return x; } static inline uint64_t bam_swap_endian_8(uint64_t v) { v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32); v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16); return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8); } static inline void *bam_swap_endian_8p(void *x) { *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x); return x; } #endif pysam-0.7.7/samtools/sam_header.c.pysam.c0000664000076400007650000005143212162637166020172 0ustar andreasandreas#include "pysam.h" #include "sam_header.h" #include #include #include #include #include #include "khash.h" KHASH_MAP_INIT_STR(str, const char *) struct _HeaderList { struct _HeaderList *last; // Hack: Used and maintained only by list_append_to_end. Maintained in the root node only. struct _HeaderList *next; void *data; }; typedef struct _HeaderList list_t; typedef list_t HeaderDict; typedef struct { char key[2]; char *value; } HeaderTag; typedef struct { char type[2]; list_t *tags; } HeaderLine; const char *o_hd_tags[] = {"SO","GO",NULL}; const char *r_hd_tags[] = {"VN",NULL}; const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL}; const char *r_sq_tags[] = {"SN","LN",NULL}; const char *u_sq_tags[] = {"SN",NULL}; const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL}; const char *r_rg_tags[] = {"ID",NULL}; const char *u_rg_tags[] = {"ID",NULL}; const char *o_pg_tags[] = {"VN","CL",NULL}; const char *r_pg_tags[] = {"ID",NULL}; const char *types[] = {"HD","SQ","RG","PG","CO",NULL}; const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL}; const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL}; const char **unique_tags[] = {NULL, u_sq_tags,u_rg_tags,NULL,NULL,NULL}; static void debug(const char *format, ...) { va_list ap; va_start(ap, format); vfprintf(pysamerr, format, ap); va_end(ap); } #if 0 // Replaced by list_append_to_end static list_t *list_prepend(list_t *root, void *data) { list_t *l = malloc(sizeof(list_t)); l->next = root; l->data = data; return l; } #endif // Relies on the root->last being correct. Do not use with the other list_* // routines unless they are fixed to modify root->last as well. static list_t *list_append_to_end(list_t *root, void *data) { list_t *l = malloc(sizeof(list_t)); l->last = l; l->next = NULL; l->data = data; if ( !root ) return l; root->last->next = l; root->last = l; return root; } static list_t *list_append(list_t *root, void *data) { list_t *l = root; while (l && l->next) l = l->next; if ( l ) { l->next = malloc(sizeof(list_t)); l = l->next; } else { l = malloc(sizeof(list_t)); root = l; } l->data = data; l->next = NULL; return root; } static void list_free(list_t *root) { list_t *l = root; while (root) { l = root; root = root->next; free(l); } } // Look for a tag "XY" in a predefined const char *[] array. static int tag_exists(const char *tag, const char **tags) { int itag=0; if ( !tags ) return -1; while ( tags[itag] ) { if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag; itag++; } return -1; } // Mimics the behaviour of getline, except it returns pointer to the next chunk of the text // or NULL if everything has been read. The lineptr should be freed by the caller. The // newline character is stripped. static const char *nextline(char **lineptr, size_t *n, const char *text) { int len; const char *to = text; if ( !*to ) return NULL; while ( *to && *to!='\n' && *to!='\r' ) to++; len = to - text + 1; if ( *to ) { // Advance the pointer for the next call if ( *to=='\n' ) to++; else if ( *to=='\r' && *(to+1)=='\n' ) to+=2; } if ( !len ) return to; if ( !*lineptr ) { *lineptr = malloc(len); *n = len; } else if ( *nkey[0] = name[0]; tag->key[1] = name[1]; tag->value = malloc(len+1); memcpy(tag->value,value_from,len+1); tag->value[len] = 0; return tag; } static HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key) { list_t *tags = hline->tags; while (tags) { HeaderTag *tag = tags->data; if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag; tags = tags->next; } return NULL; } // Return codes: // 0 .. different types or unique tags differ or conflicting tags, cannot be merged // 1 .. all tags identical -> no need to merge, drop one // 2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated // 3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2) { HeaderTag *t1, *t2; if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] ) return 0; int itype = tag_exists(hline1->type,types); if ( itype==-1 ) { debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]); return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code } if ( unique_tags[itype] ) { t1 = header_line_has_tag(hline1,unique_tags[itype][0]); t2 = header_line_has_tag(hline2,unique_tags[itype][0]); if ( !t1 || !t2 ) // this should never happen, the unique tags are required return 2; if ( strcmp(t1->value,t2->value) ) return 0; // the unique tags differ, cannot be merged } if ( !required_tags[itype] && !optional_tags[itype] ) { t1 = hline1->tags->data; t2 = hline2->tags->data; if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments return 0; } int missing=0, itag=0; while ( required_tags[itype] && required_tags[itype][itag] ) { t1 = header_line_has_tag(hline1,required_tags[itype][itag]); t2 = header_line_has_tag(hline2,required_tags[itype][itag]); if ( !t1 && !t2 ) return 2; // this should never happen else if ( !t1 || !t2 ) missing = 1; // there is some tag missing in one of the hlines else if ( strcmp(t1->value,t2->value) ) { if ( unique_tags[itype] ) return 2; // the lines have a matching unique tag but have a conflicting tag return 0; // the lines contain conflicting tags, cannot be merged } itag++; } itag = 0; while ( optional_tags[itype] && optional_tags[itype][itag] ) { t1 = header_line_has_tag(hline1,optional_tags[itype][itag]); t2 = header_line_has_tag(hline2,optional_tags[itype][itag]); if ( !t1 && !t2 ) { itag++; continue; } if ( !t1 || !t2 ) missing = 1; // there is some tag missing in one of the hlines else if ( strcmp(t1->value,t2->value) ) { if ( unique_tags[itype] ) return 2; // the lines have a matching unique tag but have a conflicting tag return 0; // the lines contain conflicting tags, cannot be merged } itag++; } if ( missing ) return 3; // there are some missing complementary tags with no conflicts, can be merged return 1; } static HeaderLine *sam_header_line_clone(const HeaderLine *hline) { list_t *tags; HeaderLine *out = malloc(sizeof(HeaderLine)); out->type[0] = hline->type[0]; out->type[1] = hline->type[1]; out->tags = NULL; tags = hline->tags; while (tags) { HeaderTag *old = tags->data; HeaderTag *new = malloc(sizeof(HeaderTag)); new->key[0] = old->key[0]; new->key[1] = old->key[1]; new->value = strdup(old->value); out->tags = list_append(out->tags, new); tags = tags->next; } return out; } static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline) { list_t *tmpl_tags; if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] ) return 0; tmpl_tags = tmpl_hline->tags; while (tmpl_tags) { HeaderTag *tmpl_tag = tmpl_tags->data; HeaderTag *out_tag = header_line_has_tag(out_hline, tmpl_tag->key); if ( !out_tag ) { HeaderTag *tag = malloc(sizeof(HeaderTag)); tag->key[0] = tmpl_tag->key[0]; tag->key[1] = tmpl_tag->key[1]; tag->value = strdup(tmpl_tag->value); out_hline->tags = list_append(out_hline->tags,tag); } tmpl_tags = tmpl_tags->next; } return 1; } static HeaderLine *sam_header_line_parse(const char *headerLine) { HeaderLine *hline; HeaderTag *tag; const char *from, *to; from = headerLine; if ( *from != '@' ) { debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine); return 0; } to = ++from; while (*to && *to!='\t') to++; if ( to-from != 2 ) { debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine); return 0; } hline = malloc(sizeof(HeaderLine)); hline->type[0] = from[0]; hline->type[1] = from[1]; hline->tags = NULL; int itype = tag_exists(hline->type, types); from = to; while (*to && *to=='\t') to++; if ( to-from != 1 ) { debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from)); free(hline); return 0; } from = to; while (*from) { while (*to && *to!='\t') to++; if ( !required_tags[itype] && !optional_tags[itype] ) { // CO is a special case, it can contain anything, including tabs if ( *to ) { to++; continue; } tag = new_tag(" ",from,to-1); } else tag = new_tag(from,from+3,to-1); if ( header_line_has_tag(hline,tag->key) ) debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine); hline->tags = list_append(hline->tags, tag); from = to; while (*to && *to=='\t') to++; if ( *to && to-from != 1 ) { debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from)); return 0; } from = to; } return hline; } // Must be of an existing type, all tags must be recognised and all required tags must be present static int sam_header_line_validate(HeaderLine *hline) { list_t *tags; HeaderTag *tag; int itype, itag; // Is the type correct? itype = tag_exists(hline->type, types); if ( itype==-1 ) { debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]); return 0; } // Has all required tags? itag = 0; while ( required_tags[itype] && required_tags[itype][itag] ) { if ( !header_line_has_tag(hline,required_tags[itype][itag]) ) { debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1], hline->type[0],hline->type[1]); return 0; } itag++; } // Are all tags recognised? tags = hline->tags; while ( tags ) { tag = tags->data; if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) ) { // Lower case tags are user-defined values. if( !(islower(tag->key[0]) || islower(tag->key[1])) ) { // Neither is lower case, but tag was not recognized. debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]); // return 0; // Even unknown tags are allowed - for forward compatibility with new attributes } // else - allow user defined tag } tags = tags->next; } return 1; } static void print_header_line(FILE *fp, HeaderLine *hline) { list_t *tags = hline->tags; HeaderTag *tag; fprintf(fp, "@%c%c", hline->type[0],hline->type[1]); while (tags) { tag = tags->data; fprintf(fp, "\t"); if ( tag->key[0]!=' ' || tag->key[1]!=' ' ) fprintf(fp, "%c%c:", tag->key[0],tag->key[1]); fprintf(fp, "%s", tag->value); tags = tags->next; } fprintf(fp,"\n"); } static void sam_header_line_free(HeaderLine *hline) { list_t *tags = hline->tags; while (tags) { HeaderTag *tag = tags->data; free(tag->value); free(tag); tags = tags->next; } list_free(hline->tags); free(hline); } void sam_header_free(void *_header) { HeaderDict *header = (HeaderDict*)_header; list_t *hlines = header; while (hlines) { sam_header_line_free(hlines->data); hlines = hlines->next; } list_free(header); } HeaderDict *sam_header_clone(const HeaderDict *dict) { HeaderDict *out = NULL; while (dict) { HeaderLine *hline = dict->data; out = list_append(out, sam_header_line_clone(hline)); dict = dict->next; } return out; } // Returns a newly allocated string char *sam_header_write(const void *_header) { const HeaderDict *header = (const HeaderDict*)_header; char *out = NULL; int len=0, nout=0; const list_t *hlines; // Calculate the length of the string to allocate hlines = header; while (hlines) { len += 4; // @XY and \n HeaderLine *hline = hlines->data; list_t *tags = hline->tags; while (tags) { HeaderTag *tag = tags->data; len += strlen(tag->value) + 1; // \t if ( tag->key[0]!=' ' || tag->key[1]!=' ' ) len += strlen(tag->value) + 3; // XY: tags = tags->next; } hlines = hlines->next; } nout = 0; out = malloc(len+1); hlines = header; while (hlines) { HeaderLine *hline = hlines->data; nout += sprintf(out+nout,"@%c%c",hline->type[0],hline->type[1]); list_t *tags = hline->tags; while (tags) { HeaderTag *tag = tags->data; nout += sprintf(out+nout,"\t"); if ( tag->key[0]!=' ' || tag->key[1]!=' ' ) nout += sprintf(out+nout,"%c%c:", tag->key[0],tag->key[1]); nout += sprintf(out+nout,"%s", tag->value); tags = tags->next; } hlines = hlines->next; nout += sprintf(out+nout,"\n"); } out[len] = 0; return out; } void *sam_header_parse2(const char *headerText) { list_t *hlines = NULL; HeaderLine *hline; const char *text; char *buf=NULL; size_t nbuf = 0; int tovalidate = 0; if ( !headerText ) return 0; text = headerText; while ( (text=nextline(&buf, &nbuf, text)) ) { hline = sam_header_line_parse(buf); if ( hline && (!tovalidate || sam_header_line_validate(hline)) ) // With too many (~250,000) reference sequences the header parsing was too slow with list_append. hlines = list_append_to_end(hlines, hline); else { if (hline) sam_header_line_free(hline); sam_header_free(hlines); if ( buf ) free(buf); return NULL; } } if ( buf ) free(buf); return hlines; } void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char value_tag[2]) { const HeaderDict *dict = (const HeaderDict*)_dict; const list_t *l = dict; khash_t(str) *tbl = kh_init(str); khiter_t k; int ret; if (_dict == 0) return tbl; // return an empty (not null) hash table while (l) { HeaderLine *hline = l->data; if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) { l = l->next; continue; } HeaderTag *key, *value; key = header_line_has_tag(hline,key_tag); value = header_line_has_tag(hline,value_tag); if ( !key || !value ) { l = l->next; continue; } k = kh_get(str, tbl, key->value); if ( k != kh_end(tbl) ) debug("[sam_header_lookup_table] They key %s not unique.\n", key->value); k = kh_put(str, tbl, key->value, &ret); kh_value(tbl, k) = value->value; l = l->next; } return tbl; } char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n) { const HeaderDict *dict = (const HeaderDict*)_dict; const list_t *l = dict; int max, n; char **ret; ret = 0; *_n = max = n = 0; while (l) { HeaderLine *hline = l->data; if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) { l = l->next; continue; } HeaderTag *key; key = header_line_has_tag(hline,key_tag); if ( !key ) { l = l->next; continue; } if (n == max) { max = max? max<<1 : 4; ret = realloc(ret, max * sizeof(void*)); } ret[n++] = key->value; l = l->next; } *_n = n; return ret; } void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **_key, const char **_value) { list_t *l = iter; if ( !l ) return NULL; while (l) { HeaderLine *hline = l->data; if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) { l = l->next; continue; } HeaderTag *key, *value; key = header_line_has_tag(hline,key_tag); value = header_line_has_tag(hline,value_tag); if ( !key && !value ) { l = l->next; continue; } *_key = key->value; *_value = value->value; return l->next; } return l; } const char *sam_tbl_get(void *h, const char *key) { khash_t(str) *tbl = (khash_t(str)*)h; khint_t k; k = kh_get(str, tbl, key); return k == kh_end(tbl)? 0 : kh_val(tbl, k); } int sam_tbl_size(void *h) { khash_t(str) *tbl = (khash_t(str)*)h; return h? kh_size(tbl) : 0; } void sam_tbl_destroy(void *h) { khash_t(str) *tbl = (khash_t(str)*)h; kh_destroy(str, tbl); } void *sam_header_merge(int n, const void **_dicts) { const HeaderDict **dicts = (const HeaderDict**)_dicts; HeaderDict *out_dict; int idict, status; if ( n<2 ) return NULL; out_dict = sam_header_clone(dicts[0]); for (idict=1; idictdata, out_hlines->data); if ( status==0 ) { out_hlines = out_hlines->next; continue; } if ( status==2 ) { print_header_line(pysamerr,tmpl_hlines->data); print_header_line(pysamerr,out_hlines->data); debug("Conflicting lines, cannot merge the headers.\n"); return 0; } if ( status==3 ) sam_header_line_merge_with(out_hlines->data, tmpl_hlines->data); inserted = 1; break; } if ( !inserted ) out_dict = list_append(out_dict, sam_header_line_clone(tmpl_hlines->data)); tmpl_hlines = tmpl_hlines->next; } } return out_dict; } char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], int *n) { int nout = 0; char **out = NULL; *n = 0; list_t *l = (list_t *)dict; if ( !l ) return NULL; int i, ntags = 0; while ( tags[ntags] ) ntags++; while (l) { HeaderLine *hline = l->data; if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) { l = l->next; continue; } out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags); for (i=0; ivalue; } nout++; l = l->next; } *n = nout; return out; } pysam-0.7.7/samtools/kstring.c.pysam.c0000664000076400007650000001244012162637166017557 0ustar andreasandreas#include "pysam.h" #include #include #include #include #include #include "kstring.h" int ksprintf(kstring_t *s, const char *fmt, ...) { va_list ap; int l; va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'. va_end(ap); if (l + 1 > s->m - s->l) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); } va_end(ap); s->l += l; return l; } char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux) { const char *p, *start; if (sep) { // set up the table if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished aux->finished = 0; if (sep[1]) { aux->sep = -1; aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0; for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f); } else aux->sep = sep[0]; } if (aux->finished) return 0; else if (str) aux->p = str - 1, aux->finished = 0; if (aux->sep < 0) { for (p = start = aux->p + 1; *p; ++p) if (aux->tab[*p>>6]>>(*p&0x3f)&1) break; } else { for (p = start = aux->p + 1; *p; ++p) if (*p == aux->sep) break; } aux->p = p; // end of token if (*p == 0) aux->finished = 1; // no more tokens return (char*)start; } // s MUST BE a null terminated string; l = strlen(s) int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) { int i, n, max, last_char, last_start, *offsets, l; n = 0; max = *_max; offsets = *_offsets; l = strlen(s); #define __ksplit_aux do { \ if (_offsets) { \ s[i] = 0; \ if (n == max) { \ max = max? max<<1 : 2; \ offsets = (int*)realloc(offsets, sizeof(int) * max); \ } \ offsets[n++] = last_start; \ } else ++n; \ } while (0) for (i = 0, last_char = last_start = 0; i <= l; ++i) { if (delimiter == 0) { if (isspace(s[i]) || s[i] == 0) { if (isgraph(last_char)) __ksplit_aux; // the end of a field } else { if (isspace(last_char) || last_char == 0) last_start = i; } } else { if (s[i] == delimiter || s[i] == 0) { if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field } else { if (last_char == delimiter || last_char == 0) last_start = i; } } last_char = s[i]; } *_max = max; *_offsets = offsets; return n; } /********************** * Boyer-Moore search * **********************/ typedef unsigned char ubyte_t; // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html static int *ksBM_prep(const ubyte_t *pat, int m) { int i, *suff, *prep, *bmGs, *bmBc; prep = (int*)calloc(m + 256, sizeof(int)); bmGs = prep; bmBc = prep + m; { // preBmBc() for (i = 0; i < 256; ++i) bmBc[i] = m; for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; } suff = (int*)calloc(m, sizeof(int)); { // suffixes() int f = 0, g; suff[m - 1] = m; g = m - 1; for (i = m - 2; i >= 0; --i) { if (i > g && suff[i + m - 1 - f] < i - g) suff[i] = suff[i + m - 1 - f]; else { if (i < g) g = i; f = i; while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; suff[i] = f - g; } } } { // preBmGs() int j = 0; for (i = 0; i < m; ++i) bmGs[i] = m; for (i = m - 1; i >= 0; --i) if (suff[i] == i + 1) for (; j < m - 1 - i; ++j) if (bmGs[j] == m) bmGs[j] = m - 1 - i; for (i = 0; i <= m - 2; ++i) bmGs[m - 1 - suff[i]] = m - 1 - i; } free(suff); return prep; } void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep) { int i, j, *prep = 0, *bmGs, *bmBc; const ubyte_t *str, *pat; str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat; prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep; if (_prep && *_prep == 0) *_prep = prep; bmGs = prep; bmBc = prep + m; j = 0; while (j <= n - m) { for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); if (i >= 0) { int max = bmBc[str[i+j]] - m + 1 + i; if (max < bmGs[i]) max = bmGs[i]; j += max; } else return (void*)(str + j); } if (_prep == 0) free(prep); return 0; } char *kstrstr(const char *str, const char *pat, int **_prep) { return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep); } char *kstrnstr(const char *str, const char *pat, int n, int **_prep) { return (char*)kmemmem(str, n, pat, strlen(pat), _prep); } /*********************** * The main() function * ***********************/ #ifdef KSTRING_MAIN #include int main() { kstring_t *s; int *fields, n, i; ks_tokaux_t aux; char *p; s = (kstring_t*)calloc(1, sizeof(kstring_t)); // test ksprintf() ksprintf(s, " abcdefg: %d ", 100); printf("'%s'\n", s->s); // test ksplit() fields = ksplit(s, 0, &n); for (i = 0; i < n; ++i) printf("field[%d] = '%s'\n", i, s->s + fields[i]); // test kstrtok() s->l = 0; for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) { kputsn(p, aux.p - p, s); kputc('\n', s); } printf("%s", s->s); // free free(s->s); free(s); free(fields); { static char *str = "abcdefgcdgcagtcakcdcd"; static char *pat = "cd"; char *ret, *s = str; int *prep = 0; while ((ret = kstrstr(s, pat, &prep)) != 0) { printf("match: %s\n", ret); s = ret + prep[0]; } free(prep); } return 0; } #endif pysam-0.7.7/samtools/kaln.h0000664000076400007650000000403012162637166015453 0ustar andreasandreas/* The MIT License Copyright (c) 2003-2006, 2008, 2009 by Heng Li Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef LH3_KALN_H_ #define LH3_KALN_H_ #include #define MINOR_INF -1073741823 typedef struct { int gap_open; int gap_ext; int gap_end_open; int gap_end_ext; int *matrix; int row; int band_width; } ka_param_t; typedef struct { int iio, iie, ido, ide; int eio, eie, edo, ede; int *matrix; int row; int band_width; } ka_param2_t; #ifdef __cplusplus extern "C" { #endif uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar); int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap); #ifdef __cplusplus } #endif extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */ extern ka_param_t ka_param_qual; // only use this for global alignment!!! extern ka_param2_t ka_param2_qual; // only use this for global alignment!!! #endif pysam-0.7.7/samtools/ksort.h0000664000076400007650000002361512162637166015702 0ustar andreasandreas/* The MIT License Copyright (c) 2008 Genome Research Ltd (GRL). Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ /* Contact: Heng Li */ /* 2012-12-11 (0.1.4): * Defined __ks_insertsort_##name as static to compile with C99. 2008-11-16 (0.1.4): * Fixed a bug in introsort() that happens in rare cases. 2008-11-05 (0.1.3): * Fixed a bug in introsort() for complex comparisons. * Fixed a bug in mergesort(). The previous version is not stable. 2008-09-15 (0.1.2): * Accelerated introsort. On my Mac (not on another Linux machine), my implementation is as fast as std::sort on random input. * Added combsort and in introsort, switch to combsort if the recursion is too deep. 2008-09-13 (0.1.1): * Added k-small algorithm 2008-09-05 (0.1.0): * Initial version */ #ifndef AC_KSORT_H #define AC_KSORT_H #include #include typedef struct { void *left, *right; int depth; } ks_isort_stack_t; #define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; } #define KSORT_INIT(name, type_t, __sort_lt) \ void ks_mergesort_##name(size_t n, type_t array[], type_t temp[]) \ { \ type_t *a2[2], *a, *b; \ int curr, shift; \ \ a2[0] = array; \ a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n); \ for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i) \ ks_heapadjust_##name(i, lsize, l); \ } \ void ks_heapsort_##name(size_t lsize, type_t l[]) \ { \ size_t i; \ for (i = lsize - 1; i > 0; --i) { \ type_t tmp; \ tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \ } \ } \ static inline void __ks_insertsort_##name(type_t *s, type_t *t) \ { \ type_t *i, *j, swap_tmp; \ for (i = s + 1; i < t; ++i) \ for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp; \ } \ } \ void ks_combsort_##name(size_t n, type_t a[]) \ { \ const double shrink_factor = 1.2473309501039786540366528676643; \ int do_swap; \ size_t gap = n; \ type_t tmp, *i, *j; \ do { \ if (gap > 2) { \ gap = (size_t)(gap / shrink_factor); \ if (gap == 9 || gap == 10) gap = 11; \ } \ do_swap = 0; \ for (i = a; i < a + n - gap; ++i) { \ j = i + gap; \ if (__sort_lt(*j, *i)) { \ tmp = *i; *i = *j; *j = tmp; \ do_swap = 1; \ } \ } \ } while (do_swap || gap > 2); \ if (gap != 1) __ks_insertsort_##name(a, a + n); \ } \ void ks_introsort_##name(size_t n, type_t a[]) \ { \ int d; \ ks_isort_stack_t *top, *stack; \ type_t rp, swap_tmp; \ type_t *s, *t, *i, *j, *k; \ \ if (n < 1) return; \ else if (n == 2) { \ if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \ return; \ } \ for (d = 2; 1ul<>1) + 1; \ if (__sort_lt(*k, *i)) { \ if (__sort_lt(*k, *j)) k = j; \ } else k = __sort_lt(*j, *i)? i : j; \ rp = *k; \ if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; } \ for (;;) { \ do ++i; while (__sort_lt(*i, rp)); \ do --j; while (i <= j && __sort_lt(rp, *j)); \ if (j <= i) break; \ swap_tmp = *i; *i = *j; *j = swap_tmp; \ } \ swap_tmp = *i; *i = *t; *t = swap_tmp; \ if (i-s > t-i) { \ if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \ s = t-i > 16? i+1 : t; \ } else { \ if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \ t = i-s > 16? i-1 : s; \ } \ } else { \ if (top == stack) { \ free(stack); \ __ks_insertsort_##name(a, a+n); \ return; \ } else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \ } \ } \ } \ /* This function is adapted from: http://ndevilla.free.fr/median/ */ \ /* 0 <= kk < n */ \ type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk) \ { \ type_t *low, *high, *k, *ll, *hh, *mid; \ low = arr; high = arr + n - 1; k = arr + kk; \ for (;;) { \ if (high <= low) return *k; \ if (high == low + 1) { \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ return *k; \ } \ mid = low + (high - low) / 2; \ if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \ if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \ if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low); \ KSORT_SWAP(type_t, *mid, *(low+1)); \ ll = low + 1; hh = high; \ for (;;) { \ do ++ll; while (__sort_lt(*ll, *low)); \ do --hh; while (__sort_lt(*low, *hh)); \ if (hh < ll) break; \ KSORT_SWAP(type_t, *ll, *hh); \ } \ KSORT_SWAP(type_t, *low, *hh); \ if (hh <= k) low = ll; \ if (hh >= k) high = hh - 1; \ } \ } \ void ks_shuffle_##name(size_t n, type_t a[]) \ { \ int i, j; \ for (i = n; i > 1; --i) { \ type_t tmp; \ j = (int)(drand48() * i); \ tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp; \ } \ } #define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t) #define ks_introsort(name, n, a) ks_introsort_##name(n, a) #define ks_combsort(name, n, a) ks_combsort_##name(n, a) #define ks_heapsort(name, n, a) ks_heapsort_##name(n, a) #define ks_heapmake(name, n, a) ks_heapmake_##name(n, a) #define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a) #define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k) #define ks_shuffle(name, n, a) ks_shuffle_##name(n, a) #define ks_lt_generic(a, b) ((a) < (b)) #define ks_lt_str(a, b) (strcmp((a), (b)) < 0) typedef const char *ksstr_t; #define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic) #define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str) #endif pysam-0.7.7/samtools/kstring.h0000664000076400007650000001055312162637166016216 0ustar andreasandreas/* The MIT License Copyright (c) by Attractive Chaos Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #ifndef KSTRING_H #define KSTRING_H #include #include #include #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif typedef struct { uint64_t tab[4]; int sep, finished; const char *p; // end of the current token } ks_tokaux_t; #ifdef __cplusplus extern "C" { #endif int ksprintf(kstring_t *s, const char *fmt, ...); int ksplit_core(char *s, int delimiter, int *_max, int **_offsets); char *kstrstr(const char *str, const char *pat, int **_prep); char *kstrnstr(const char *str, const char *pat, int n, int **_prep); void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep); /* kstrtok() is similar to strtok_r() except that str is not * modified and both str and sep can be NULL. For efficiency, it is * actually recommended to set both to NULL in the subsequent calls * if sep is not changed. */ char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux); #ifdef __cplusplus } #endif static inline void ks_resize(kstring_t *s, size_t size) { if (s->m < size) { s->m = size; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } } static inline int kputsn(const char *p, int l, kstring_t *s) { if (s->l + l + 1 >= s->m) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } memcpy(s->s + s->l, p, l); s->l += l; s->s[s->l] = 0; return l; } static inline int kputs(const char *p, kstring_t *s) { return kputsn(p, strlen(p), s); } static inline int kputc(int c, kstring_t *s) { if (s->l + 1 >= s->m) { s->m = s->l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } s->s[s->l++] = c; s->s[s->l] = 0; return c; } static inline int kputw(int c, kstring_t *s) { char buf[16]; int l, x; if (c == 0) return kputc('0', s); if(c < 0) for (l = 0, x = c; x < 0; x /= 10) buf[l++] = '0' - (x%10); else for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0'; if (c < 0) buf[l++] = '-'; if (s->l + l + 1 >= s->m) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x]; s->s[s->l] = 0; return 0; } static inline int kputuw(unsigned c, kstring_t *s) { char buf[16]; int l, i; unsigned x; if (c == 0) return kputc('0', s); for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0'; if (s->l + l + 1 >= s->m) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i]; s->s[s->l] = 0; return 0; } static inline int kputl(long c, kstring_t *s) { char buf[32]; long l, x; if (c == 0) return kputc('0', s); for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0'; if (c < 0) buf[l++] = '-'; if (s->l + l + 1 >= s->m) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); } for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x]; s->s[s->l] = 0; return 0; } static inline int *ksplit(kstring_t *s, int delimiter, int *n) { int max = 0, *offsets = 0; *n = ksplit_core(s->s, delimiter, &max, &offsets); return offsets; } #endif pysam-0.7.7/samtools/bam_tview_html.c.pysam.c0000664000076400007650000002035612162637166021104 0ustar andreasandreas#include "pysam.h" #include #include "bam_tview.h" #define UNDERLINE_FLAG 10 typedef struct HtmlTview { tview_t view; int row_count; tixel_t** screen; FILE* out; int attributes;/* color... */ } html_tview_t; #define FROM_TV(ptr) ((html_tview_t*)ptr) static void html_destroy(tview_t* base) { int i; html_tview_t* tv=(html_tview_t*)base; if(tv->screen!=NULL) { for(i=0;i< tv->row_count;++i) free(tv->screen[i]); free(tv->screen); } base_tv_destroy(base); free(tv); } /* void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...); void (*my_)(struct AbstractTview*,int,int,int); void (*my_attron)(struct AbstractTview*,int); void (*my_attroff)(struct AbstractTview*,int); void (*my_clear)(struct AbstractTview*); int (*my_colorpair)(struct AbstractTview*,int); */ static void html_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...) { int i,nchars=0; unsigned int size=tv->mcol+2; char* str=malloc(size); if(str==0) exit(EXIT_FAILURE); va_list argptr; va_start(argptr, fmt); nchars=vsnprintf(str,size, fmt, argptr); va_end(argptr); for(i=0;i< nchars;++i) { tv->my_mvaddch(tv,y,x+i,str[i]); } free(str); } static void html_mvaddch(struct AbstractTview* tv,int y,int x,int ch) { tixel_t* row=NULL; html_tview_t* ptr=FROM_TV(tv); if( x >= tv->mcol ) return; //out of screen while(ptr->row_count<=y) { int x; row=(tixel_t*)calloc(tv->mcol,sizeof(tixel_t)); if(row==0) exit(EXIT_FAILURE); for(x=0;xmcol;++x) {row[x].ch=' ';row[x].attributes=0;} ptr->screen=(tixel_t**)realloc(ptr->screen,sizeof(tixel_t*)*(ptr->row_count+1)); ptr->screen[ptr->row_count++]=row; } row=ptr->screen[y]; row[x].ch=ch; row[x].attributes=ptr->attributes; } static void html_attron(struct AbstractTview* tv,int flag) { html_tview_t* ptr=FROM_TV(tv); ptr->attributes |= flag; } static void html_attroff(struct AbstractTview* tv,int flag) { html_tview_t* ptr=FROM_TV(tv); ptr->attributes &= ~(flag); } static void html_clear(struct AbstractTview* tv) { html_tview_t* ptr=FROM_TV(tv); if(ptr->screen!=NULL) { int i; for(i=0;i< ptr->row_count;++i) free(ptr->screen[i]); free(ptr->screen); ptr->screen=NULL; } ptr->row_count=0; ptr->attributes=0; } static int html_colorpair(struct AbstractTview* tv,int flag) { return (1 << (flag)); } static int html_drawaln(struct AbstractTview* tv, int tid, int pos) { int y,x; html_tview_t* ptr=FROM_TV(tv); html_clear(tv); base_draw_aln(tv, tid, pos); fputs("",ptr->out); fprintf(ptr->out,"%s:%d", tv->header->target_name[tid], pos+1 ); //style fputs("",ptr->out); fputs("",ptr->out); fprintf(ptr->out,"
%s:%d
", tv->header->target_name[tid], pos+1 ); fputs("
",ptr->out);
    for(y=0;y< ptr->row_count;++y)
    	{
    	
    	for(x=0;x< tv->mcol;++x)
	    	{
	    	
		
		if(x== 0 || ptr->screen[y][x].attributes != ptr->screen[y][x-1].attributes)
	    		{
	    		int css=0;
			fprintf(ptr->out,"1) fprintf(pysamerr,"css=%d pow2=%d vs %d\n",css,(1 << (css)),ptr->screen[y][x].attributes);
	    			if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
	    				{
	    				
	    				fprintf(ptr->out," class='tviewc%s%d'",
	    					(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)) )!=0?"u":""),
	    					css);
	    				break;
	    				}
	    			++css;
	    			}


	    		fputs(">",ptr->out);
	    		}
		
		int ch=ptr->screen[y][x].ch;
		switch(ch)
			{
			case '<': fputs("<",ptr->out);break;
			case '>': fputs(">",ptr->out);break;
			case '&': fputs("&",ptr->out);break;
			default: fputc(ch,ptr->out); break;
			}
	    	
	    	
	    	if(x+1 == tv->mcol  || ptr->screen[y][x].attributes!=ptr->screen[y][x+1].attributes)
	    		{
	    		fputs("",ptr->out);
	    		}
	    	}
    	if(y+1 < ptr->row_count) fputs("
",ptr->out);
    	}
    fputs("
",ptr->out); return 0; } #define ANSI_COLOR_RED "\x1b[31m" #define ANSI_COLOR_GREEN "\x1b[32m" #define ANSI_COLOR_YELLOW "\x1b[33m" #define ANSI_COLOR_BLUE "\x1b[34m" #define ANSI_COLOR_MAGENTA "\x1b[35m" #define ANSI_COLOR_CYAN "\x1b[36m" #define ANSI_COLOR_BLACK "\x1b[0m" #define ANSI_COLOR_RESET ANSI_COLOR_BLACK #define ANSI_UNDERLINE_SET "\033[4m" #define ANSI_UNDERLINE_UNSET "\033[0m" static int text_drawaln(struct AbstractTview* tv, int tid, int pos) { int y,x; html_tview_t* ptr=FROM_TV(tv); html_clear(tv); base_draw_aln(tv, tid, pos); int is_term= isatty(fileno(ptr->out)); for(y=0;y< ptr->row_count;++y) { for(x=0;x< tv->mcol;++x) { if(is_term) { int css=0; while(css<32) { if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0) { break; } ++css; } switch(css) { //CSS(0, "black"); case 1: fputs(ANSI_COLOR_BLUE,ptr->out); break; case 2: fputs(ANSI_COLOR_GREEN,ptr->out); break; case 3: fputs(ANSI_COLOR_YELLOW,ptr->out); break; //CSS(4, "black"); case 5: fputs(ANSI_COLOR_GREEN,ptr->out); break; case 6: fputs(ANSI_COLOR_CYAN,ptr->out); break; case 7: fputs(ANSI_COLOR_YELLOW,ptr->out); break; case 8: fputs(ANSI_COLOR_RED,ptr->out); break; case 9: fputs(ANSI_COLOR_BLUE,ptr->out); break; default:break; } if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0) { fputs(ANSI_UNDERLINE_SET,ptr->out); } } int ch=ptr->screen[y][x].ch; fputc(ch,ptr->out); if(is_term) { fputs(ANSI_COLOR_RESET,ptr->out); if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0) { fputs(ANSI_UNDERLINE_UNSET,ptr->out); } } } fputc('\n',ptr->out); } return 0; } static int html_loop(tview_t* tv) { //tv->my_drawaln(tv, tv->curr_tid, tv->left_pos); return 0; } static int html_underline(tview_t* tv) { return (1 << UNDERLINE_FLAG); } /* static void init_pair(html_tview_t *tv,int id_ge_1, const char* pen, const char* paper) { } */ tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples) { char* colstr=getenv("COLUMNS"); html_tview_t *tv = (html_tview_t*)calloc(1, sizeof(html_tview_t)); tview_t* base=(tview_t*)tv; if(tv==0) { fprintf(pysamerr,"Calloc failed\n"); return 0; } tv->row_count=0; tv->screen=NULL; tv->out=stdout; tv->attributes=0; base_tv_init(base,fn,fn_fa,samples); /* initialize callbacks */ #define SET_CALLBACK(fun) base->my_##fun=html_##fun; SET_CALLBACK(destroy); SET_CALLBACK(mvprintw); SET_CALLBACK(mvaddch); SET_CALLBACK(attron); SET_CALLBACK(attroff); SET_CALLBACK(clear); SET_CALLBACK(colorpair); SET_CALLBACK(drawaln); SET_CALLBACK(loop); SET_CALLBACK(underline); #undef SET_CALLBACK if(colstr!=0) { base->mcol=atoi(colstr); if(base->mcol<10) base->mcol=80; } base->mrow=99999; /* init_pair(tv,1, "blue", "white"); init_pair(tv,2, "green", "white"); init_pair(tv,3, "yellow", "white"); init_pair(tv,4, "white", "white"); init_pair(tv,5, "green", "white"); init_pair(tv,6, "cyan", "white"); init_pair(tv,7, "yellow", "white"); init_pair(tv,8, "red", "white"); init_pair(tv,9, "blue", "white"); */ return base; } tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples) { tview_t* tv=html_tv_init(fn,fn_fa,samples); tv->my_drawaln=text_drawaln; return tv; } pysam-0.7.7/KNOWN_BUGS0000664000076400007650000000000011700526652014136 0ustar andreasandreaspysam-0.7.7/tests/0000775000076400007650000000000012241575073013655 5ustar andreasandreaspysam-0.7.7/tests/ex5.sam0000664000076400007650000000042511700526652015057 0ustar andreasandreas@HD VN:1.0 @SQ SN:chr1 LN:100 @SQ SN:chr2 LN:100 read_28833_29006_6945 0 * * * * * 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< read_28701_28881_323b 0 * * * * * 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< pysam-0.7.7/tests/example_btag.sam0000664000076400007650000000556512075110060017004 0ustar andreasandreas@SQ LN:200000000 SN:chr1 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:S,100,1,91,0,7,101,0,201,96,204,0,0,87,109,0,7,97,112,1,12,78,197,0,7,100,95,101,202,0,6,0,1,186,0,84,0,244,0,0,324,0,107,195,101,113,0,102,0,104,3,0,101,1,0,212,6,0,0,1,0,74,1,11,0,196,2,197,103,0,108,98,2,7,0,1,2,194,0,180,0,108,0,203,104,16,5,205,0,0,0,1,1,100,98,0,0,204,6,0,79,0,0,101,7,109,90,265,1,27,10,109,102,9,0,292,0,110,0,0,102,112,0,0,84,100,103,2,81,126,0,2,90,0,15,96,15,1,0,2,0,107,92,0,0,101,3,98,15,102,13,116,116,90,93,198,0,0,0,199,92,26,495,100,5,0,100,5,209,0,92,107,90,0,0,0,0,109,194,7,94,200,0,40,197,0,11,0,0,112,110,6,4,200,28,0,196,0,203,1,129,0,0,1,0,94,0,1,0,107,5,201,3,3,100,0,121,0,7,0,1,105,306,3,86,8,183,0,12,163,17,83,22,0,0,1,8,109,103,0,0,295,0,200,16,172,3,16,182,3,11,0,0,223,111,103,0,5,225,0,95 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:s,-100,200,-300,-400 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:c,-100,12 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:C,12,15 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 QW85I:468:729 0 chr1 156268499 63 140M15H * 0 0 GTCCAGTCTCCTGTAATTCTTGGGCTTGACTAGGCTTCCGACAACCTGGAGGCATTGCTCTTTCAGGGTATACACTGCAGTGTGATGTTGGCAAAAACAGGCTGTCCATTAACATTGGAAGATGGCACAAACAATTCAGT >>>>>>>====>=>>;:8,,((1*0536;;=<>;:;>>>>>>>>>>>>>>>>>>>><9=556.2<<<8===<<<9;9=>=>>>>>>>>>>>>>>>>.>>>===>>>>>>>4=>>==;<<896=>===<>>588-1.19<= RG:Z:QW85I PG:Z:tmap MD:Z:140 NM:i:0 AS:i:140 FZ:B:f,-1.0,5.0,2.5 XA:Z:map2-1 XS:i:53 XT:i:38 XF:i:1 XE:i:0 pysam-0.7.7/tests/ex1.fa0000664000076400007650000000623111700526652014662 0ustar andreasandreas>chr1 CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC TCCCTCGTCTTCTTA >chr2 TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC CAGAAAAAAATATTTACAGTAACT pysam-0.7.7/tests/vcf-examples/0000775000076400007650000000000012241575073016247 5ustar andreasandreaspysam-0.7.7/tests/vcf-examples/7.vcf0000664000076400007650000122720012005337141017107 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##fileDate=20110524 ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 20 82176 rs11906362 T C 318 NOT_DESIGNED BCM.AC=16;DB;SRC=VQSR+2-OF-7 20 249843 rs112456910 C T 1304 PASS BCM.AC=14;DB;SEQUENOM.AC=12;SRC=VQSR+INTERSECTION GT 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/1 . . 0/0 0/0 . 0/0 . . . 0/0 . 0/0 0/0 0/1 0/0 . . . 0/0 . 0/0 . . . . . . . . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 . . 0/1 . . 0/0 . 0/1 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 . . . . . 0/0 . . . . . 0/0 . 0/1 . . . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . . . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 . . . 0/0 0/1 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 . 0/0 0/0 0/0 . . . . . . . 0/0 . 0/0 . . . . . . . . . . 0/0 . 0/0 . . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 . . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 . 0/1 0/1 0/0 . . 0/0 0/0 . . 0/0 0/1 . . 0/1 . . . 0/0 0/0 0/0 . . . . . 0/0 . 20 688672 rs116071340 C T 56 PASS BCM.AC=1;DB;SEQUENOM.AC=2;SRC=VQSR+2-OF-7 GT . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 987773 rs6077519 T G 474 PASS DB;HW_VIOLATION;SEQUENOM.AC=73;SRC=VQSR-ONLY GT . 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/1 . 0/0 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G T 26 NOT_DESIGNED BCM.AC=20;SRC=VQSR+2-OF-7 20 1333317 . 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C T 100 PASS SEQUENOM.AC=3;SRC=2-OF-7-ONLY GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1577285 . G A 4 HIGH_NO_CALL_RATE SEQUENOM.AC=0;SRC=VQSR-ONLY GT . . . 0/0 0/0 . 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 . . . 0/0 . . . . . . 0/0 . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . . . 0/0 0/0 . . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . . . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 . . . 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . . . 0/0 . . . . . . . . 0/0 . . . 0/0 . . . . . . . . . . . . 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . . 0/0 . 0/0 0/0 . . 0/0 . . . . . . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . . 0/0 0/0 . . . . . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 . . . . . 0/0 0/0 0/0 . . 0/0 0/0 20 1577845 . 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T A 100 PASS SEQUENOM.AC=0;SRC=2-OF-7-ONLY GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62724959 . G T 10 NOT_DESIGNED SRC=VQSR-ONLY 20 62888718 . T C 57 POLYMORPHIC_SAMPLES_FAILED BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62918298 . G A 33 NOT_DESIGNED SRC=VQSR+2-OF-7 20 62961477 . T C 17 AMBIGUOUS_SEQUENOM_CALLS SEQUENOM.AC=0;SRC=VQSR+2-OF-7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/vcf-examples/3.vcf0000664000076400007650000025452711754437212017130 0ustar andreasandreas##fileformat=VCFv4.0 ##filedate=2010-06-21 ##reference=NCBI36 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= #CHROM POS ID REF ALT QUAL FILTER INFO 1 1000153 . TCACAC TC 100 PASS AF=0.115095;HP=1;NF=16;NR=13;NS=52;CA=0;DP=615 1 1000906 . CAG CG 48 PASS AF=0.0772696;HP=1;NF=2;NR=9;NS=51;CA=0;DP=281 1 1000950 rs60561655;-/G CGG CG 100 PASS AF=0.447771;HP=5;DB;NF=10;NR=20;NS=50;CA=M;DP=291 1 1010786 rs36095298;-/G,mills,venter AC AGC 100 PASS AF=0.774334;HP=1;DB;NF=21;NR=27;NS=51;CA=0;DP=306 1 1026158 . TG TGGGGGG 100 PASS AF=0.115637;HP=1;NF=5;NR=2;NS=52;CA=0;DP=591 1 1028860 mills,venter ACTCC AC 10 PASS AF=0.0107751;HP=1;NF=5;NR=4;NS=52;CA=0;DP=522 1 1040517 . CA CAA 100 PASS AF=0.0577672;HP=1;NF=7;NR=4;NS=52;CA=0;DP=426 1 1043690 rs5772037;-/G,venter TG TGG 100 PASS AF=0.065857;HP=3;DB;NF=5;NR=8;NS=51;CA=0;DP=427 1 1049375 . TA TACACACCTGAGCACACACACCTGTGCA 100 PASS AF=0.0808078;HP=1;NF=1;NR=1;NS=51;CA=M;DP=643 1 1055459 venter ACC AC 100 PASS AF=0.936429;HP=2;NF=13;NR=24;NS=51;CA=M;DP=342 1 1056251 rs34287831;-/A,venter CT CTT 100 PASS AF=0.725164;HP=1;DB;NF=31;NR=20;NS=52;CA=0;DP=375 1 1057459 rs55853944;-/AG,venter CAGG CG 100 PASS AF=0.525146;HP=1;DB;NF=16;NR=18;NS=51;CA=0;DP=331 1 1057537 rs35574593;-/CC,watson TG TGGG 100 PASS AF=0.591248;HP=1;DB;NF=30;NR=12;NS=50;CA=0;DP=341 1 1058532 rs34990026;-/A GTT GT 100 PASS AF=0.702381;HP=4;DB;NF=29;NR=32;NS=52;CA=0;DP=405 1 1058695 rs56086046;-/GCCTGCCTGCCCGGCC,watson CGCCGCCTGCCTGCCCGG CG 100 PASS AF=0.601284;HP=1;DB;NF=24;NR=23;NS=51;CA=0;DP=365 1 1073880 . AC ACC 13 PASS AF=0.0555821;HP=2;NF=1;NR=6;NS=52;CA=0;DP=457 1 1087270 mills,venter,watson CCCCAC CC 100 PASS AF=0.990156;HP=4;NF=32;NR=27;NS=50;CA=0;DP=339 1 1088683 rs5772039;-/C,venter TCC TC 100 PASS AF=0.957928;HP=9;DB;NF=31;NR=26;NS=49;CA=0;DP=336 1 1093553 . TC TCAC 100 PASS AF=0.962343;HP=5;NF=44;NR=17;NS=51;CA=0;DP=324 1 1111698 rs57346441;-/TG,watson CA CTGA 100 PASS AF=0.0986662;HP=1;DB;NF=8;NR=5;NS=52;CA=0;DP=528 1 1117471 . GT GTT 48 PASS AF=0.04843;HP=6;NF=20;NR=8;NS=52;CA=0;DP=510 1 1118641 . CT CTTAT 38 PASS AF=0.0574453;HP=1;NF=5;NR=1;NS=51;CA=0;DP=424 1 1119225 rs60117456;-/C AC ACC 50 PASS AF=0.0255886;HP=4;DB;NF=8;NR=5;NS=52;CA=0;DP=522 1 1121774 . GCTGTTCAGACCTG GG 100 PASS AF=0.0749767;HP=1;NF=6;NR=6;NS=51;CA=0;DP=508 1 1123178 . AACA AA 14 PASS AF=0.0195065;HP=3;NF=2;NR=3;NS=49;CA=0;DP=329 1 1134362 . GGAG GG 100 PASS AF=0.142028;HP=2;NF=12;NR=17;NS=51;CA=0;DP=407 1 1140087 . TCA TA 19 PASS AF=0.0635822;HP=1;NF=2;NR=5;NS=51;CA=0;DP=446 1 1141951 . CTG CG 100 PASS AF=0.100135;HP=1;NF=7;NR=7;NS=52;CA=0;DP=463 1 1148304 rs34808371;-/GT,venter GCAC GC 100 PASS AF=0.0786699;HP=1;DB;NF=11;NR=18;NS=52;CA=0;DP=687 1 1148425 rs57524763;-/AC AACA AA 100 PASS AF=0.0744913;HP=2;DB;NF=17;NR=8;NS=51;CA=0;DP=647 1 1149524 . GTTTTAT GT 100 PASS AF=0.0475567;HP=4;NF=19;NR=14;NS=50;CA=0;DP=395 1 1150963 . CGCCACAGACACGGGCCACACACTCCACATG CG 100 PASS AF=0.111384;HP=1;NF=46;NR=28;NS=50;CA=0;DP=510 1 1151863 . GT GCT 100 PASS AF=0.126132;HP=1;NF=8;NR=7;NS=52;CA=0;DP=416 1 1153674 rs3831195;-/ACAG GG GGACAG 18 PASS AF=0.0388728;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=418 1 1154612 . GT GCT 100 PASS AF=0.0630518;HP=1;NF=7;NR=4;NS=52;CA=0;DP=531 1 1155143 . GCAC GC 100 PASS AF=0.0991605;HP=1;NF=25;NR=23;NS=52;CA=0;DP=540 1 1155183 . CATG CG 100 PASS AF=0.0714383;HP=1;NF=5;NR=8;NS=52;CA=0;DP=527 1 1156953 rs57672822;-/ACCCCGGGA CCCCCGGGAAC CC 59 PASS AF=0.0847102;HP=5;DB;NF=5;NR=8;NS=50;CA=0;DP=312 1 1164370 . AA AACATGCATCCA 100 PASS AF=0.0550752;HP=2;NF=2;NR=1;NS=51;CA=0;DP=481 1 1166826 . AC ACC 11 PASS AF=0.0735648;HP=1;NF=1;NR=10;NS=52;CA=0;DP=379 1 1167781 rs3835300;-/T CTG CG 100 PASS AF=0.0719128;HP=1;DB;NF=3;NR=3;NS=50;CA=0;DP=360 1 1180776 rs35025185;-/T,mills CTT CT 15 PASS AF=0.0182173;HP=3;DB;NF=5;NR=1;NS=52;CA=0;DP=526 1 1184391 . GC GCAC 16 PASS AF=0.0187867;HP=1;NF=2;NR=6;NS=51;CA=M;DP=521 1 1204971 . TGG TG 100 PASS AF=0.0564084;HP=6;NF=11;NR=6;NS=50;CA=0;DP=419 1 1207801 rs35647244;-/GT,watson CC CCAC 100 PASS AF=0.034013;HP=2;DB;NF=9;NR=4;NS=52;CA=0;DP=624 1 1213486 . GTCT GT 100 PASS AF=0.504039;HP=1;NF=9;NR=5;NS=50;CA=M;DP=372 1 1217527 rs3831920;-/CTCA,watson TTGAGT TT 100 PASS AF=0.098042;HP=2;DB;NF=11;NR=14;NS=51;CA=0;DP=444 1 1224625 . AGG AG 40 PASS AF=0.0395551;HP=5;NF=4;NR=4;NS=51;CA=0;DP=406 1 1228918 rs35156558;-/GGA,venter CC CCCTC 100 PASS AF=0.999996;HP=5;DB;NF=24;NR=30;NS=49;CA=0;DP=268 1 1232491 . CTACCTGACCTTC CC 13 PASS AF=0.0510512;HP=1;NF=5;NR=5;NS=52;CA=0;DP=510 1 1236119 . CGGCTCTGGGTCACAGGTG CG 17 PASS AF=0.0581287;HP=2;NF=6;NR=8;NS=49;CA=M;DP=277 1 1245266 rs5772041;-/G,venter TGG TG 100 PASS AF=0.928175;HP=4;DB;NF=39;NR=39;NS=52;CA=0;DP=431 1 1286232 venter,watson GACA GA 100 PASS AF=0.878082;HP=1;NF=31;NR=15;NS=50;CA=0;DP=249 1 1292184 watson TG TGTGTGCAG 100 PASS AF=0.92351;HP=1;NF=36;NR=17;NS=51;CA=0;DP=633 1 1475307 rs35008066;-/G,venter GCC GC 59 PASS AF=0.0854422;HP=2;DB;NF=2;NR=3;NS=52;CA=0;DP=372 1 1476800 rs3835461;-/C AG AGG 100 PASS AF=0.239098;HP=1;DB;NF=13;NR=18;NS=52;CA=0;DP=491 1 1482738 rs34962853;-/AT,watson CATA CA 100 PASS AF=0.1747;HP=1;DB;NF=28;NR=14;NS=51;CA=0;DP=441 1 1483969 rs3835460;-/T,mills CG CAG 100 PASS AF=0.180671;HP=5;DB;NF=6;NR=13;NS=52;CA=0;DP=512 1 1484993 rs35384209;-/CT CA CAGA 100 PASS AF=0.182804;HP=1;DB;NF=9;NR=15;NS=52;CA=0;DP=441 1 1485720 . TC TCGTAC 39 PASS AF=0.0207216;HP=1;NF=1;NR=3;NS=51;CA=0;DP=498 1 1487504 rs35885836;-/AGAA,venter,watson TTTTCT TT 100 PASS AF=0.210263;HP=4;DB;NF=16;NR=20;NS=52;CA=0;DP=574 1 1490348 rs3835459;-/CATGATCCGCCTGCCTT CAAGGCAGGCGGATCATGA CA 59 PASS AF=0.230233;HP=2;DB;NF=5;NR=66;NS=51;CA=M;DP=377 1 1490873 . GT GGGCCCGACGGTGCT 100 PASS AF=0.133846;HP=1;NF=8;NR=3;NS=52;CA=0;DP=572 1 1495811 venter ACC AC 100 PASS AF=0.232263;HP=8;NF=12;NR=29;NS=52;CA=0;DP=481 1 1502734 rs35576478;-/G,venter AC ACC 100 PASS AF=0.221604;HP=4;DB;NF=16;NR=9;NS=51;CA=0;DP=388 1 1507556 . AC ACC 42 PASS AF=0.0176775;HP=1;NF=1;NR=4;NS=51;CA=0;DP=511 1 1508235 . CT CTT 100 PASS AF=0.2555;HP=1;NF=18;NR=15;NS=51;CA=0;DP=535 1 1508689 . CG CGG 100 PASS AF=0.0922424;HP=5;NF=19;NR=17;NS=51;CA=0;DP=568 1 1510533 . TTTTGT TT 100 PASS AF=0.423696;HP=7;NF=37;NR=39;NS=52;CA=0;DP=387 1 1511216 . TA TAATAATAATAAAA 39 PASS AF=0.542394;HP=2;NF=7;NR=3;NS=51;CA=0;DP=331 1 1512041 . CAAAAGTAAA CA 33 PASS AF=0.0333379;HP=4;NF=12;NR=13;NS=52;CA=0;DP=440 1 1514403 . TTTTAT TT 100 PASS AF=0.771875;HP=5;NF=24;NR=58;NS=50;CA=0;DP=243 1 1520133 rs34595829;-/GT,venter GA GACA 100 PASS AF=0.432871;HP=1;DB;NF=24;NR=19;NS=52;CA=0;DP=966 1 1520238 venter,watson TG TGAGACAG 100 PASS AF=0.606404;HP=1;NF=52;NR=36;NS=52;CA=M;DP=847 1 1520271 . CA CAGA 100 PASS AF=0.169509;HP=1;NF=48;NR=39;NS=52;CA=M;DP=736 1 1520357 . CAGAGAGA CA 100 PASS AF=0.218715;HP=1;NF=44;NR=30;NS=52;CA=M;DP=708 1 1520549 . CAGA CA 100 PASS AF=0.257166;HP=1;NF=41;NR=40;NS=52;CA=0;DP=790 1 1520595 . CAGA CA 100 PASS AF=0.107822;HP=1;NF=52;NR=44;NS=52;CA=M;DP=804 1 1520983 . GA GAGAGAGACA 34 PASS AF=0.0372679;HP=1;NF=2;NR=3;NS=52;CA=0;DP=610 1 1521139 . GA GAGACA 100 PASS AF=0.667375;HP=1;NF=10;NR=7;NS=52;CA=M;DP=537 1 1521387 . GAGACA GA 100 PASS AF=0.361313;HP=1;NF=13;NR=34;NS=52;CA=M;DP=598 1 1521833 . GACA GA 100 PASS AF=0.193306;HP=1;NF=23;NR=17;NS=52;CA=0;DP=737 1 1522371 . CC CCCTCAGCTGGACTC 100 PASS AF=0.480499;HP=3;NF=11;NR=12;NS=51;CA=0;DP=535 1 1530305 . AG AGG 15 PASS AF=0.0737746;HP=3;NF=13;NR=4;NS=51;CA=0;DP=569 1 1536491 rs36101309;-/GA ATCT AT 100 PASS AF=0.128408;HP=1;DB;NF=22;NR=14;NS=51;CA=0;DP=621 1 1537805 venter TT TCT 100 PASS AF=0.350404;HP=8;NF=3;NR=18;NS=52;CA=M;DP=419 1 1539301 . CAAAAGA CA 56 PASS AF=0.0156055;HP=4;NF=9;NR=2;NS=51;CA=0;DP=577 1 1549566 venter ATT AT 100 PASS AF=0.505899;HP=3;NF=25;NR=27;NS=52;CA=0;DP=451 1 1554815 . TGG TG 100 PASS AF=0.158582;HP=6;NF=12;NR=6;NS=48;CA=0;DP=271 1 1575329 . GCAAC GC 12 PASS AF=0.0174116;HP=1;NF=27;NR=21;NS=52;CA=0;DP=554 1 1575977 rs35072492;-/A TCC TC 100 PASS AF=0.626664;HP=3;DB;NF=23;NR=50;NS=51;CA=0;DP=361 1 1577203 venter,watson AA AAAACA 100 PASS AF=0.979791;HP=4;NF=59;NR=37;NS=52;CA=0;DP=498 1 1584062 rs5772057;-/T,venter CT CTT 100 PASS AF=0.992883;HP=1;DB;NF=34;NR=22;NS=46;CA=0;DP=291 1 1589954 . TTGT TT 100 PASS AF=0.0452889;HP=8;NF=5;NR=13;NS=51;CA=0;DP=424 1 1611607 venter ATA AA 100 PASS AF=0.528232;HP=1;NF=7;NR=10;NS=50;CA=M;DP=243 1 1615408 venter AC ACGC 100 PASS AF=0.553544;HP=9;NF=16;NR=20;NS=51;CA=M;DP=247 1 1618248 . CTGA CA 100 PASS AF=0.0412633;HP=1;NF=5;NR=2;NS=51;CA=0;DP=789 1 1637509 venter CG CTG 100 PASS AF=0.956642;HP=1;NF=57;NR=41;NS=52;CA=M;DP=533 1 1637828 rs34259364;-/AT,mills CG CATG 100 PASS AF=0.24683;HP=1;DB;NF=5;NR=57;NS=52;CA=0;DP=744 1 1638199 . GA GATGTTAA 100 PASS AF=0.962724;HP=1;NF=22;NR=22;NS=52;CA=0;DP=480 1 1638366 venter AT ATT 100 PASS AF=0.471703;HP=4;NF=50;NR=16;NS=52;CA=0;DP=738 1 1638469 rs34392519;-/AGC,mills GA GAGCA 100 PASS AF=0.428728;HP=1;DB;NF=34;NR=23;NS=52;CA=0;DP=804 1 1639339 rs36127854;-/CT,venter TA TAGA 100 PASS AF=0.27562;HP=1;DB;NF=10;NR=15;NS=52;CA=0;DP=961 1 1639610 . ATTCTC AC 59 PASS AF=0.0697107;HP=2;NF=31;NR=24;NS=52;CA=M;DP=817 1 1640937 venter CG CTCGCTCTGTCACCCAGGCTG 100 PASS AF=0.639983;HP=2;NF=4;NR=3;NS=52;CA=M;DP=638 1 1641995 rs34986248;-/ATT,venter,watson CT CTTAT 100 PASS AF=0.924551;HP=2;DB;NF=33;NR=29;NS=52;CA=0;DP=414 1 1654133 rs34171153;-/ATCG TA TATCGA 100 PASS AF=0.2409;HP=1;DB;NF=10;NR=13;NS=52;CA=0;DP=463 1 1656307 rs35516110;-/GTTT,venter GT GGTTTT 100 PASS AF=0.686901;HP=6;DB;NF=22;NR=20;NS=51;CA=0;DP=293 1 1674207 venter CC CCCTC 100 PASS AF=0.303909;HP=3;NF=26;GC;NR=29;NS=52;CA=0;DP=534 1 1675781 . TCCCTGGGACCGAAGTCGCCCCAC TC 100 PASS AF=0.270579;HP=3;NF=25;NR=24;NS=52;CA=0;DP=473 1 1679986 rs35357728;-/TG,mills,venter,watson AA AACA 100 PASS AF=0.956895;HP=4;DB;NF=60;NR=58;NS=52;CA=0;DP=520 1 1684058 . AAATGA AA 100 PASS AF=0.508762;HP=4;NF=48;NR=55;NS=52;CA=0;DP=471 1 1684177 . TG TGGGGGGGG 100 PASS AF=0.126497;HP=1;NF=5;NR=3;NS=51;CA=0;DP=449 1 1691268 rs35459537;-/AAAAACAAAAAC,mills,venter CAAAACAAAAACAA CA 100 PASS AF=0.305762;HP=4;DB;NF=54;NR=62;NS=51;CA=0;DP=443 1 1697760 mills,venter GAAACA GA 100 PASS AF=0.276545;HP=3;NF=21;NR=43;NS=52;CA=0;DP=564 1 1700966 rs34974144;-/AT,venter TT TTGT 100 PASS AF=0.37365;HP=3;DB;NF=34;NR=30;NS=52;CA=0;DP=445 1 1715347 . TG TGGGGGG 24 PASS AF=0.0415083;HP=1;NF=4;NR=5;NS=52;CA=0;DP=519 1 1717050 rs56070879;-/ACAAAAAA,venter TC TCAAAAAAAC 100 PASS AF=0.90619;HP=1;DB;NF=11;NR=7;NS=52;CA=0;DP=442 1 1729683 . ACT AT 100 PASS AF=0.104273;HP=1;NF=9;NR=11;NS=52;CA=0;DP=587 1 1729941 rs55730045;-/TTTG,watson TTTTGT TT 100 PASS AF=0.270089;HP=5;DB;NF=25;NR=44;NS=52;CA=M;DP=458 1 1733706 rs4012956;-/GT,mills,venter TA TACA 100 PASS AF=0.737658;HP=1;DB;NF=58;NR=26;NS=52;CA=M;DP=547 1 1750193 rs34820549;-/TG,venter TA TACA 100 PASS AF=0.417596;HP=1;DB;NF=42;NR=29;NS=52;CA=0;DP=495 1 1761838 . GCAC GC 17 PASS AF=0.0186129;HP=1;NF=23;NR=23;NS=52;CA=0;DP=566 1 1767123 . TACACACACACACACACACACACACACACACA TA 100 PASS AF=0.205885;HP=1;NF=32;NR=32;NS=52;CA=0;DP=560 1 1767308 . AG ATG 12 PASS AF=0.363076;HP=2;NF=25;NR=12;NS=52;CA=0;DP=611 1 1768358 . ACA AA 11 NoQCALL AF=0.0311546;HP=1;NF=1;NR=4;NS=52;CA=0;DP=502 1 1768592 . AC ACAACAAAATCCCTTTTTC 100 PASS AF=0.0974177;HP=1;NF=2;NR=5;NS=52;CA=0;DP=597 1 1769336 rs34011234;-/TA,venter,watson CT CTAT 100 PASS AF=0.385782;HP=1;DB;NF=21;NR=42;NS=52;CA=0;DP=534 1 1769673 rs56979938;-/A,venter AGA AA 21 PASS AF=0.232442;HP=1;DB;NF=9;NR=3;NS=52;CA=0;DP=465 1 1771291 . TG TGG 100 PASS AF=0.18937;HP=2;NF=5;NR=15;NS=52;CA=0;DP=590 1 1778545 . TA TAAA 100 PASS AF=0.155668;HP=3;NF=5;NR=12;NS=52;CA=0;DP=621 1 1778604 rs34483468;-/AGCC,venter GG GGGCTG 100 PASS AF=0.135521;HP=4;DB;NF=22;NR=28;NS=52;CA=0;DP=629 1 1786587 watson ACCA AA 26 PASS AF=0.0677562;HP=2;NF=15;NR=22;NS=52;CA=M;DP=404 1 1797136 rs59528461;-/C,venter TCC TC 100 PASS AF=0.94689;HP=10;DB;NF=58;NR=57;NS=52;CA=0;DP=531 1 1797791 rs35226472;-/CT,venter CG CGAG 100 PASS AF=0.383219;HP=1;DB;NF=64;NR=38;NS=52;CA=0;DP=673 1 1802225 rs34339560;-/A,mills,venter CAA CA 100 PASS AF=0.973419;HP=2;DB;NF=64;NR=71;NS=52;CA=0;DP=635 1 1802305 . GGAG GG 100 PASS AF=0.273326;HP=2;NF=41;NR=34;NS=52;CA=0;DP=695 1 1806743 . TTAGAT TT 100 PASS AF=0.179706;HP=2;NF=9;NR=6;NS=52;CA=0;DP=377 1 1809681 . AG AGG 21 PASS AF=0.133833;HP=2;NF=7;NR=3;NS=52;CA=0;DP=482 1 1810283 . AC ACC 30 PASS AF=0.0430128;HP=2;NF=4;NR=11;NS=52;CA=0;DP=523 1 1810555 . CTTAAT CT 100 PASS AF=0.0498379;HP=2;NF=9;NR=7;NS=52;CA=0;DP=521 1 1812953 rs34135959;-/TCTC CA CAGAGA 100 PASS AF=0.311555;HP=1;DB;NF=6;NR=8;NS=42;CA=0;DP=242 1 1819911 . CATG CG 100 PASS AF=0.0319085;HP=1;NF=3;NR=6;NS=52;CA=0;DP=765 1 1819947 rs60517384;-/AAGTTGGATATACACACAT CACACACATAAGTTGGATATA CA 100 PASS AF=0.0935091;HP=1;DB;NF=59;NR=69;NS=52;CA=0;DP=854 1 1825723 venter AA AAAATAAATAAATA 100 PASS AF=0.348026;HP=4;NF=9;NR=10;NS=52;CA=0;DP=373 1 1835530 . GTGAGAGTTGTTG GG 100 PASS AF=0.15298;HP=1;NF=12;NR=1;NS=51;CA=0;DP=528 1 1838692 rs5772055;-/AC,mills AA AACA 100 PASS AF=0.0441449;HP=3;DB;NF=2;NR=3;NS=51;CA=0;DP=360 1 1843475 rs3039777;-/ACTG,venter,watson TC TCTGAC 100 PASS AF=0.999998;HP=1;DB;NF=38;NR=39;NS=50;CA=0;DP=422 1 1850674 . AGG AG 100 PASS AF=0.474687;HP=3;NF=7;NR=1;NS=49;CA=0;DP=271 1 1855740 watson GT GTGTAT 100 PASS AF=0.646893;HP=1;NF=42;NR=28;NS=51;CA=0;DP=653 1 1856762 . CACAGG CG 14 PASS AF=0.0324715;HP=1;NF=1;NR=2;NS=50;CA=M;DP=379 1 1857166 . TACA TA 100 PASS AF=0.0531955;HP=1;NF=39;NR=29;NS=52;CA=0;DP=634 1 1859140 mills ACACCAGGTCCACCTCTGGACACAGGTCCACCC AC 100 PASS AF=0.180806;HP=1;NF=26;NR=15;NS=52;CA=0;DP=672 1 1859353 rs35385292;-/TC,venter ACTC AC 100 PASS AF=0.493919;HP=1;DB;NF=26;NR=38;NS=52;CA=M;DP=641 1 1859424 rs34242289;-/CA,venter TCAG TG 100 PASS AF=0.3962;HP=1;DB;NF=40;NR=32;NS=52;CA=M;DP=695 1 1859520 . TCAC TC 100 PASS AF=0.234548;HP=1;NF=26;NR=23;NS=52;CA=0;DP=729 1 1859631 rs35205487;-/GA,venter AC ACTC 100 PASS AF=0.347295;HP=1;DB;NF=15;NR=28;NS=52;CA=0;DP=710 1 1859792 rs34050188;-/AT,watson CG CATG 100 PASS AF=0.715253;HP=1;DB;NF=35;NR=44;NS=52;CA=0;DP=590 1 1864576 . CG CGG 13 PASS AF=0.0158703;HP=1;NF=3;NR=2;NS=51;CA=0;DP=556 1 1867274 rs34832935;-/C TGG TG 100 PASS AF=0.304336;HP=8;DB;NF=38;NR=23;NS=51;CA=0;DP=538 1 1869711 rs56005703;-/ATAT,watson AA AATATA 100 PASS AF=0.652198;HP=3;DB;NF=16;NR=16;NS=51;CA=0;DP=349 1 1870233 . TC TCCCTCCCTTCTTTCCTTCCCTTTCCCTCC 100 PASS AF=0.408049;HP=2;NF=11;NR=9;NS=52;CA=0;DP=814 1 1870305 . CC CCTTTCCCTCCCTTACTCCTTCCTTCCTTC 100 PASS AF=0.121733;HP=4;NF=1;NR=5;NS=52;CA=0;DP=680 1 1870363 . CT CTT 100 PASS AF=0.11398;HP=2;NF=4;NR=6;NS=52;CA=0;DP=680 1 1870863 rs35875775;-/C,venter TT TGT 100 PASS AF=0.744276;HP=2;DB;NF=43;NR=22;NS=52;CA=0;DP=455 1 1873164 . GT GTT 100 PASS AF=0.387355;HP=3;NF=20;NR=18;NS=52;CA=0;DP=523 1 1873889 rs58267869;-/AAGA AA AAAAGA 100 PASS AF=0.252999;HP=5;DB;NF=57;NR=31;NS=52;CA=0;DP=536 1 1874122 rs35595511;-/T TAA TA 100 PASS AF=0.338059;HP=9;DB;NF=38;NR=38;NS=51;CA=0;DP=519 1 1876064 watson AG AGAGTG 100 PASS AF=0.0829624;HP=1;NF=6;NR=5;NS=52;CA=0;DP=465 1 1876204 . AC ACAGC 100 PASS AF=0.256855;HP=1;NF=14;NR=10;NS=52;CA=0;DP=483 1 1876616 . GC GCTGGTGCGCGTC 100 PASS AF=0.0656988;HP=1;NF=5;NR=2;NS=51;CA=0;DP=420 1 1876971 rs3838975;-/G GCC GC 21 PASS AF=0.201137;HP=2;DB;NF=15;NR=6;NS=52;CA=0;DP=439 1 1877704 . CCTGC CC 19 PASS AF=0.0183173;HP=2;NF=7;NR=13;NS=52;CA=0;DP=436 1 1884832 rs34937714;-/T CA CAA 100 PASS AF=0.254902;HP=3;DB;NF=27;NR=6;NS=52;CA=0;DP=449 1 1886549 rs3838974;-/T GG GAG 100 PASS AF=0.153123;HP=4;DB;NF=11;NR=10;NS=52;CA=0;DP=456 1 1889260 rs55954278;-/ATGA GT GTGAAT 100 PASS AF=0.630203;HP=1;DB;NF=12;NR=17;NS=52;CA=0;DP=656 1 1889311 . GTGAAT GT 100 PASS AF=0.167491;HP=1;NF=33;NR=18;NS=52;CA=0;DP=606 1 1889402 rs34520694;-/GTGA AT ATGAGT 100 PASS AF=0.306146;HP=1;DB;NF=24;NR=32;NS=52;CA=0;DP=916 1 1889884 rs56985589;-/G TGC TC 100 PASS AF=0.347999;HP=1;DB;NF=20;NR=28;NS=51;CA=0;DP=537 1 1889966 rs61233860;-/CCT,watson TC TCTCC 100 PASS AF=0.211403;HP=1;DB;NF=12;NR=14;NS=52;CA=0;DP=554 1 1892548 . ACTC AC 21 PASS AF=0.0207771;HP=1;NF=4;NR=3;NS=52;CA=0;DP=750 1 1900826 . AACA AA 100 PASS AF=0.122368;HP=2;NF=13;NR=6;NS=52;CA=M;DP=435 1 1908846 venter CT CTT 100 PASS AF=0.30139;HP=10;NF=11;NR=28;NS=51;CA=0;DP=350 1 1910458 . TGAG TG 15 PASS AF=0.0208928;HP=1;NF=23;NR=12;NS=52;CA=0;DP=514 1 1927207 rs61162553;-/GTTCTCTCTCTCTCTCTCTC,venter CTCTCTCTCTCTCTCTCTCGTT CT 100 PASS AF=0.399955;HP=1;DB;NF=34;NR=47;NS=51;CA=0;DP=427 1 1929307 rs36066718;-/T CAA CA 30 PASS AF=0.114706;HP=10;DB;NF=24;NR=15;NS=52;CA=0;DP=520 1 1933578 . CA CAAAATAAAATA 100 PASS AF=0.562689;HP=4;NF=21;NR=28;NS=52;CA=0;DP=359 1 1947079 rs3831907;-/C CGG CG 100 PASS AF=0.131218;HP=3;DB;NF=4;NR=10;NS=52;CA=0;DP=316 1 1949721 rs35354651;-/G GC GCC 100 PASS AF=0.218024;HP=1;DB;NF=11;NR=5;NS=51;CA=0;DP=306 1 1965555 rs56225932;-/CA,venter TACA TA 100 PASS AF=0.743144;HP=1;DB;NF=50;NR=67;NS=52;CA=0;DP=679 1 1966402 venter,watson GC GCCGCC 100 PASS AF=0.988372;HP=2;NF=36;NR=16;NS=46;CA=0;DP=232 1 1989567 . AC ACC 12 PASS AF=0.0334278;HP=6;NF=10;NR=9;NS=52;CA=0;DP=367 1 1992350 . CA CACCTGGGCGTGTGA 56 PASS AF=0.19029;HP=1;NF=6;NR=3;NS=52;CA=0;DP=412 1 1993852 rs34106910;-/G,venter GCC GC 100 PASS AF=0.178292;HP=2;DB;NF=15;NR=7;NS=51;CA=0;DP=388 1 1996153 . GT GTT 59 PASS AF=0.126167;HP=8;NF=7;NR=14;NS=51;CA=0;DP=436 1 2010531 rs35300904;-/C,venter CA CGA 100 PASS AF=0.2131;HP=1;DB;NF=18;NR=7;NS=52;CA=0;DP=418 1 2019409 rs55716481;-/AGTGACTAAGGTGACCAGG,venter CA CAGGTGACCAGGAGTGACTAA 100 PASS AF=0.901172;HP=1;DB;NF=17;NR=16;NS=52;CA=0;DP=600 1 2019867 rs58602729;-/CT CCTC CC 100 PASS AF=0.15521;HP=3;DB;NF=6;NR=12;NS=52;CA=0;DP=542 1 2019961 mills CGTTTTGTTTTG CG 100 PASS AF=0.239816;HP=1;NF=44;NR=59;NS=52;CA=0;DP=513 1 2027926 . CT CTT 100 PASS AF=0.591615;HP=1;NF=7;NR=4;NS=51;CA=M;DP=262 1 2028042 . CT CTT 100 PASS AF=0.242884;HP=1;NF=28;NR=12;NS=51;CA=M;DP=738 1 2031773 . GA GGGTA 100 PASS AF=0.197429;HP=1;NF=15;NR=7;NS=51;CA=0;DP=405 1 2036771 . AC ACCCC 100 PASS AF=0.173415;HP=3;NF=1;NR=5;NS=52;CA=0;DP=532 1 2040362 venter CT CTT 100 PASS AF=0.61548;HP=3;NF=31;NR=33;NS=52;CA=0;DP=522 1 2042747 . CG CGGGGG 100 PASS AF=0.132985;HP=2;NF=11;NR=6;NS=51;CA=0;DP=880 1 2042976 . GT GTTATT 100 PASS AF=0.225391;HP=2;NF=13;NR=25;NS=51;CA=M;DP=882 1 2045297 . GT GTAGTTATT 36 PASS AF=0.513037;HP=2;NF=5;NR=16;NS=46;CA=M;DP=269 1 2048642 rs56348719;-/A CAG CG 100 PASS AF=0.626672;HP=1;DB;NF=15;NR=37;NS=51;CA=0;DP=337 1 2055895 watson AT AATT 100 PASS AF=0.183323;HP=1;NF=10;NR=14;NS=52;CA=0;DP=511 1 2058884 watson GCCTC GC 100 PASS AF=0.258368;HP=2;NF=23;NR=18;NS=51;CA=0;DP=533 1 2068674 . CTCTAT CT 100 PASS AF=0.0693035;HP=1;NF=7;NR=5;NS=52;CA=0;DP=600 1 2076576 . GTGAT GT 100 PASS AF=0.0691863;HP=1;NF=32;NR=24;NS=52;CA=0;DP=918 1 2076741 . GTGAT GT 49 PASS AF=0.200249;HP=1;NF=13;NR=21;NS=51;CA=0;DP=758 1 2076895 . GTGAT GT 100 PASS AF=0.134423;HP=1;NF=21;NR=19;NS=51;CA=0;DP=658 1 2076954 rs60433546;-/ATG AA AATGA 100 PASS AF=0.310432;HP=2;DB;NF=12;NR=27;NS=52;CA=0;DP=664 1 2079377 rs3835418;-/T CT CTT 100 PASS AF=0.201153;HP=1;DB;NF=13;NR=15;NS=52;CA=0;DP=451 1 2081537 rs56068331;-/GTGT CGTGTG CG 13 PASS AF=0.276967;HP=1;DB;NF=58;NR=66;NS=52;CA=0;DP=516 1 2085600 rs3835419;-/CTGGGCCAACCC GA GACCCCTGGGCCAA 100 PASS AF=0.243746;HP=1;DB;NF=11;NR=6;NS=52;CA=0;DP=535 1 2087974 . GCC GC 15 PASS AF=0.0623565;HP=8;NF=7;NR=14;NS=52;CA=0;DP=325 1 2089182 rs34571180;-/CTC,mills,venter GCCTC GC 100 PASS AF=0.116512;HP=2;DB;NF=9;NR=4;NS=51;CA=0;DP=440 1 2089950 . CG CGGGG 100 PASS AF=0.178382;HP=2;NF=20;NR=7;NS=51;CA=0;DP=444 1 2091793 rs56317708;-/GATA,venter,watson AA AAGATA 100 PASS AF=0.896718;HP=2;DB;NF=37;NR=55;NS=52;CA=0;DP=525 1 2094394 watson TCCACC TC 100 PASS AF=0.191274;HP=2;NF=15;NR=11;NS=52;CA=0;DP=554 1 2099298 . TG TGG 100 PASS AF=0.234547;HP=1;NF=15;NR=4;NS=51;CA=0;DP=434 1 2101678 . AGACG AG 100 PASS AF=0.0220699;HP=1;NF=10;NR=4;NS=51;CA=0;DP=533 1 2104518 rs55672189;-/CGTCTC,venter AG AGTCTCCG 32 PASS AF=0.0318159;HP=1;DB;NF=1;NR=2;NS=51;CA=0;DP=303 1 2110593 rs34825103;-/C TG TGG 100 PASS AF=0.0674605;HP=1;DB;NF=1;NR=4;NS=52;CA=M;DP=336 1 2114205 . TT TTTGT 14 PASS AF=0.0440601;HP=4;NF=24;NR=27;NS=52;CA=0;DP=414 1 2118677 rs35613376;-/T,venter GA GAA 100 PASS AF=0.110597;HP=1;DB;NF=4;NR=6;NS=51;CA=0;DP=395 1 2129208 venter CGTGTGTGTGTGTGTGTGTGTG CG 100 PASS AF=0.312577;HP=1;NF=50;NR=42;NS=51;CA=0;DP=395 1 2136104 rs34745034;-/AC,venter,watson CTGT CT 100 PASS AF=0.148774;HP=1;DB;NF=9;NR=15;NS=51;CA=0;DP=394 1 2147798 . CGG CG 100 PASS AF=0.069257;HP=5;NF=3;NR=7;NS=51;CA=0;DP=433 1 2156467 rs34646035;-/A,venter GG GTG 100 PASS AF=0.0650203;HP=2;DB;NF=3;NR=2;NS=51;CA=0;DP=299 1 2163248 rs34969427;-/CA,venter,watson CT CTGT 59 PASS AF=0.323344;HP=1;DB;NF=36;NR=42;NS=52;CA=0;DP=622 1 2168152 rs34184068;-/C TG TGG 100 PASS AF=0.267631;HP=8;DB;NF=12;NR=25;NS=52;CA=0;DP=462 1 2173905 rs59705675;-/C,venter GCC GC 100 PASS AF=0.519185;HP=4;DB;NF=28;NR=31;NS=52;CA=0;DP=472 1 2178426 . ATCTCT AT 59 PASS AF=0.0153899;HP=1;NF=1;NR=2;NS=52;CA=0;DP=558 1 2180516 . TG TGGG 15 PASS AF=0.10873;HP=1;NF=7;NR=3;NS=52;CA=0;DP=495 1 2193017 rs35691128;-/C,venter TG TGG 100 PASS AF=0.296206;HP=9;DB;NF=9;NR=11;NS=52;CA=0;DP=367 1 2204648 . AGGGG AG 100 PASS AF=0.0847086;HP=8;NF=9;NR=7;NS=52;CA=0;DP=441 1 2211603 . TG TGGGGGGGGGG 100 PASS AF=0.176;HP=1;NF=5;NR=9;NS=52;CA=0;DP=507 1 2211835 rs35471620;-/C,venter CG CGG 100 PASS AF=0.403922;HP=3;DB;NF=20;NR=20;NS=51;CA=0;DP=363 1 2213004 rs35841716;-/G,mills,venter TGG TG 100 PASS AF=0.938006;HP=7;DB;NF=35;NR=9;NS=52;CA=0;DP=297 1 2214726 . GC GCC 100 PASS AF=0.415474;HP=9;NF=18;NR=19;NS=51;CA=0;DP=416 1 2220552 rs35472917;-/C,venter AGG AG 100 PASS AF=0.609848;HP=9;DB;NF=24;NR=22;NS=51;CA=0;DP=385 1 2221276 . GC GCC 23 PASS AF=0.0895016;HP=2;NF=1;NR=11;NS=50;CA=0;DP=396 1 2222657 . AC ACC 16 PASS AF=0.0530452;HP=2;NF=1;NR=3;NS=51;CA=0;DP=404 1 2223900 . CAGGA CA 100 PASS AF=0.105506;HP=1;NF=9;NR=6;NS=52;CA=0;DP=517 1 2232109 . CAGG CG 100 PASS AF=0.220422;HP=1;NF=14;NR=13;NS=51;CA=0;DP=430 1 2233476 rs34394327;-/CGTTT,mills,venter,watson CC CCGTTTC 100 PASS AF=0.982218;HP=3;DB;NF=18;NR=31;NS=52;CA=0;DP=378 1 2238242 rs56200665;-/C,mills GG GCG 100 PASS AF=0.745403;HP=4;DB;NF=37;NR=40;NS=51;CA=0;DP=419 1 2242260 rs34121936;-/C AGG AG 100 PASS AF=0.107749;HP=4;DB;NF=7;NR=6;NS=51;CA=0;DP=427 1 2246276 rs61120130;-/TGC,venter GG GGCTG 100 PASS AF=0.447977;HP=3;DB;NF=13;NR=17;NS=51;CA=0;DP=403 1 2246469 . TT TTCCCTCCCTTCCTTCCTTCCCTCCCT 100 PASS AF=0.0710328;HP=3;NF=8;NR=6;NS=51;CA=B;DP=731 1 2246586 rs59175712;-/CT CC CCTC 100 PASS AF=0.378253;HP=2;DB;NF=33;NR=29;NS=50;CA=0;DP=515 1 2248450 rs61135926;-/CACA AA AACACA 100 PASS AF=0.367115;HP=3;DB;NF=24;NR=19;NS=51;CA=0;DP=445 1 2248486 . CAGA CA 100 PASS AF=0.108968;HP=1;NF=14;NR=11;NS=51;CA=M;DP=382 1 2248806 rs59142249;-/A CA CAA 100 PASS AF=0.0756571;HP=1;DB;NF=4;NR=12;NS=51;CA=0;DP=728 1 2255198 . TGCTGGAAAGAACAG TG 100 PASS AF=0.115149;HP=1;NF=9;NR=12;NS=51;CA=0;DP=470 1 2267148 . ACACACAGA AA 100 PASS AF=0.128331;HP=1;NF=4;NR=6;NS=51;CA=0;DP=681 1 2268675 . TG TGG 10 PASS AF=0.0406249;HP=1;NF=7;NR=3;NS=52;CA=0;DP=508 1 2269958 . GCACGCACACGCAC GC 40 PASS AF=0.0297002;HP=1;NF=6;NR=7;NS=50;CA=0;DP=288 1 2270248 . CCTG CG 100 PASS AF=0.21901;HP=4;NF=14;NR=17;NS=52;CA=0;DP=478 1 2272049 . AGGGGTGGCACGG AG 100 PASS AF=0.0657391;HP=4;NF=20;NR=19;NS=52;CA=0;DP=465 1 2272576 rs35424701;-/T TA TAA 100 PASS AF=0.0794139;HP=1;DB;NF=5;NR=5;NS=51;CA=0;DP=426 1 2273487 . TAA TA 10 PASS AF=0.0158231;HP=10;NF=25;NR=9;NS=51;CA=0;DP=564 1 2282631 rs59328016;-/G AG AGG 100 PASS AF=0.230902;HP=1;DB;NF=1;NR=6;NS=52;CA=M;DP=310 1 2282847 rs34534255;-/AG AC ACTC 100 PASS AF=0.108076;HP=1;DB;NF=5;NR=4;NS=50;CA=0;DP=293 1 2284162 . CA CAA 12 PASS AF=0.0508845;HP=10;NF=7;NR=7;NS=52;CA=0;DP=406 1 2285124 . TAAAAA TA 100 PASS AF=0.226133;HP=8;NF=14;NR=5;NS=52;CA=0;DP=315 1 2288255 rs56670882;-/TACATAGAAAAA,venter,watson CAAAATACATAGAA CA 100 PASS AF=0.154865;HP=4;DB;NF=46;NR=50;NS=51;CA=0;DP=466 1 2291012 venter ATAATT AT 100 PASS AF=0.140631;HP=1;NF=7;NR=9;NS=51;CA=0;DP=365 1 2292525 rs60502597;-/CACAACAAC,venter CA CACAACCACAA 100 PASS AF=0.411828;HP=1;DB;NF=18;NR=3;NS=52;CA=0;DP=515 1 2305015 rs35699260;-/T,venter CAG CG 100 PASS AF=0.283002;HP=1;DB;NF=14;NR=17;NS=51;CA=0;DP=451 1 2310430 . AA AAAGA 100 PASS AF=0.382413;HP=6;NF=20;NR=11;NS=52;CA=0;DP=408 1 2314333 venter CG CGGACGCCAGGCAGAGGACTTCATCCCAGGCTTCAGTGCTCCTG 100 PASS AF=0.736856;HP=2;NF=1;NR=2;NS=52;CA=0;DP=679 1 2319273 rs57204595;-/C ACC AC 100 PASS AF=0.125223;HP=2;DB;NF=7;NR=13;NS=52;CA=0;DP=523 1 2322519 . TCCT TT 100 PASS AF=0.200476;HP=2;NF=2;NR=10;NS=50;CA=0;DP=413 1 2322562 . TCCACCCTCC TC 100 PASS AF=0.3747;HP=2;NF=8;NR=15;NS=51;CA=0;DP=325 1 2322680 . CT CTT 100 PASS AF=0.284453;HP=1;NF=26;NR=24;NS=52;CA=M;DP=388 1 2323804 venter TC TCC 100 PASS AF=0.865363;HP=3;NF=38;NR=47;NS=50;CA=0;DP=438 1 2325452 . CG CGG 39 PASS AF=0.0242463;HP=3;NF=5;NR=8;NS=51;CA=0;DP=547 1 2332518 . GA GAA 100 PASS AF=0.0862532;HP=1;NF=5;NR=13;NS=51;CA=0;DP=414 1 2337697 rs55744642;-/CGACA,venter,watson GG GGGACAG 100 PASS AF=0.867582;HP=3;DB;NF=16;NR=23;NS=51;CA=0;DP=383 1 2338712 rs34210450;-/AGCTTCCC,mills,venter GC GCCCAGCTTC 100 PASS AF=0.431742;HP=3;DB;NF=24;NR=15;NS=52;CA=0;DP=504 1 2341261 . TCC TC 20 PASS AF=0.13716;HP=9;NF=4;NR=20;NS=51;CA=0;DP=258 1 2343280 rs60532031;-/AAAAG,watson GA GAAGAAA 100 PASS AF=0.0544808;HP=2;DB;NF=2;NR=10;NS=49;CA=0;DP=348 1 2343570 venter AA AAAACA 100 PASS AF=0.0882931;HP=6;NF=28;NR=18;NS=52;CA=0;DP=434 1 2344468 . TTTTGT TT 100 PASS AF=0.233529;HP=7;NF=49;NR=55;NS=52;CA=0;DP=493 1 2345597 rs35560781;-/T,venter TAA TA 100 PASS AF=0.501718;HP=6;DB;NF=36;NR=26;NS=52;CA=0;DP=532 1 2352446 . CGTG CG 16 PASS AF=0.0185013;HP=1;NF=10;NR=25;NS=52;CA=0;DP=432 1 2352629 rs35263617;-/CA,venter CG CGTG 100 PASS AF=0.4693;HP=1;DB;NF=44;NR=38;NS=51;CA=0;DP=539 1 2355283 rs35314501;-/G TC TCC 100 PASS AF=0.408524;HP=4;DB;NF=21;NR=18;NS=52;CA=0;DP=436 1 2356275 rs34090130;-/G,mills AGG AG 100 PASS AF=0.172214;HP=6;DB;NF=16;NR=9;NS=51;CA=0;DP=415 1 2356753 rs58056215;-/TGGAGGC TGGCTGGAG TG 100 PASS AF=0.178356;HP=2;DB;NF=43;NR=59;NS=51;CA=0;DP=429 1 2357119 . TGG TG 100 PASS AF=0.179635;HP=6;NF=12;NR=18;NS=52;CA=0;DP=495 1 2357323 . TCCCT TT 100 PASS AF=0.0931072;HP=3;NF=8;NR=9;NS=52;CA=0;DP=484 1 2357636 . CTCCACCTTT CT 100 PASS AF=0.252701;HP=1;NF=11;NR=9;NS=47;CA=M;DP=266 1 2358758 . CAA CA 26 PASS AF=0.0241071;HP=3;NF=1;NR=3;NS=51;CA=0;DP=486 1 2360543 rs34299371;-/G,venter GCC GC 100 PASS AF=0.460241;HP=7;DB;NF=18;NR=28;NS=51;CA=0;DP=403 1 2365835 rs35499456;-/A GT GTT 100 PASS AF=0.299753;HP=3;DB;NF=19;NR=20;NS=52;CA=0;DP=431 1 2370798 . AAACCA AA 100 PASS AF=0.315002;HP=4;NF=56;NR=52;NS=52;CA=0;DP=505 1 2379981 rs35697743;-/C,venter TGC TC 100 PASS AF=0.0396508;HP=1;DB;NF=1;NR=5;NS=50;CA=0;DP=425 1 2383170 rs35931789;-/T,venter CC CAC 100 PASS AF=0.441832;HP=7;DB;NF=24;NR=21;NS=52;CA=0;DP=453 1 2383775 . ACC AC 19 PASS AF=0.0298335;HP=5;NF=6;NR=2;NS=52;CA=0;DP=442 1 2388741 watson GCCTTCCTCAC GC 100 PASS AF=0.134128;HP=2;NF=6;NR=9;NS=47;CA=0;DP=257 1 2394261 rs34886292;-/T,venter CA CAA 100 PASS AF=0.640008;HP=1;DB;NF=28;NR=33;NS=51;CA=0;DP=459 1 2395694 venter AGG AG 100 PASS AF=0.518622;HP=3;NF=29;NR=23;NS=50;CA=0;DP=387 1 2406522 rs35886782;-/CTCTGGACGCT,venter,watson TG TGCTCTCTGGACG 100 PASS AF=0.531691;HP=1;DB;NF=12;NR=19;NS=51;CA=0;DP=452 1 2429911 rs3831090;-/AT,mills TT TTAT 100 PASS AF=0.138967;HP=3;DB;NF=24;NR=13;NS=52;CA=0;DP=328 1 2458287 . CGTG CG 100 PASS AF=0.0696687;HP=1;NF=38;NR=32;NS=52;CA=0;DP=613 1 2458465 . AGTG AG 31 PASS AF=0.0212179;HP=1;NF=18;NR=32;NS=51;CA=0;DP=600 1 2460527 . TG TGCGGCCCATCTCAG 51 PASS AF=0.164756;HP=1;NF=1;NR=4;NS=51;CA=0;DP=496 1 2477778 . AC ACCC 100 PASS AF=0.157812;HP=2;NF=2;NR=11;NS=51;CA=0;DP=389 1 2501833 rs34000217;-/ATT AA AAATA 100 PASS AF=0.437274;HP=5;DB;NF=19;NR=23;NS=51;CA=0;DP=337 1 2503512 rs59345997;-/CAAA AAAACA AA 100 PASS AF=0.46764;HP=4;DB;NF=44;NR=29;NS=52;CA=0;DP=456 1 2506681 . TG TGGG 46 PASS AF=0.310909;HP=9;NF=14;NR=8;NS=51;CA=0;DP=273 1 2513520 rs5772070;-/G,mills CGG CG 100 PASS AF=0.652792;HP=8;DB;NF=8;NR=34;NS=51;CA=0;DP=275 1 2517761 . TGC TC 100 PASS AF=0.0839269;HP=1;NF=3;NR=6;NS=50;CA=0;DP=359 1 2520201 rs34705971;-/C,venter AG AGG 100 PASS AF=0.612406;HP=1;DB;NF=42;NR=46;NS=52;CA=0;DP=518 1 2521983 . TCAAACAAACAAAC TC 100 PASS AF=0.365407;HP=1;NF=35;NR=29;NS=52;CA=0;DP=501 1 2522019 . CT CTGTT 100 PASS AF=0.523695;HP=1;NF=28;NR=12;NS=52;CA=0;DP=410 1 2522313 rs34791736;-/A,venter CT CTT 100 PASS AF=0.621139;HP=1;DB;NF=47;NR=24;NS=52;CA=0;DP=472 1 2524952 rs35090174;-/CT ACTC AC 100 PASS AF=0.224915;HP=1;DB;NF=19;NR=15;NS=51;CA=0;DP=517 1 2529806 . CATA CA 100 PASS AF=0.236462;HP=1;NF=22;NR=13;NS=51;CA=0;DP=625 1 2529841 . CACATA CA 100 PASS AF=0.190786;HP=1;NF=20;NR=19;NS=51;CA=0;DP=663 1 2530205 rs61132608;-/CATATA,watson CA CACATATA 100 PASS AF=0.547698;HP=1;DB;NF=20;NR=28;NS=52;CA=0;DP=660 1 2543402 rs5772073;-/GAG,mills TAGGA TA 100 PASS AF=0.24689;HP=1;DB;NF=12;NR=31;NS=52;CA=0;DP=543 1 2547236 rs58240187;-/AGA,venter,watson GG GGAAG 100 PASS AF=0.531939;HP=2;DB;NF=25;NR=25;NS=52;CA=0;DP=444 1 2551119 rs35955733;-/CCC,venter,watson GCCCC GC 100 PASS AF=0.606107;HP=9;DB;NF=24;NR=35;NS=52;CA=0;DP=492 1 2551885 rs36036408;-/AC,venter CGTG CG 100 PASS AF=0.356574;HP=1;DB;NF=39;NR=38;NS=52;CA=0;DP=803 1 2552076 . CGTG CG 100 PASS AF=0.066645;HP=1;NF=25;NR=15;NS=51;CA=0;DP=782 1 2552384 . CTGT CT 12 PASS AF=0.0121638;HP=1;NF=13;NR=25;NS=52;CA=0;DP=612 1 2556252 . ACACTC AC 59 PASS AF=0.143579;HP=1;NF=12;NR=9;NS=49;CA=0;DP=331 1 2578474 . CCACACCCCCAG CG 100 PASS AF=0.930867;HP=3;NF=16;NR=12;NS=51;CA=M;DP=281 1 2688911 rs34425096;-/TC,venter TTCT TT 100 PASS AF=0.26327;HP=5;DB;NF=17;NR=12;NS=52;CA=0;DP=451 1 2691366 rs36213670;-/CTCTGGGCCA,mills,venter GCTCTGGGCCAC GC 39 PASS AF=0.191253;HP=1;DB;NF=21;NR=36;NS=52;CA=0;DP=344 1 2691723 rs57511628;-/ACCCCAGGAGATCCCTGC TA TACCCCAGGAGATCCCTGCA 100 PASS AF=0.332823;HP=1;DB;NF=6;NR=7;NS=52;CA=0;DP=453 1 2703254 . CA CAA 100 PASS AF=0.111948;HP=3;NF=8;NR=13;NS=51;CA=0;DP=502 1 2703885 . AC ACC 100 PASS AF=0.0959517;HP=6;NF=24;NR=11;NS=51;CA=0;DP=531 1 2725125 rs34936518;-/C,venter GCT GT 100 PASS AF=0.375093;HP=1;DB;NF=33;NR=32;NS=52;CA=0;DP=621 1 2725735 . AACACA AA 24 PASS AF=0.0139746;HP=2;NF=16;NR=4;NS=51;CA=0;DP=639 1 2726135 rs34620269;-/CA GCAC GC 100 PASS AF=0.0410325;HP=1;DB;NF=28;NR=22;NS=52;CA=0;DP=626 1 2726213 . GC GCAC 13 PASS AF=0.0257105;HP=1;NF=8;NR=9;NS=52;CA=0;DP=552 1 2746483 . AC ACC 40 PASS AF=0.0544668;HP=1;NF=4;NR=12;NS=51;CA=0;DP=544 1 2747281 . TG TGAGAG 100 PASS AF=0.152256;HP=1;NF=11;NR=8;NS=52;CA=0;DP=855 1 2754002 rs36202379;-/CTGCTTGT,mills,watson ATTGTCTGCT AT 100 PASS AF=0.260861;HP=2;DB;NF=32;NR=35;NS=52;CA=0;DP=496 1 2755160 rs34916159;-/A TA TAA 100 PASS AF=0.532865;HP=7;DB;NF=10;NR=34;NS=52;CA=0;DP=533 1 2755983 . GCC GC 100 PASS AF=0.106339;HP=3;NF=18;NR=26;NS=52;CA=M;DP=700 1 2765711 . AA AAGGAAGGA 100 PASS AF=0.686149;HP=2;NF=11;NR=8;NS=50;CA=0;DP=364 1 2765863 . AG AGG 100 PASS AF=0.999885;HP=1;NF=14;NR=36;NS=49;CA=0;DP=364 1 2765952 . AG AGG 100 PASS AF=0.0789769;HP=1;NF=29;NR=29;NS=51;CA=B;DP=851 1 2779479 . TTTTCTTCTCTTTCT TT 100 PASS AF=0.712577;HP=4;NF=29;NR=22;NS=50;CA=0;DP=322 1 2794338 rs34131736;-/T CTG CG 100 PASS AF=0.089184;HP=1;DB;NF=7;NR=4;NS=51;CA=0;DP=440 1 2801123 . TCCTCCCCACCCTGAC TC 48 PASS AF=0.0412327;HP=2;NF=13;NR=18;NS=51;CA=0;DP=343 1 2803308 watson CATG CG 100 PASS AF=0.160766;HP=1;NF=23;NR=20;NS=52;CA=0;DP=816 1 2805468 rs56260225;-/ACAA AAAACA AA 100 PASS AF=0.859977;HP=4;DB;NF=62;NR=35;NS=51;CA=0;DP=433 1 2806441 rs34966309;-/G CG CGG 100 PASS AF=0.211987;HP=4;DB;NF=20;NR=11;NS=52;CA=0;DP=441 1 2810388 . GCC GC 100 PASS AF=0.11183;HP=2;NF=8;NR=5;NS=51;CA=0;DP=431 1 2822166 . TACATGCACACA TA 100 PASS AF=0.150719;HP=1;NF=43;NR=52;NS=52;CA=0;DP=844 1 2822270 rs59677991;-/GC GGCG GG 18 NoQCALL AF=0.0194725;HP=2;DB;NF=15;NR=5;NS=52;CA=0;DP=806 1 2822473 . CACACAC CC 100 PASS AF=0.138944;HP=1;NF=6;NR=7;NS=52;CA=0;DP=951 1 2827616 . CAAGC CC 52 PASS AF=0.132317;HP=2;NF=8;NR=4;NS=51;CA=0;DP=300 1 2828576 . CG CTG 100 PASS AF=0.168378;HP=1;NF=8;NR=2;NS=52;CA=0;DP=325 1 2829365 rs35758696;-/A TAA TA 100 PASS AF=0.216995;HP=6;DB;NF=20;NR=20;NS=51;CA=0;DP=531 1 2833106 . TG TGTTGGG 100 PASS AF=0.237115;HP=1;NF=11;NR=4;NS=52;CA=0;DP=336 1 2834384 . AC ACC 32 PASS AF=0.0617917;HP=1;NF=3;NR=5;NS=52;CA=0;DP=592 1 2835704 rs35824541;-/G AGG AG 100 PASS AF=0.188967;HP=3;DB;NF=15;NR=11;NS=52;CA=0;DP=691 1 2836635 rs56691957;-/AT CATG CG 100 PASS AF=0.126742;HP=1;DB;NF=8;NR=13;NS=52;CA=0;DP=611 1 2851063 . ATGTGTGTCT AT 100 PASS AF=0.224053;HP=1;NF=34;NR=32;NS=52;CA=0;DP=798 1 2859183 rs34869376;-/CT ACTC AC 100 PASS AF=0.228335;HP=1;DB;NF=11;NR=14;NS=52;CA=0;DP=446 1 2859269 rs34009406;-/C AC ACC 100 PASS AF=0.168197;HP=2;DB;NF=8;NR=14;NS=52;CA=0;DP=460 1 2862455 rs34488344;-/T GT GTT 100 PASS AF=0.140555;HP=10;DB;NF=25;NR=16;NS=52;CA=0;DP=484 1 2866073 . AC ACC 56 PASS AF=0.0758065;HP=1;NF=2;NR=11;NS=51;CA=0;DP=513 1 2871504 . TA TACTAA 100 PASS AF=0.128765;HP=1;NF=11;NR=12;NS=52;CA=0;DP=676 1 2871601 rs60410855;-/TCCA CC CCCATC 100 PASS AF=0.11635;HP=3;DB;NF=19;NR=14;NS=52;CA=0;DP=682 1 2874709 . GT GTT 100 PASS AF=0.138394;HP=9;NF=8;NR=12;NS=51;CA=0;DP=534 1 2876814 rs5772089;-/A,mills,venter GG GAG 100 PASS AF=0.999994;HP=10;DB;NF=39;NR=42;NS=50;CA=0;DP=343 1 2877421 rs35085736;-/C,venter GC GCC 100 PASS AF=0.582204;HP=6;DB;NF=29;NR=37;NS=50;CA=0;DP=426 1 2881114 . GG GTG 100 PASS AF=0.586283;HP=5;NF=16;NR=5;NS=47;CA=M;DP=256 1 2883970 . GG GCG 16 PASS AF=0.516075;HP=4;NF=6;NR=2;NS=51;CA=M;DP=332 1 2885504 . TCC TC 29 PASS AF=0.140908;HP=9;NF=12;NR=8;NS=51;CA=0;DP=353 1 2886983 . AG AGG 50 PASS AF=0.0436199;HP=3;NF=7;NR=2;NS=50;CA=0;DP=401 1 2887864 rs57379840;-/T,venter CG CTG 100 PASS AF=0.770236;HP=2;DB;NF=41;NR=25;NS=51;CA=0;DP=375 1 2892284 . CAT CT 100 PASS AF=0.0885935;HP=1;NF=23;NR=17;NS=52;CA=0;DP=685 1 2892433 venter AT ATCCATCCTCCATCCT 100 PASS AF=0.814532;HP=1;NF=13;NR=12;NS=52;CA=0;DP=620 1 2892472 . CCCATC CC 100 PASS AF=0.181828;HP=3;NF=50;NR=61;NS=52;CA=0;DP=633 1 2899352 . CTA CA 100 PASS AF=0.0433393;HP=1;NF=5;NR=2;NS=51;CA=0;DP=512 1 2902379 . TAGA TA 40 PASS AF=0.0165292;HP=1;NF=3;NR=2;NS=51;CA=0;DP=476 1 2903930 rs36097640;-/A TAA TA 12 PASS AF=0.0522384;HP=8;DB;NF=13;NR=15;NS=51;CA=0;DP=535 1 2907194 rs35693840;-/G AG AGG 100 PASS AF=0.136995;HP=5;DB;NF=14;NR=8;NS=52;CA=0;DP=516 1 2916313 . AC ACC 40 PASS AF=0.0606632;HP=1;NF=1;NR=13;NS=52;CA=0;DP=529 1 2923107 . GA GGGGGGAA 35 PASS AF=0.311458;HP=1;NF=1;NR=2;NS=50;CA=0;DP=285 1 2923994 . AAGGA AA 100 PASS AF=0.136914;HP=3;NF=4;NR=16;NS=52;CA=0;DP=475 1 2926544 rs58065168;-/G TG TGG 100 PASS AF=0.231871;HP=7;DB;NF=23;NR=13;NS=51;CA=0;DP=445 1 2927774 . GTCT GT 100 PASS AF=0.039848;HP=1;NF=24;NR=39;NS=52;CA=0;DP=466 1 2928267 rs4013154;-/TCT CAGAA CA 100 PASS AF=0.176094;HP=1;DB;NF=10;GC;NR=20;NS=52;CA=0;DP=390 1 2931584 . GTGGTGTTTTCATT GT 100 PASS AF=0.171247;HP=1;NF=23;NR=10;NS=52;CA=0;DP=486 1 2932462 . GT GTGAT 56 PASS AF=0.766604;HP=1;NF=33;NR=13;NS=52;CA=M;DP=790 1 2932531 . GT GTGGTGAT 56 PASS AF=0.365205;HP=1;NF=19;NR=4;NS=52;CA=M;DP=738 1 2938240 rs57953122;-/AAGCC AC ACCAAGC 100 PASS AF=0.229942;HP=2;DB;NF=5;NR=7;NS=52;CA=0;DP=387 1 2939820 rs35035410;-/C,venter GCC GC 100 PASS AF=0.270114;HP=6;DB;NF=15;NR=21;NS=52;CA=0;DP=477 1 2940602 . GA GAA 100 PASS AF=0.245189;HP=10;NF=31;NR=30;NS=52;CA=0;DP=516 1 2941986 . ACCC AC 100 PASS AF=0.242307;HP=10;NF=20;NR=20;NS=52;CA=0;DP=471 1 2943041 rs34450334;-/G,mills CGG CG 100 PASS AF=0.212427;HP=8;DB;NF=13;NR=12;NS=52;CA=0;DP=523 1 2943605 rs5772091;-/C,mills GC GCC 100 PASS AF=0.155328;HP=1;DB;NF=7;NR=7;NS=52;CA=0;DP=349 1 2946559 . TT TTGT 100 PASS AF=0.174249;HP=3;NF=13;NR=14;NS=52;CA=0;DP=596 1 2948391 . TT TTTTTCT 100 PASS AF=0.137955;HP=5;NF=19;NR=16;NS=52;CA=0;DP=557 1 2949076 rs33910396;-/G,mills CG CGG 100 PASS AF=0.102902;HP=1;DB;NF=3;NR=8;NS=52;CA=0;DP=413 1 2950056 . TC TCAAACAAAC 100 PASS AF=0.133966;HP=1;NF=9;NR=9;NS=51;CA=0;DP=587 1 2950689 rs60031908;-/A CAA CA 100 PASS AF=0.200188;HP=8;DB;NF=20;NR=25;NS=51;CA=0;DP=517 1 2958314 . CC CCCATC 100 PASS AF=0.190271;HP=3;NF=39;NR=18;NS=52;CA=M;DP=454 1 2961502 rs60708459;-/T AT ATT 100 PASS AF=0.219472;HP=3;DB;NF=14;NR=16;NS=52;CA=0;DP=460 1 2968615 . AG AGG 100 PASS AF=0.288912;HP=2;NF=11;NR=13;NS=51;CA=0;DP=324 1 2982005 . GT GGGTT 100 PASS AF=0.189932;HP=5;NF=6;NR=5;NS=52;CA=0;DP=460 1 2984462 rs34471979;-/C,venter TCC TC 100 PASS AF=0.423837;HP=2;DB;NF=20;NR=27;NS=51;CA=0;DP=459 1 2985828 rs5772093;-/TTCGGGG,mills,venter,watson CT CTTCGGGGT 100 PASS AF=0.888966;HP=1;DB;NF=22;NR=15;NS=49;CA=0;DP=372 1 2987353 . AGTG AG 39 PASS AF=0.0534166;HP=1;NF=13;NR=12;NS=51;CA=0;DP=341 1 2990018 . TC TGC 51 PASS AF=0.347647;HP=1;NF=9;NR=5;NS=52;CA=0;DP=328 1 2992552 rs55740340;-/TTGT,mills,venter,watson CT CTGTTT 100 PASS AF=0.633228;HP=1;DB;NF=31;NR=31;NS=52;CA=0;DP=471 1 2994869 . TT TTTAT 48 PASS AF=0.246512;HP=4;NF=8;NR=15;NS=49;CA=0;DP=238 1 2996339 rs60239912;-/TCATTCAT CT CTCATTCATT 100 PASS AF=0.288255;HP=1;DB;NF=27;NR=24;NS=52;CA=0;DP=550 1 2996940 . TG TGGG 52 PASS AF=0.252534;HP=1;NF=5;NR=3;NS=51;CA=0;DP=485 1 2997430 rs58914207;-/TC TTCT TT 17 PASS AF=0.0239916;HP=3;DB;NF=1;NR=3;NS=51;CA=0;DP=533 1 2998548 rs3067411;-/GC,mills,watson TT TGCT 100 PASS AF=0.513959;HP=2;DB;NF=16;NR=33;NS=51;CA=0;DP=457 1 2998746 rs33948447;-/CTGAGGGTAT,mills,watson CCTGAGGGTATC CC 100 PASS AF=0.567187;HP=2;DB;NF=32;NR=26;NS=51;CA=0;DP=446 1 2998922 rs3067390;-/CA,mills,watson CTGT CT 100 PASS AF=0.344398;HP=1;DB;NF=25;NR=25;NS=52;CA=0;DP=544 1 3001309 . TCTTCC TC 100 PASS AF=0.122521;HP=1;NF=13;NR=16;NS=51;CA=0;DP=463 1 3003643 rs34727240;-/A CA CAA 100 PASS AF=0.30407;HP=4;DB;NF=23;NR=14;NS=51;CA=0;DP=462 1 3003980 . ATTCT AT 100 PASS AF=0.0770408;HP=2;NF=12;NR=8;NS=51;CA=0;DP=436 1 3015507 rs36215320;-/AATAAT,mills AAATAATA AA 100 PASS AF=0.341849;HP=4;DB;NF=19;NR=21;NS=52;CA=M;DP=287 1 3020627 . GC GCGCGCAC 45 PASS AF=0.0864166;HP=1;NF=3;NR=4;NS=52;CA=0;DP=675 1 3020729 . GCAC GC 100 PASS AF=0.270815;HP=1;NF=26;NR=22;NS=52;CA=0;DP=511 1 3020780 . GCAC GC 100 PASS AF=0.0529136;HP=1;NF=14;NR=13;NS=52;CA=0;DP=580 1 3020851 rs36140038;-/G,venter CC CGC 100 PASS AF=0.0570603;HP=2;DB;NF=7;NR=8;NS=52;CA=0;DP=580 1 3020930 . GCAC GC 100 PASS AF=0.0608239;HP=1;NF=21;NR=20;NS=52;CA=0;DP=662 1 3020996 . ACT AT 100 PASS AF=0.0376658;HP=1;NF=4;NR=2;NS=52;CA=0;DP=646 1 3021049 rs58793198;-/CA AA AACA 100 PASS AF=0.0822964;HP=2;DB;NF=19;NR=18;NS=52;CA=0;DP=756 1 3024532 . TGTGTGCG TG 100 PASS AF=0.0453628;HP=1;NF=12;NR=35;NS=51;CA=0;DP=585 1 3035092 venter,watson CTCCCACCATGCTACTGGAGACCAT CT 100 PASS AF=0.175148;HP=1;NF=41;NR=54;NS=51;CA=0;DP=464 1 3035605 rs56967751;-/TG,venter,watson AG AGTG 100 PASS AF=0.387697;HP=1;DB;NF=30;NR=25;NS=51;CA=0;DP=671 1 3035812 . CGTG CG 100 PASS AF=0.051827;HP=1;NF=28;NR=20;NS=51;CA=0;DP=643 1 3035887 . ATGT AT 50 PASS AF=0.0421027;HP=1;NF=24;NR=34;NS=52;CA=0;DP=556 1 3036291 rs36033160;-/CCG CT CCCGT 100 PASS AF=0.0605711;HP=1;DB;NF=3;NR=5;NS=51;CA=0;DP=428 1 3037949 rs34840011;-/A,venter TA TAA 100 PASS AF=0.096326;HP=8;DB;NF=5;NR=6;NS=52;CA=0;DP=462 1 3046082 rs35271327;-/T AT ATT 19 PASS AF=0.0473995;HP=7;DB;NF=9;NR=8;NS=52;CA=0;DP=430 1 3049499 . ACC AC 27 PASS AF=0.0269129;HP=3;NF=3;NR=1;NS=51;CA=0;DP=373 1 3053337 . TGG TG 100 PASS AF=0.205181;HP=7;NF=15;NR=19;NS=52;CA=0;DP=424 1 3058772 . TCATCC TC 100 PASS AF=0.716787;HP=1;NF=61;NR=51;NS=52;CA=0;DP=435 1 3069377 . CATGGT CT 100 PASS AF=0.42044;HP=1;NF=3;NR=14;NS=48;CA=M;DP=257 1 3076481 rs35945121;-/T,mills ATT AT 100 PASS AF=0.33892;HP=10;DB;NF=9;NR=38;NS=52;CA=0;DP=438 1 3079028 . TA TCA 100 PASS AF=0.0528803;HP=1;NF=5;NR=3;NS=51;CA=0;DP=475 1 3084256 watson AGTTTAGATACTG AG 100 PASS AF=0.123981;HP=1;NF=18;NR=14;NS=52;CA=0;DP=554 1 3087172 rs34468831;-/A GAA GA 100 PASS AF=0.0618762;HP=3;DB;NF=2;NR=5;NS=50;CA=0;DP=475 1 3087517 . CACACGCAGTCTTA CA 100 PASS AF=0.637316;HP=1;NF=41;NR=37;NS=52;CA=0;DP=973 1 3087777 . TA TACA 100 PASS AF=0.377666;HP=1;NF=43;NR=55;NS=52;CA=M;DP=966 1 3087871 . CACGGTCTTA CA 100 PASS AF=0.589214;HP=1;NF=16;NR=14;NS=51;CA=0;DP=710 1 3087938 . AG AGTCTTACACAAGCGG 100 PASS AF=0.469462;HP=1;NF=28;NR=29;NS=52;CA=M;DP=816 1 3088154 . GG GCAG 100 PASS AF=0.0511127;HP=2;NF=11;NR=10;NS=52;CA=M;DP=894 1 3088232 rs35125658;-/TT GG GCAG 100 PASS AF=0.0967781;HP=2;DB;NF=3;NR=24;NS=51;CA=M;DP=938 1 3088301 . CT CTTGCACACGCAGTTT 47 PASS AF=0.0188781;HP=2;NF=5;NR=2;NS=51;CA=M;DP=684 1 3105704 rs35372326;-/G,mills CGG CG 100 PASS AF=0.0956114;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=378 1 3107408 rs5772098;-/G,mills AG AGG 100 PASS AF=0.107417;HP=5;DB;NF=19;NR=15;NS=52;CA=0;DP=504 1 3107714 rs34461209;-/G,venter TG TGG 100 PASS AF=0.61875;HP=3;DB;NF=21;NR=28;NS=52;CA=0;DP=454 1 3108534 rs59512254;-/GA GGAG GG 100 PASS AF=0.184609;HP=2;DB;NF=17;NR=11;NS=52;CA=0;DP=510 1 3121064 . TG TGAG 59 PASS AF=0.0221492;HP=1;NF=7;NR=3;NS=52;CA=0;DP=555 1 3131583 rs57750843;-/A GAA GA 100 PASS AF=0.166149;HP=9;DB;NF=21;NR=20;NS=52;CA=0;DP=490 1 3131742 . GT GGGGGGGGGTT 27 PASS AF=0.243052;HP=3;NF=2;NR=1;NS=49;CA=0;DP=394 1 3135855 rs34340862;-/TAA,mills CT CTAAT 100 PASS AF=0.183257;HP=1;DB;NF=11;NR=9;NS=51;CA=0;DP=520 1 3146366 . GGAG GG 100 PASS AF=0.040688;HP=4;NF=13;NR=14;NS=51;CA=0;DP=434 1 3152159 . AT ATT 100 PASS AF=0.0396994;HP=4;NF=8;NR=9;NS=52;CA=0;DP=489 1 3157729 venter,watson AG AGGGGTGAGGTG 100 PASS AF=0.830079;HP=4;NF=30;NR=23;NS=51;CA=0;DP=548 1 3158807 . AGG AG 100 PASS AF=0.705976;HP=6;NF=35;NR=30;NS=52;CA=0;DP=371 1 3158885 . CATG CG 100 PASS AF=0.09216;HP=1;NF=6;NR=6;NS=51;CA=0;DP=375 1 3163280 . CAAAATA CA 100 PASS AF=0.148526;HP=4;NF=13;NR=1;NS=49;CA=M;DP=326 1 3164018 rs5772100;-/A,mills,venter TAA TA 100 PASS AF=0.999998;HP=3;DB;NF=67;NR=69;NS=52;CA=0;DP=511 1 3174387 . CAGG CG 17 PASS AF=0.0141709;HP=1;NF=1;NR=2;NS=51;CA=0;DP=428 1 3176024 . GACAGTCCCAGAGGAGCA GA 44 PASS AF=0.0444872;HP=1;NF=3;NR=10;NS=52;CA=M;DP=480 1 3177102 . AG AGAGGAGGACAGTCGGGGAGGACAGTCCCGG 100 PASS AF=0.346135;HP=1;NF=8;NR=13;NS=52;CA=0;DP=550 1 3179862 rs35987870;-/GTGG ATGTGT AT 100 PASS AF=0.0762534;HP=1;DB;NF=17;NR=17;NS=51;CA=0;DP=618 1 3183094 rs33953525;-/GGTGCCGTGAACAGAGCCAGCGAGG,mills AG AGGTGCCGTGAACAGAGCCAGCGAGGG 100 PASS AF=0.665581;HP=2;DB;NF=15;NR=15;NS=52;CA=0;DP=424 1 3183166 rs35451643;-/C,venter TCC TC 100 PASS AF=0.123295;HP=4;DB;NF=12;NR=6;NS=52;CA=0;DP=460 1 3184208 rs59663829;-/GCACACACAA TA TGCACACACAAA 100 PASS AF=0.152939;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=733 1 3186299 . ACC AC 100 PASS AF=0.951135;HP=8;NF=16;NR=14;NS=51;CA=0;DP=311 1 3202609 . TG TGGGGGGG 11 PASS AF=0.122471;HP=1;NF=3;NR=3;NS=52;CA=0;DP=479 1 3292566 . TC TCGGGGTGCCC 12 PASS AF=0.209628;HP=1;NF=22;NR=17;NS=51;CA=0;DP=462 1 3292669 . AAGA AA 100 PASS AF=0.312194;HP=8;NF=13;NR=14;NS=51;CA=0;DP=483 1 3293018 rs35846516;-/A,venter GAA GA 100 PASS AF=0.791047;HP=9;DB;NF=59;NR=44;NS=51;CA=0;DP=507 1 3293422 rs34150215;-/A,mills,venter TA TAA 100 PASS AF=0.418316;HP=7;DB;NF=27;NR=18;NS=52;CA=0;DP=481 1 3307979 rs35082175;-/A,venter CAT CT 100 PASS AF=0.379363;HP=1;DB;NF=36;NR=25;NS=52;CA=0;DP=659 1 3308056 . CATA CA 100 PASS AF=0.0313721;HP=1;NF=4;NR=5;NS=52;CA=0;DP=699 1 3308306 rs34659426;-/AA CAAA CA 100 PASS AF=0.238591;HP=3;DB;NF=23;NR=22;NS=52;CA=0;DP=732 1 3308692 . GC GCC 100 PASS AF=0.610676;HP=6;NF=23;NR=26;NS=52;CA=0;DP=447 1 3309461 . ACCCTCCTCTGAGTCTTCCTCCCCTTCCCGTGC AC 100 PASS AF=0.218197;HP=3;NF=28;NR=41;NS=51;CA=0;DP=430 1 3313004 . ATT AT 18 PASS AF=0.117282;HP=10;NF=22;NR=12;NS=51;CA=0;DP=407 1 3315219 rs35154920;-/GT CG CGTG 100 PASS AF=0.407055;HP=1;DB;NF=23;NR=17;NS=52;CA=0;DP=498 1 3315279 rs34306698;-/AT CG CATG 100 PASS AF=0.27165;HP=1;DB;NF=18;NR=10;NS=51;CA=0;DP=460 1 3315552 rs61650876;-/ATGT CATGTG CG 100 PASS AF=0.074251;HP=1;DB;NF=10;NR=7;NS=52;CA=0;DP=612 1 3315608 . CGTG CG 44 PASS AF=0.0200264;HP=1;NF=15;NR=25;NS=52;CA=0;DP=622 1 3316180 rs34769314;-/GTGA TGTGAG TG 100 PASS AF=0.13026;HP=1;DB;NF=29;NR=21;NS=52;CA=0;DP=930 1 3316258 rs57503175;-/TGTATGTGCGTGTGTGTGGTGTG GG GGTGTGTGGTGTGTGTATGTGCGTG 100 PASS AF=0.277124;HP=3;DB;NF=3;NR=11;NS=52;CA=0;DP=898 1 3316338 rs34133894;-/GT GGTG GG 100 PASS AF=0.121606;HP=2;DB;NF=18;NR=27;NS=52;CA=0;DP=901 1 3316408 . TGG TG 100 PASS AF=0.153074;HP=7;NF=23;NR=10;NS=52;CA=0;DP=898 1 3316476 rs60842130;-/GTG TGTGG TG 43 PASS AF=0.0151943;HP=1;DB;NF=4;NR=1;NS=52;CA=0;DP=732 1 3317481 rs34240659;-/AT CATA CA 100 PASS AF=0.127605;HP=1;DB;NF=14;NR=8;NS=52;CA=0;DP=538 1 3319964 . ACC AC 100 PASS AF=0.0511239;HP=5;NF=12;NR=4;NS=52;CA=0;DP=505 1 3327173 rs56093721;-/A,venter TAA TA 100 PASS AF=0.89527;HP=9;DB;NF=37;NR=68;NS=52;CA=0;DP=540 1 3328302 . AG AGGGGGG 53 PASS AF=0.124625;HP=2;NF=13;NR=2;NS=52;CA=0;DP=585 1 3335208 . CGG CG 100 PASS AF=0.0438559;HP=2;NF=3;NR=3;NS=52;CA=0;DP=448 1 3335551 rs34869178;-/T CTC CC 100 PASS AF=0.0947355;HP=1;DB;NF=4;NR=8;NS=52;CA=0;DP=487 1 3342021 rs34485545;-/A TA TAA 100 PASS AF=0.154806;HP=9;DB;NF=25;NR=23;NS=52;CA=0;DP=444 1 3347098 venter CG CAG 100 PASS AF=0.931731;HP=1;NF=49;NR=54;NS=52;CA=0;DP=497 1 3348129 rs55866341;-/G,venter CG CGG 100 PASS AF=0.883294;HP=1;DB;NF=55;NR=55;NS=52;CA=0;DP=521 1 3352897 . AA ACA 46 PASS AF=0.0385898;HP=6;NF=2;NR=6;NS=51;CA=0;DP=407 1 3353821 rs34792713;-/T AT ATT 36 PASS AF=0.0290672;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=428 1 3356271 . TTCCT TT 15 PASS AF=0.00990969;HP=3;NF=1;NR=1;NS=52;CA=0;DP=537 1 3356391 rs4018597;-/TA TT TTAT 100 PASS AF=0.0517593;HP=2;DB;NF=13;NR=11;NS=52;CA=0;DP=475 1 3356436 rs5772104;-/GT CGTG CG 100 PASS AF=0.82813;HP=1;DB;NF=59;NR=53;NS=51;CA=0;DP=449 1 3356871 . CATG CG 26 PASS AF=0.0193592;HP=1;NF=1;NR=3;NS=51;CA=0;DP=430 1 3359412 rs34037774;-/G,venter TGG TG 59 PASS AF=0.0301496;HP=2;DB;NF=4;NR=5;NS=52;CA=0;DP=451 1 3370575 rs35597752;-/TG,venter,watson CTGT CT 100 PASS AF=0.760154;HP=1;DB;NF=43;NR=36;NS=52;CA=0;DP=405 1 3372018 rs34109718;-/G,venter CGG CG 100 PASS AF=0.891318;HP=3;DB;NF=46;NR=36;NS=51;CA=0;DP=349 1 3383745 rs57207202;-/C AC ACC 100 PASS AF=0.182529;HP=4;DB;NF=9;NR=7;NS=47;CA=D;DP=229 1 3384084 rs5772105;-/G,mills,venter CG CGG 100 PASS AF=0.937697;HP=2;DB;NF=49;NR=47;NS=50;CA=0;DP=457 1 3385833 rs5772106;-/CC,mills,venter,watson ACCC AC 100 PASS AF=0.778535;HP=5;DB;NF=33;NR=14;NS=51;CA=0;DP=418 1 3387275 rs56102150;-/TC,venter CC CCTC 100 PASS AF=0.999995;HP=4;DB;NF=16;NR=36;NS=50;CA=0;DP=364 1 3388739 rs58188396;-/GGGGGGCGGGTAGCC GG GGGGGGGCGGGTAGCCG 40 PASS AF=0.263678;HP=7;DB;NF=3;NR=2;NS=48;CA=0;DP=326 1 3393157 . AAAAAATA AA 100 PASS AF=0.0549314;HP=6;NF=23;NR=18;NS=51;CA=0;DP=468 1 3393524 . GGTGTG GG 23 PASS AF=0.017751;HP=2;NF=1;NR=19;NS=49;CA=0;DP=266 1 3409800 . AAGA AA 100 PASS AF=0.0431791;HP=3;NF=1;NR=8;NS=51;CA=0;DP=643 1 3410131 rs58666986;-/GTGT ATGTGT AT 100 PASS AF=0.0433727;HP=1;DB;NF=7;NR=13;NS=52;CA=0;DP=603 1 3411485 rs60864742;-/ACACCGGTAGCAAGGCA,mills ACACCGGTAGCAAGGCACC AC 100 PASS AF=0.0858716;HP=1;DB;NF=8;NR=17;NS=52;CA=0;DP=523 1 3417374 . GCACACGCCCCCACCC GC 20 PASS AF=0.0294079;HP=1;NF=4;NR=3;NS=50;CA=0;DP=447 1 3429498 rs56204236;-/G CG CGG 100 PASS AF=0.596026;HP=10;DB;NF=6;NR=7;NS=51;CA=0;DP=322 1 3435396 . CACAGA CA 100 PASS AF=0.0433621;HP=1;NF=2;NR=6;NS=52;CA=0;DP=457 1 3442767 rs36106109;-/G CG CGG 100 PASS AF=0.112939;HP=5;DB;NF=5;NR=6;NS=50;CA=0;DP=369 1 3451064 rs36030995;-/C GC GCC 100 PASS AF=0.385449;HP=5;DB;NF=22;NR=12;NS=50;CA=0;DP=388 1 3456931 rs35289361;-/G AG AGG 100 PASS AF=0.0676076;HP=4;DB;NF=11;NR=9;NS=52;CA=0;DP=554 1 3467274 watson GGGCTG GG 100 PASS AF=0.132596;HP=3;NF=16;NR=12;NS=51;CA=0;DP=428 1 3475422 rs61428836;-/G TG TGG 100 PASS AF=0.0480433;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=468 1 3482055 . CA CGTCTTATA 100 PASS AF=0.593516;HP=1;NF=10;NR=11;NS=49;CA=M;DP=256 1 3482413 mills,watson TCTCC TC 100 PASS AF=0.414589;HP=1;NF=24;NR=32;NS=51;CA=0;DP=496 1 3485140 venter,watson CCAAC CC 100 PASS AF=0.714294;HP=2;NF=21;NR=32;NS=52;CA=0;DP=460 1 3486991 rs35452084;-/G,venter AGG AG 100 PASS AF=0.744909;HP=4;DB;NF=15;NR=35;NS=50;CA=0;DP=363 1 3492812 . CGTG CG 14 PASS AF=0.0148914;HP=1;NF=22;NR=26;NS=51;CA=0;DP=585 1 3494290 . AC ACAGGACCGGCC 100 PASS AF=0.117184;HP=1;NF=2;NR=22;NS=52;CA=0;DP=464 1 3496820 rs34860893;-/C,mills,venter ACC AC 100 PASS AF=0.924032;HP=7;DB;NF=33;NR=48;NS=52;CA=0;DP=386 1 3504928 rs36094767;-/C,venter TC TCC 100 PASS AF=0.786142;HP=4;DB;NF=23;NR=43;NS=51;CA=0;DP=405 1 3511572 rs3072238;-/TCAC,venter ACACTC AC 100 PASS AF=0.160871;HP=1;DB;NF=22;NR=22;NS=52;CA=0;DP=824 1 3511789 rs59801836;-/CTCA,watson ACACTC AC 100 PASS AF=0.620819;HP=1;DB;NF=54;NR=52;NS=52;CA=0;DP=740 1 3511919 . TACA TA 100 PASS AF=0.049568;HP=1;NF=20;NR=22;NS=52;CA=0;DP=729 1 3511980 rs57128321;-/ACTC,venter,watson AC ACACTC 100 PASS AF=0.937206;HP=1;DB;NF=63;NR=38;NS=52;CA=0;DP=712 1 3512089 rs61705210;-/TCACAC,venter,watson AACTCACA AA 100 PASS AF=0.658764;HP=3;DB;NF=65;NR=52;NS=52;CA=0;DP=808 1 3516936 rs60239345;-/CA,venter CG CCAG 100 PASS AF=0.999997;HP=1;DB;NF=52;NR=26;NS=52;CA=0;DP=391 1 3519155 rs35740208;-/G,venter AGG AG 100 PASS AF=0.108418;HP=3;DB;NF=7;NR=11;NS=51;CA=0;DP=505 1 3523781 rs56339243;-/GGCTCC,venter,watson AC ACCGGCTC 100 PASS AF=0.603986;HP=3;DB;NF=20;NR=23;NS=52;CA=0;DP=449 1 3526023 . GGCACTTCCCGCCCCCGTCACCCCTGCCGCCATG GG 100 PASS AF=0.227609;HP=2;NF=10;NR=15;NS=52;CA=0;DP=454 1 3526486 rs35020651;-/C,venter TC TCC 100 PASS AF=0.389171;HP=3;DB;NF=32;NR=20;NS=52;CA=0;DP=470 1 3530060 . TGG TG 100 PASS AF=0.033793;HP=3;NF=6;NR=1;NS=52;CA=0;DP=540 1 3531966 rs3838971;-/C TG TGG 100 PASS AF=0.155382;HP=6;DB;NF=14;NR=11;NS=49;CA=0;DP=292 1 3534095 rs35816205;-/A,mills,venter TAA TA 100 PASS AF=0.160054;HP=3;DB;NF=9;NR=10;NS=52;CA=0;DP=455 1 3535035 rs58849058;-/TCTGGGAGCTCCTCCCCCT,venter,watson GTTCTGGGAGCTCCTCCCCCT GT 100 PASS AF=0.609724;HP=2;DB;NF=50;NR=48;NS=52;CA=0;DP=487 1 3535985 . CCAAAC CC 100 PASS AF=0.116123;HP=2;NF=10;NR=13;NS=51;CA=0;DP=553 1 3536124 rs55905548;-/GGCG,venter,watson CCGGGC CC 100 PASS AF=0.45742;HP=3;DB;NF=28;NR=31;NS=51;CA=0;DP=499 1 3543853 . TC TCC 100 PASS AF=0.156605;HP=6;NF=12;NR=13;NS=52;CA=0;DP=527 1 3549495 . AC ACCCCC 34 PASS AF=0.0959154;HP=1;NF=1;NR=3;NS=52;CA=0;DP=496 1 3553372 rs34514629;-/C,venter GCA GA 100 PASS AF=0.652107;HP=1;DB;NF=45;NR=47;NS=52;CA=0;DP=551 1 3556485 rs3831025;-/CAGCCTGC,venter,watson AGCAGGCTGC AC 100 PASS AF=0.38103;HP=1;DB;NF=13;NR=9;NS=49;CA=0;DP=292 1 3556883 . CA CATA 14 PASS AF=0.0221011;HP=1;NF=9;NR=13;NS=50;CA=0;DP=436 1 3563429 . CG CGGGGG 56 PASS AF=0.17049;HP=2;NF=3;NR=7;NS=52;CA=0;DP=586 1 3564334 rs3034639;-/GT,mills GA GACA 100 PASS AF=0.227635;HP=1;DB;NF=10;NR=13;NS=50;CA=0;DP=364 1 3564964 rs5772113;-/G TGG TG 100 PASS AF=0.220888;HP=2;DB;NF=11;NR=18;NS=50;CA=0;DP=408 1 3565238 venter GGTCTCCTACAGTCATATTTTGGGGTGACGTATTCTAG GG 100 PASS AF=0.145422;HP=2;NF=1;NR=10;NS=52;CA=M;DP=323 1 3566253 rs57149403;-/GTCCAGC AC ACGTCCAGC 100 PASS AF=0.0476733;HP=1;DB;NF=3;NR=3;NS=52;CA=0;DP=363 1 3567114 . ATG AG 100 PASS AF=0.0358982;HP=1;NF=3;NR=5;NS=52;CA=0;DP=555 1 3568146 rs3034606;-/TA GTAT GT 100 PASS AF=0.533957;HP=1;DB;NF=12;NR=29;NS=51;CA=0;DP=247 1 3570893 rs34305694;-/C TCC TC 100 PASS AF=0.0467251;HP=2;DB;NF=5;NR=3;NS=52;CA=0;DP=443 1 3574939 . CG CGTGTGTG 23 PASS AF=0.401022;HP=1;NF=46;NR=32;NS=52;CA=0;DP=481 1 3586002 . ACTC AC 100 PASS AF=0.157197;HP=1;NF=17;NR=24;NS=52;CA=0;DP=691 1 3586231 rs61542341;-/GTCTCT CTCTCTGT CT 12 PASS AF=0.0310208;HP=1;DB;NF=1;NR=11;NS=52;CA=M;DP=400 1 3586281 . CTTT CT 21 PASS AF=0.115475;HP=3;NF=1;NR=3;NS=51;CA=M;DP=469 1 3589610 rs57492244;-/G TGG TG 100 PASS AF=0.0691843;HP=7;DB;NF=11;NR=8;NS=51;CA=0;DP=527 1 3593995 rs57765962;-/AT,watson AATG AG 100 PASS AF=0.127015;HP=2;DB;NF=10;NR=8;NS=52;CA=0;DP=423 1 3603570 . GCGGGGCCCACCTCGCACCCGCGGCCCACGTCGCACCC GC 100 PASS AF=0.0758905;HP=1;NF=8;NR=12;NS=51;CA=0;DP=414 1 3606881 rs5772119;-/A,venter TAG TG 100 PASS AF=0.333638;HP=1;DB;NF=12;NR=36;NS=51;CA=0;DP=522 1 3618309 rs3841787;-/TG,watson CATG CG 100 PASS AF=0.219932;HP=1;DB;NF=14;NR=14;NS=50;CA=0;DP=449 1 3619353 venter GCCCCTGCC GC 100 PASS AF=0.290838;HP=4;NF=18;NR=8;NS=51;CA=0;DP=322 1 3629994 rs35939665;-/CTGC,mills,venter,watson TCTGCC TC 100 PASS AF=0.953969;HP=1;DB;NF=43;NR=31;NS=51;CA=0;DP=364 1 3630547 rs35380007;-/A,venter TA TAA 100 PASS AF=0.373122;HP=2;DB;NF=20;NR=12;NS=51;CA=0;DP=293 1 3632819 rs61728692;-/CGGA GT GCGGAT 100 PASS AF=0.63605;HP=1;DB;NF=18;NR=3;NS=48;CA=0;DP=238 1 3632891 . GGATTG GG 46 PASS AF=0.024415;HP=2;NF=4;NR=2;NS=49;CA=0;DP=381 1 3633325 . CG CGATGGATGGGTGG 100 PASS AF=0.870192;HP=1;NF=3;NR=4;NS=52;CA=0;DP=751 1 3635416 rs3034587;-/CTCTCT,mills,venter AA AAGAGAGA 100 PASS AF=0.707697;HP=3;DB;NF=37;NR=27;NS=52;CA=0;DP=538 1 3643833 . AC ACCC 25 PASS AF=0.0664372;HP=1;NF=3;NR=3;NS=51;CA=0;DP=511 1 3648954 rs3216059;-/G AG AGG 100 PASS AF=0.42719;HP=4;DB;NF=35;NR=35;NS=51;CA=0;DP=551 1 3660684 . GA GCA 100 PASS AF=0.136632;HP=1;NF=2;NR=10;NS=49;CA=0;DP=480 1 3663009 rs35440871;-/AA CAAG CG 100 PASS AF=0.2595;HP=2;DB;NF=19;NR=14;NS=51;CA=0;DP=498 1 3665663 rs60798590;-/TATTTAAAAAT,watson CA CAATTATTTAAAA 33 PASS AF=0.0338921;HP=2;DB;NF=8;NR=3;NS=51;CA=0;DP=388 1 3665995 . TTTGAAACT TT 33 PASS AF=0.00986571;HP=4;NF=1;NR=3;NS=52;CA=0;DP=507 1 3668078 . AGG AG 100 PASS AF=0.341281;HP=8;NF=21;NR=29;NS=52;CA=0;DP=467 1 3677245 rs36002367;-/AG AAGA AA 100 PASS AF=0.137474;HP=3;DB;NF=6;NR=10;NS=52;CA=0;DP=521 1 3680208 . TG TGG 10 PASS AF=0.0239017;HP=1;NF=7;NR=5;NS=51;CA=0;DP=448 1 3681294 venter CC CGCAC 100 PASS AF=0.200075;HP=8;NF=7;NR=2;NS=50;CA=0;DP=245 1 3682989 rs35616712;-/C TCC TC 100 PASS AF=0.0813904;HP=3;DB;NF=9;NR=3;NS=51;CA=0;DP=447 1 3684305 venter CG CGG 100 PASS AF=0.0596707;HP=3;NF=4;NR=6;NS=51;CA=0;DP=416 1 3686623 rs35661250;-/AG CA CAGA 100 PASS AF=0.0609898;HP=1;DB;NF=5;NR=6;NS=52;CA=0;DP=626 1 3691009 rs35756038;-/A,venter CAA CA 100 PASS AF=0.444393;HP=2;DB;NF=24;NR=32;NS=52;CA=0;DP=562 1 3696676 . CCTG CG 100 PASS AF=0.102585;HP=4;NF=7;NR=6;NS=52;CA=0;DP=502 1 3697316 rs34679063;-/C,venter GC GCC 100 PASS AF=0.8246;HP=1;DB;NF=51;NR=32;NS=52;CA=0;DP=438 1 3704105 . TT TTAATTTTTATATTAACCGTGTTAATAT 100 PASS AF=0.377269;HP=2;NF=17;NR=26;NS=52;CA=0;DP=476 1 3708451 watson TG TGGAGG 43 PASS AF=0.0406373;HP=2;NF=3;NR=4;NS=52;CA=0;DP=587 1 3710853 rs35447451;-/G,venter AG AGG 100 PASS AF=0.272856;HP=4;DB;NF=25;NR=31;NS=52;CA=0;DP=507 1 3711553 rs36007194;-/T AT ATT 100 PASS AF=0.093968;HP=10;DB;NF=11;NR=13;NS=52;CA=0;DP=515 1 3712668 rs35364504;-/GA,venter GGAG GG 100 PASS AF=0.369523;HP=5;DB;NF=18;NR=34;NS=51;CA=0;DP=320 1 3713867 venter TTTTATTTAT TT 100 PASS AF=0.301438;HP=5;NF=21;NR=36;NS=49;CA=0;DP=294 1 3714365 rs58666367;-/CTCAT,venter,watson GA GATCTCA 100 PASS AF=0.431722;HP=1;DB;NF=24;NR=17;NS=52;CA=0;DP=484 1 3721514 rs3838969;-/A,venter CG CTG 100 PASS AF=0.472733;HP=2;DB;NF=27;NR=26;NS=52;CA=0;DP=461 1 3726918 rs34085838;-/G CG CGG 100 PASS AF=0.242958;HP=1;DB;NF=17;NR=14;NS=52;CA=0;DP=479 1 3728638 rs61301856;-/GA,venter,watson TGAG TG 100 PASS AF=0.446341;HP=1;DB;NF=54;NR=33;NS=52;CA=0;DP=666 1 3729131 rs56900717;-/A TT TAT 100 PASS AF=0.489357;HP=2;DB;NF=33;NR=22;NS=52;CA=0;DP=466 1 3733293 rs5772126;-/G,venter TG TGG 100 PASS AF=0.701257;HP=2;DB;NF=17;NR=26;NS=51;CA=0;DP=451 1 3733413 . CA CAA 100 PASS AF=0.107016;HP=5;NF=12;NR=16;NS=52;CA=0;DP=523 1 3735276 venter TA TAAA 100 PASS AF=0.491527;HP=1;NF=29;NR=33;NS=52;CA=0;DP=477 1 3737219 rs61056063;-/A AGA AA 11 PASS AF=0.205567;HP=1;DB;NF=13;NR=6;NS=51;CA=0;DP=431 1 3740075 rs35801288;-/C ACA AA 100 PASS AF=0.438207;HP=1;DB;NF=35;NR=12;NS=52;CA=0;DP=395 1 3741588 rs34966926;-/T,venter GT GTT 100 PASS AF=0.212825;HP=10;DB;NF=21;NR=22;NS=51;CA=0;DP=541 1 3748510 mills TTTTTTAT TT 53 PASS AF=0.0323102;HP=7;NF=21;NR=15;NS=51;CA=0;DP=420 1 3759325 . CG CGGCCAAGGAG 100 PASS AF=0.391954;HP=2;NF=19;NR=18;NS=52;CA=0;DP=465 1 3759824 . CG CGGG 22 PASS AF=0.0355289;HP=5;NF=4;NR=8;NS=52;CA=0;DP=591 1 3760224 rs61309375;-/A,venter CAG CG 100 PASS AF=0.303624;HP=1;DB;NF=27;NR=13;NS=51;CA=0;DP=447 1 3773150 . CTT CT 12 NoQCALL AF=0.0786801;HP=2;NF=1;NR=9;NS=52;CA=0;DP=540 1 3774838 . GT GTT 11 PASS AF=0.0109686;HP=1;NF=2;NR=1;NS=52;CA=0;DP=492 1 3774974 venter CG CTG 100 PASS AF=0.552417;HP=1;NF=26;NR=38;NS=52;CA=0;DP=559 1 3776839 . TGG TG 100 PASS AF=0.0926011;HP=3;NF=5;NR=5;NS=52;CA=0;DP=441 1 3780438 venter CT CTTT 100 PASS AF=0.113197;HP=2;NF=10;NR=13;NS=52;CA=0;DP=654 1 3780687 rs34664006;-/G TGT TT 50 PASS AF=0.0614825;HP=1;DB;NF=4;NR=8;NS=50;CA=M;DP=299 1 3784253 venter ACTGTGCCGGCTTTCTATTC AC 100 PASS AF=0.0567473;HP=1;NF=81;NR=75;NS=52;CA=0;DP=627 1 3786092 . TACTCA TA 100 PASS AF=0.0330531;HP=1;NF=1;NR=6;NS=52;CA=0;DP=497 1 3788460 rs35600694;-/ATA,watson CA CAATA 100 PASS AF=0.42686;HP=1;DB;NF=20;NR=17;NS=51;CA=0;DP=533 1 3788666 rs34172576;-/T,venter GT GTT 100 PASS AF=0.481873;HP=1;DB;NF=26;NR=12;NS=52;CA=0;DP=409 1 3804956 rs60302317;-/CAACA AACAACA AA 46 PASS AF=0.0866272;HP=2;DB;NF=6;NR=2;NS=52;CA=M;DP=556 1 3805210 rs58663935;-/AAAG CA CAAAGA 100 PASS AF=0.0920558;HP=3;DB;NF=9;NR=2;NS=52;CA=0;DP=523 1 3805480 . GAA GA 55 PASS AF=0.0675729;HP=8;NF=13;NR=11;NS=52;CA=0;DP=539 1 3805914 . CCAGACACTGGCACCCCCCTTC CC 100 PASS AF=0.0288464;HP=2;NF=5;NR=4;NS=52;CA=0;DP=613 1 3806447 rs35704040;-/C,mills GCC GC 100 PASS AF=0.0700176;HP=6;DB;NF=4;NR=8;NS=52;CA=0;DP=350 1 3807398 rs35759189;-/G,venter AGG AG 100 PASS AF=0.324114;HP=3;DB;NF=21;NR=8;NS=50;CA=0;DP=355 1 3808303 venter GT GTTCTTTTCTTT 100 PASS AF=0.475205;HP=2;NF=19;NR=9;NS=52;CA=0;DP=264 1 3809301 . TACA TA 100 PASS AF=0.028676;HP=1;NF=26;NR=22;NS=52;CA=0;DP=553 1 3813066 rs34938659;-/T ATT AT 100 PASS AF=0.131264;HP=2;DB;NF=8;NR=6;NS=52;CA=0;DP=521 1 3814885 . TCACACACACACACACAC TC 34 PASS AF=0.149965;HP=1;NF=6;NR=2;NS=52;CA=M;DP=644 1 3818483 . AC ACC 29 PASS AF=0.0676027;HP=3;NF=1;NR=7;NS=50;CA=0;DP=412 1 3820456 . TGG TG 12 PASS AF=0.0215117;HP=4;NF=5;NR=1;NS=51;CA=0;DP=417 1 3824944 . GCTC GC 100 PASS AF=0.174164;HP=1;NF=9;NR=17;NS=50;CA=0;DP=277 1 3825911 . CG CGGGGGG 100 PASS AF=0.29134;HP=2;NF=24;NR=12;NS=52;CA=0;DP=514 1 3827024 . TTCCCT TT 16 PASS AF=0.0318298;HP=2;NF=34;NR=70;NS=51;CA=M;DP=394 1 3827604 . TG TGG 40 PASS AF=0.0159039;HP=1;NF=2;NR=5;NS=52;CA=0;DP=571 1 3833062 watson TC TCCACC 100 PASS AF=0.312659;HP=2;NF=17;NR=16;NS=52;CA=0;DP=463 1 3833266 venter,watson AT ATCAGT 100 PASS AF=0.497122;HP=1;NF=10;NR=19;NS=51;CA=0;DP=412 1 3833395 . CTATCTT CT 24 PASS AF=0.0218407;HP=1;NF=7;NR=3;NS=50;CA=0;DP=400 1 3833485 . GTCTAT GT 100 PASS AF=0.417779;HP=1;NF=11;NR=12;NS=50;CA=0;DP=323 1 3833578 watson TTATCT TT 100 PASS AF=0.329625;HP=2;NF=27;NR=26;NS=51;CA=0;DP=388 1 3833880 watson CA CATCTA 100 PASS AF=0.347946;HP=1;NF=11;NR=13;NS=52;CA=0;DP=458 1 3906706 . TGG TG 100 PASS AF=0.149111;HP=3;NF=11;NR=9;NS=52;CA=0;DP=498 1 3907565 rs34088401;-/C,mills TCC TC 100 PASS AF=0.191109;HP=6;DB;NF=11;NR=14;NS=51;CA=0;DP=478 1 3909253 . AC ACC 100 PASS AF=0.0974891;HP=2;NF=10;NR=9;NS=52;CA=0;DP=591 1 3909917 rs35302885;-/T,venter CTT CT 100 PASS AF=0.766256;HP=7;DB;NF=45;NR=61;NS=52;CA=0;DP=605 1 3916501 rs55698528;-/A,venter GA GAA 100 PASS AF=0.624637;HP=1;DB;NF=37;NR=28;NS=52;CA=0;DP=488 1 3920626 rs59758170;-/TAAATAAATA AATAAATAAATA AA 100 PASS AF=0.276985;HP=3;DB;NF=6;NR=6;NS=50;CA=M;DP=308 1 3923069 . TCG TG 100 PASS AF=0.224119;HP=1;NF=23;NR=7;NS=52;CA=0;DP=488 1 3925431 rs34400281;-/T,venter CTT CT 100 PASS AF=0.372459;HP=2;DB;NF=14;NR=10;NS=51;CA=0;DP=500 1 3933527 . ATTCCCCACAGTGTCTATGGGGACTCTAGCACGGTCAGGGACCCT AT 100 PASS AF=0.0367516;HP=2;NF=29;NR=33;NS=51;CA=0;DP=622 1 3934862 venter GCAC GC 100 PASS AF=0.565308;HP=1;NF=47;NR=42;NS=51;CA=0;DP=648 1 3935044 . TCAC TC 40 PASS AF=0.0156518;HP=1;NF=25;NR=8;NS=52;CA=0;DP=717 1 3937578 rs56700097;-/A,venter TG TAG 100 PASS AF=0.540707;HP=1;DB;NF=40;NR=17;NS=52;CA=0;DP=392 1 3938627 rs58820377;-/ATAG TTAGAT TT 100 PASS AF=0.0846429;HP=2;DB;NF=10;NR=11;NS=52;CA=0;DP=489 1 3945777 . CAGA CA 100 PASS AF=0.442957;HP=1;NF=49;NR=35;NS=52;CA=M;DP=511 1 3967107 venter GAGAA GA 100 PASS AF=0.226936;HP=1;NF=10;NR=15;NS=52;CA=0;DP=543 1 3971955 rs56102422;-/T AT ATT 100 PASS AF=0.275646;HP=10;DB;NF=12;NR=15;NS=52;CA=0;DP=477 1 3973109 rs56883229;-/T,venter ATT AT 100 PASS AF=0.374332;HP=8;DB;NF=7;NR=38;NS=52;CA=0;DP=398 1 3974590 . ATT AT 100 PASS AF=0.373956;HP=8;NF=19;NR=19;NS=51;CA=0;DP=352 1 3976220 . TTCCAGCTGTTGGACTGGCAAACAGT TT 100 PASS AF=0.155908;HP=3;NF=51;NR=67;NS=52;CA=0;DP=702 1 3983232 . GC GCC 100 PASS AF=0.153929;HP=3;NF=2;NR=12;NS=51;CA=0;DP=479 1 3989673 rs34117538;-/T CTT CT 100 PASS AF=0.138005;HP=7;DB;NF=10;NR=16;NS=52;CA=0;DP=480 1 3991472 . GT GTT 41 PASS AF=0.0921994;HP=10;NF=23;NR=19;NS=52;CA=0;DP=490 1 3995340 . GAATA GA 100 PASS AF=0.126804;HP=2;NF=18;NR=25;NS=51;CA=0;DP=456 1 3995701 rs35842317;-/A GA GAA 100 PASS AF=0.287765;HP=3;DB;NF=16;NR=28;NS=52;CA=0;DP=515 1 3998289 rs34690250;-/C AT ATT 31 PASS AF=0.0505667;HP=1;DB;NF=5;NR=6;NS=50;CA=0;DP=373 1 3998556 rs35439065;-/C,venter AC ACC 100 PASS AF=0.152989;HP=1;DB;NF=17;NR=4;NS=52;CA=0;DP=565 1 4003805 . CCCTTC CC 100 PASS AF=0.497734;HP=3;NF=13;NR=9;NS=52;CA=M;DP=357 1 4004467 . TA TAA 100 PASS AF=0.178845;HP=10;NF=39;NR=12;NS=52;CA=0;DP=482 1 4005161 . AAGA AA 10 PASS AF=0.109604;HP=8;NF=5;NR=3;NS=52;CA=0;DP=418 1 4009724 . GGAGAGGGAGAAG GG 100 PASS AF=0.0443217;HP=4;NF=7;NR=9;NS=51;CA=0;DP=347 1 4010638 rs59300943;-/T CT CTT 100 PASS AF=0.238748;HP=5;DB;NF=17;NR=13;NS=52;CA=0;DP=424 1 4018608 . GGGAG GG 14 PASS AF=0.0210215;HP=3;NF=11;NR=22;NS=52;CA=0;DP=439 1 4020045 rs60135555;-/AAA,venter TA TAAAA 55 PASS AF=0.669408;HP=9;DB;NF=19;NR=3;NS=52;CA=0;DP=315 1 4021381 . CTGGGAAC CC 26 PASS AF=0.0682584;HP=1;NF=1;NR=7;NS=52;CA=0;DP=500 1 4022270 . TG TCG 59 PASS AF=0.0269606;HP=6;NF=2;NR=3;NS=52;CA=0;DP=522 1 4022431 rs58149124;-/CC,watson TC TCCC 100 PASS AF=0.833755;HP=1;DB;NF=29;NR=41;NS=52;CA=0;DP=574 1 4024133 rs56013829;-/GTCA,venter ACAGTC AC 100 PASS AF=0.444062;HP=1;DB;NF=29;NR=25;NS=52;CA=0;DP=599 1 4024168 rs56372495;-/AC,venter TCAC TC 100 PASS AF=0.370935;HP=1;DB;NF=14;NR=39;NS=52;CA=0;DP=645 1 4024408 rs55816119;-/TT,watson TC TCAC 100 PASS AF=0.479654;HP=1;DB;NF=17;NR=29;NS=52;CA=0;DP=726 1 4024524 . ACTC AC 100 PASS AF=0.220192;HP=1;NF=11;NR=5;NS=52;CA=0;DP=721 1 4024673 . TT TTCACT 100 PASS AF=0.173855;HP=2;NF=11;NR=13;NS=52;CA=0;DP=887 1 4024704 . TCAG TG 100 PASS AF=0.0291681;HP=1;NF=6;NR=1;NS=52;CA=0;DP=750 1 4024735 venter TC TCAC 100 PASS AF=0.247468;HP=1;NF=19;NR=5;NS=52;CA=0;DP=775 1 4024928 . CTCAGT CT 100 PASS AF=0.0974879;HP=1;NF=11;NR=7;NS=52;CA=0;DP=919 1 4025065 . TCAC TC 100 PASS AF=0.273013;HP=1;NF=7;NR=12;NS=52;CA=0;DP=714 1 4025127 . ACTC AC 100 PASS AF=0.380734;HP=1;NF=17;NR=20;NS=52;CA=M;DP=574 1 4025165 . TC TCACTCAC 100 PASS AF=0.0820414;HP=1;NF=1;NR=9;NS=52;CA=M;DP=574 1 4025232 watson TC TCAC 100 PASS AF=0.631924;HP=1;NF=15;NR=11;NS=52;CA=M;DP=459 1 4025339 . TTCACT TT 53 PASS AF=0.159738;HP=2;NF=17;NR=14;NS=51;CA=0;DP=609 1 4025399 . CA CATA 100 PASS AF=0.0862676;HP=1;NF=4;NR=7;NS=52;CA=0;DP=506 1 4025472 . CA CATTTA 39 PASS AF=0.0270865;HP=1;NF=2;NR=1;NS=52;CA=0;DP=538 1 4025543 venter,watson TC TCAC 100 PASS AF=0.26036;HP=1;NF=9;NR=12;NS=52;CA=0;DP=482 1 4025589 . AC ACTC 53 PASS AF=0.0696821;HP=1;NF=1;NR=1;NS=52;CA=0;DP=575 1 4025678 watson TACTCA TA 100 PASS AF=0.299176;HP=1;NF=14;NR=7;NS=52;CA=0;DP=549 1 4025718 . CATT CT 100 PASS AF=0.0815807;HP=1;NF=8;NR=6;NS=52;CA=0;DP=570 1 4025810 watson TC TCAC 100 PASS AF=0.240222;HP=1;NF=8;NR=8;NS=52;CA=0;DP=442 1 4025920 . ACTCACACTC AC 15 PASS AF=0.0440807;HP=1;NF=5;NR=6;NS=52;CA=0;DP=439 1 4025988 . ATCACT AT 100 PASS AF=0.115745;HP=1;NF=7;NR=3;NS=52;CA=M;DP=409 1 4026021 . ATTCGC AC 19 PASS AF=0.0230633;HP=2;NF=4;NR=4;NS=52;CA=0;DP=408 1 4026091 . ACAGTC AC 100 PASS AF=0.239672;HP=1;NF=10;NR=12;NS=52;CA=0;DP=418 1 4026188 . GTCACTCGTT GT 100 PASS AF=0.0942528;HP=1;NF=17;NR=15;NS=51;CA=M;DP=704 1 4026243 . AC ACTCACTC 100 PASS AF=0.0701669;HP=1;NF=8;NR=2;NS=52;CA=0;DP=852 1 4026341 . AC ACTC 100 PASS AF=0.180464;HP=1;NF=7;NR=12;NS=52;CA=0;DP=797 1 4026433 . AC ACTCACAGTC 100 PASS AF=0.0755971;HP=1;NF=10;NR=4;NS=52;CA=0;DP=727 1 4026489 . CCACTC CC 100 PASS AF=0.152175;HP=2;NF=20;NR=14;NS=52;CA=0;DP=896 1 4026521 . AT ACT 18 PASS AF=0.0348752;HP=1;NF=8;NR=8;NS=52;CA=0;DP=896 1 4026676 . ACACTC AC 100 PASS AF=0.345964;HP=1;NF=25;NR=27;NS=52;CA=0;DP=805 1 4026745 . ACTC AC 100 PASS AF=0.277096;HP=1;NF=6;NR=11;NS=52;CA=0;DP=625 1 4026831 . AC ACTC 100 PASS AF=0.158736;HP=1;NF=13;NR=9;NS=52;CA=0;DP=585 1 4026904 . TACTCA TA 59 PASS AF=0.094457;HP=1;NF=7;NR=4;NS=52;CA=0;DP=594 1 4026996 . TT TTCACT 100 PASS AF=0.0816069;HP=2;NF=19;NR=16;NS=52;CA=0;DP=668 1 4027100 watson GT GTCACT 100 PASS AF=0.51624;HP=1;NF=22;NR=20;NS=52;CA=0;DP=958 1 4027153 . AC ACTCACACTC 100 PASS AF=0.221157;HP=1;NF=11;NR=7;NS=52;CA=0;DP=694 1 4027249 . ACACTCGCTCAGTC AC 100 PASS AF=0.191741;HP=1;NF=20;NR=16;NS=52;CA=0;DP=528 1 4027301 . TCAC TC 100 PASS AF=0.21653;HP=1;NF=6;NR=9;NS=52;CA=0;DP=511 1 4027378 . TT TTCACT 100 PASS AF=0.23813;HP=2;NF=19;NR=16;NS=52;CA=0;DP=565 1 4027440 . TT TTCACT 100 PASS AF=0.351897;HP=2;NF=28;NR=13;NS=52;CA=0;DP=736 1 4031776 venter,watson GC GCTGCTCC 100 PASS AF=0.57914;HP=1;NF=17;NR=13;NS=52;CA=0;DP=475 1 4046995 rs60127181;-/ATG,watson GC GGATC 100 PASS AF=0.863384;HP=1;DB;NF=37;NR=32;NS=51;CA=0;DP=427 1 4053051 . AC AACC 10 PASS AF=0.0731381;HP=1;NF=2;NR=3;NS=52;CA=0;DP=453 1 4056743 rs57501900;-/T,venter ATT AT 100 PASS AF=0.863012;HP=6;DB;NF=63;NR=45;NS=52;CA=0;DP=485 1 4078234 venter,watson CTGCCTGTGTGAGCAAGAT CT 100 PASS AF=0.308447;HP=1;NF=26;NR=18;NS=52;CA=0;DP=484 1 4080449 rs35774756;-/T GTT GT 100 PASS AF=0.285891;HP=2;DB;NF=20;NR=24;NS=51;CA=0;DP=526 1 4082493 rs35701497;-/G CGG CG 100 PASS AF=0.277913;HP=4;DB;NF=14;NR=16;NS=52;CA=0;DP=416 1 4086137 . CA CTA 100 PASS AF=0.0260425;HP=1;NF=4;NR=2;NS=52;CA=0;DP=569 1 4088196 . TTCT TT 100 PASS AF=0.0658972;HP=3;NF=67;NR=77;NS=51;CA=B;DP=647 1 4091673 rs56198003;-/TTA GTTAT GT 100 PASS AF=0.0274099;HP=2;DB;NF=4;NR=7;NS=52;CA=0;DP=489 1 4093407 rs35442233;-/G,venter TGG TG 100 PASS AF=0.056726;HP=4;DB;NF=4;NR=5;NS=51;CA=0;DP=432 1 4097902 rs5772141;-/ATT,mills,venter,watson CA CATTA 100 PASS AF=0.999995;HP=1;DB;NF=38;NR=34;NS=52;CA=0;DP=432 1 4106716 . AC ACACACACACACGC 100 PASS AF=0.316911;HP=1;NF=1;NR=1;NS=52;CA=0;DP=601 1 4114274 rs60603556;-/CAT,watson AATCA AA 100 PASS AF=0.135224;HP=3;DB;NF=17;NR=9;NS=51;CA=0;DP=587 1 4114592 rs56285575;-/ACA,venter AAACA AA 100 PASS AF=0.254759;HP=3;DB;NF=21;NR=18;NS=52;CA=0;DP=554 1 4114812 . TTAT TT 33 PASS AF=0.14738;HP=3;NF=5;NR=4;NS=52;CA=0;DP=411 1 4114996 . AA AATTATTA 11 PASS AF=0.228122;HP=2;NF=26;NR=29;NS=49;CA=0;DP=276 1 4120825 . GAA GA 43 PASS AF=0.147904;HP=2;NF=11;NR=17;NS=51;CA=0;DP=328 1 4121802 . ATGT AT 11 PASS AF=0.0113836;HP=1;NF=24;NR=16;NS=52;CA=0;DP=570 1 4131826 . ATTGTTT AT 100 PASS AF=0.999996;HP=2;NF=38;NR=35;NS=52;CA=0;DP=456 1 4134659 rs35271731;-/G TG TGG 100 PASS AF=0.417516;HP=5;DB;NF=21;NR=19;NS=52;CA=0;DP=429 1 4139315 rs35859581;-/T,venter GT GTT 100 PASS AF=0.371694;HP=2;DB;NF=12;NR=16;NS=52;CA=0;DP=444 1 4144542 . CAA CA 100 PASS AF=0.0915309;HP=2;NF=7;NR=8;NS=52;CA=M;DP=461 1 4149378 rs35644791;-/CCT,venter,watson AC ACCTC 100 PASS AF=0.955034;HP=2;DB;NF=35;NR=24;NS=52;CA=0;DP=461 1 4150078 . ATC AC 100 PASS AF=0.0248618;HP=1;NF=3;NR=1;NS=52;CA=0;DP=489 1 4158176 rs61115653;-/A CA CAA 100 PASS AF=0.109858;HP=9;DB;NF=9;NR=8;NS=52;CA=0;DP=480 1 4158371 rs35550030;-/G AGA AA 100 PASS AF=0.282272;HP=1;DB;NF=22;NR=13;NS=52;CA=0;DP=508 1 4160853 . AG AGTG 100 PASS AF=0.883963;HP=1;NF=52;NR=40;NS=52;CA=0;DP=475 1 4163479 rs35439066;-/T,venter ATT AT 100 PASS AF=0.421487;HP=7;DB;NF=35;NR=40;NS=52;CA=0;DP=580 1 4165518 rs5772143;-/A,mills CAT CT 100 PASS AF=0.0997002;HP=1;DB;NF=8;NR=9;NS=52;CA=0;DP=569 1 4168412 . TG TGG 100 PASS AF=0.0597927;HP=5;NF=7;NR=5;NS=50;CA=0;DP=411 1 4174019 . CCTTTC CC 100 PASS AF=0.223832;HP=2;NF=5;NR=11;NS=51;CA=M;DP=369 1 4176371 rs5772145;-/GGGCT,mills,venter,watson GG GGGGCTG 100 PASS AF=0.965127;HP=4;DB;NF=37;NR=39;NS=51;CA=0;DP=577 1 4180359 rs35134459;-/T,venter CG CTG 100 PASS AF=0.994644;HP=2;DB;NF=70;NR=40;NS=52;CA=0;DP=510 1 4198168 . GCCATTTACATCCCACC GC 100 PASS AF=0.0947023;HP=2;NF=47;NR=53;NS=52;CA=0;DP=625 1 4203370 . TCAC TC 22 PASS AF=0.151126;HP=1;NF=40;NR=22;NS=51;CA=0;DP=481 1 4224147 . ATGT AT 100 PASS AF=0.459042;HP=1;NF=45;NR=57;NS=52;CA=0;DP=508 1 4236168 venter,watson GT GTCCTGTT 100 PASS AF=0.465028;HP=1;NF=21;NR=21;NS=51;CA=0;DP=473 1 4238553 . TAG TG 100 PASS AF=0.0884036;HP=1;NF=3;NR=3;NS=52;CA=0;DP=313 1 4243904 . TG TGGGGG 28 PASS AF=0.177328;HP=1;NF=6;NR=9;NS=52;CA=0;DP=598 1 4252300 . AATTTA AA 27 PASS AF=0.0160294;HP=2;NF=16;NR=12;NS=52;CA=0;DP=550 1 4256051 . CC CCTCAC 100 PASS AF=0.423907;HP=2;NF=10;NR=6;NS=52;CA=M;DP=450 1 4256251 rs56817136;-/AATCCATC TC TCATCAATCC 27 PASS AF=0.483921;HP=1;DB;NF=24;NR=28;NS=52;CA=M;DP=501 1 4256338 rs59859709;-/CCAT CCCATC CC 100 PASS AF=0.420087;HP=3;DB;NF=47;NR=73;NS=52;CA=0;DP=510 1 4258560 rs35749795;-/G,venter TGG TG 100 PASS AF=0.563751;HP=3;DB;NF=30;NR=43;NS=52;CA=0;DP=533 1 4270968 rs5772150;-/A,mills,venter TAA TA 100 PASS AF=0.863858;HP=2;DB;NF=66;NR=65;NS=52;CA=0;DP=554 1 4272781 rs34523387;-/CA,venter,watson TCAC TC 100 PASS AF=0.221206;HP=1;DB;NF=55;NR=32;NS=52;CA=0;DP=555 1 4276688 rs56762609;-/A CA CAA 25 PASS AF=0.0168189;HP=4;DB;NF=5;NR=7;NS=52;CA=0;DP=567 1 4278344 rs33957131;-/A,mills TAT TT 100 PASS AF=0.260307;HP=1;DB;NF=13;NR=14;NS=52;CA=M;DP=390 1 4280264 rs35972891;-/G,venter TG TGG 100 PASS AF=0.36321;HP=6;DB;NF=16;NR=21;NS=52;CA=0;DP=487 1 4280920 rs3058085;-/AGA,mills,venter,watson AT ATCTT 100 PASS AF=0.75024;HP=1;DB;NF=34;NR=50;NS=52;CA=0;DP=518 1 4281851 rs59086076;-/TTGT CTGTTT CT 100 PASS AF=0.15371;HP=1;DB;NF=12;NR=13;NS=52;CA=0;DP=454 1 4287207 rs3986843;-/CCT CA CAGGA 100 PASS AF=0.100002;HP=1;DB;NF=8;NR=1;NS=52;CA=0;DP=451 1 4289708 . GTGTTAG GG 37 PASS AF=0.0904846;HP=1;NF=3;NR=9;NS=52;CA=0;DP=447 1 4291813 . CGC CC 41 PASS AF=0.05598;HP=1;NF=1;NR=9;NS=52;CA=0;DP=504 1 4291856 rs33950418;-/C,mills ACA AA 53 PASS AF=0.0424203;HP=1;DB;NF=2;NR=10;NS=52;CA=M;DP=504 1 4292024 rs33982329;-/CA,mills CG CATG 100 PASS AF=0.0974178;HP=1;DB;NF=14;NR=14;NS=52;CA=0;DP=697 1 4296830 . CTT CT 100 PASS AF=0.101792;HP=2;NF=15;NR=4;NS=52;CA=0;DP=805 1 4298115 rs34054009;-/G,venter AG AGG 100 PASS AF=0.314255;HP=2;DB;NF=25;NR=10;NS=52;CA=0;DP=565 1 4310246 rs35999105;-/A TA TAA 100 PASS AF=0.229765;HP=5;DB;NF=23;NR=13;NS=52;CA=0;DP=488 1 4310305 venter GA GAA 39 PASS AF=0.078696;HP=9;NF=15;NR=5;NS=52;CA=0;DP=455 1 4312461 . GAAAGAAA GA 24 PASS AF=0.0372797;HP=3;NF=23;NR=6;NS=52;CA=M;DP=401 1 4313453 . GG GTG 23 PASS AF=0.026167;HP=2;NF=2;NR=5;NS=52;CA=0;DP=614 1 4315016 rs34078493;-/T,venter CT CTT 100 PASS AF=0.459017;HP=1;DB;NF=25;NR=37;NS=52;CA=0;DP=493 1 4316236 rs35864764;-/TC ATCT AT 100 PASS AF=0.164629;HP=1;DB;NF=18;NR=15;NS=52;CA=0;DP=434 1 4317119 rs35907112;-/AG AAGA AA 100 PASS AF=0.210583;HP=3;DB;NF=19;NR=13;NS=52;CA=0;DP=652 1 4319781 rs34098980;-/AAAAA,mills,venter CC CAAAAAC 100 PASS AF=0.451406;HP=2;DB;NF=9;NR=1;NS=52;CA=0;DP=605 1 4323411 . GT GTT 41 PASS AF=0.0448346;HP=6;NF=4;NR=5;NS=52;CA=0;DP=498 1 4326343 . CG CGGGGGGGGGGG 100 PASS AF=0.212625;HP=2;NF=5;NR=11;NS=52;CA=0;DP=475 1 4329138 . GTGAT GT 47 PASS AF=0.0168095;HP=1;NF=35;NR=37;NS=52;CA=0;DP=675 1 4329500 venter ATGGTGATGGT AT 100 PASS AF=0.0491;HP=1;NF=35;NR=49;NS=52;CA=0;DP=718 1 4333035 . CCACTC CC 100 PASS AF=0.0536691;HP=2;NF=18;NR=17;NS=52;CA=0;DP=614 1 4333090 . CCCATC CC 100 PASS AF=0.896174;HP=3;NF=52;NR=56;NS=52;CA=0;DP=564 1 4333868 rs34013096;-/CCAT AC ACCATC 100 PASS AF=0.411752;HP=2;DB;NF=63;NR=59;NS=52;CA=0;DP=556 1 4352929 . TAA TA 100 PASS AF=0.0606075;HP=5;NF=10;NR=5;NS=51;CA=0;DP=422 1 4360308 . CAA CA 100 PASS AF=0.160821;HP=3;NF=12;NR=13;NS=52;CA=0;DP=502 1 4360675 rs55750624;-/A GAA GA 100 PASS AF=0.209252;HP=2;DB;NF=18;NR=10;NS=52;CA=0;DP=456 1 4362123 rs57250327;-/AAATT TA TAATTAA 100 PASS AF=0.202867;HP=2;DB;NF=23;NR=24;NS=52;CA=0;DP=404 1 4372014 rs34773421;-/A,venter TAA TA 100 PASS AF=0.507594;HP=2;DB;NF=43;NR=31;NS=52;CA=0;DP=496 1 4373092 . CATTTA CA 100 PASS AF=0.155807;HP=1;NF=19;NR=10;NS=52;CA=0;DP=440 1 4375952 . TCT TT 100 PASS AF=0.0215948;HP=1;NF=3;NR=2;NS=52;CA=0;DP=530 1 4376164 rs57973702;-/TG,venter CG CGTG 100 PASS AF=0.555727;HP=1;DB;NF=33;NR=60;NS=52;CA=0;DP=552 1 4382255 . GT GTT 100 PASS AF=0.134524;HP=8;NF=12;NR=14;NS=52;CA=0;DP=445 1 4382929 . CG CGCCGTGCCCTGCTCAG 100 PASS AF=0.293977;HP=1;NF=3;NR=1;NS=52;CA=0;DP=423 1 4386769 rs34696074;-/G TGG TG 100 PASS AF=0.524405;HP=3;DB;NF=43;NR=31;NS=51;CA=0;DP=586 1 4386900 rs35831569;-/GTGA,watson TG TGTGAG 100 PASS AF=0.786341;HP=1;DB;NF=49;NR=47;NS=52;CA=0;DP=728 1 4387089 rs35106948;-/GA,venter,watson TGAG TG 100 PASS AF=0.76407;HP=1;DB;NF=42;NR=48;NS=52;CA=0;DP=730 1 4398343 rs56075652;-/AGCTAG,mills,venter,watson GGAGCTAG GG 100 PASS AF=0.850798;HP=2;DB;NF=51;NR=52;NS=52;CA=0;DP=535 1 4403445 . ATC AC 100 PASS AF=0.0257077;HP=1;NF=3;NR=3;NS=52;CA=0;DP=579 1 4413424 . GGAAG GG 100 PASS AF=0.0911622;HP=2;NF=13;NR=11;NS=52;CA=0;DP=539 1 4415363 rs35655214;-/A,mills,venter CAA CA 100 PASS AF=0.279808;HP=10;DB;NF=16;NR=13;NS=52;CA=0;DP=623 1 4419729 rs34301403;-/T,venter CT CTT 100 PASS AF=0.276688;HP=3;DB;NF=23;NR=17;NS=52;CA=0;DP=491 1 4429935 . ACC AC 100 PASS AF=0.121066;HP=2;NF=8;NR=7;NS=52;CA=0;DP=509 1 4432975 rs35185885;-/TTAT,venter TT TTTTAT 100 PASS AF=0.370788;HP=4;DB;NF=7;NR=50;NS=51;CA=0;DP=329 1 4433724 . AC ACC 100 PASS AF=0.191535;HP=2;NF=16;NR=17;NS=52;CA=0;DP=609 1 4434361 . GA GATGATATTGAAA 100 PASS AF=0.175787;HP=1;NF=8;NR=5;NS=52;CA=0;DP=496 1 4439328 rs55695069;-/TGTG,watson TGTGAG TG 100 PASS AF=0.115075;HP=1;DB;NF=13;NR=10;NS=51;CA=0;DP=510 1 4444447 . GC GCC 100 PASS AF=0.126735;HP=1;NF=8;NR=6;NS=52;CA=0;DP=442 1 4444562 watson TTCG TG 100 PASS AF=0.167206;HP=3;NF=13;NR=9;NS=52;CA=0;DP=477 1 4448379 rs55971665;-/A,venter GAA GA 100 PASS AF=0.999997;HP=5;DB;NF=29;NR=34;NS=51;CA=0;DP=398 1 4456774 rs34368344;-/CTCA,watson TCTCAC TC 100 PASS AF=0.4985;HP=1;DB;NF=46;NR=35;NS=52;CA=0;DP=679 1 4456823 . TT TTTTCTCTCT 100 PASS AF=0.281015;HP=3;NF=18;NR=7;NS=52;CA=0;DP=566 1 4460399 . CAGA CA 17 PASS AF=0.0162627;HP=1;NF=4;NR=1;NS=52;CA=0;DP=437 1 4461064 . TG TGGG 100 PASS AF=0.136493;HP=8;NF=11;NR=12;NS=52;CA=0;DP=516 1 4461120 . GAGTCA GA 100 PASS AF=0.106497;HP=1;NF=4;NR=10;NS=52;CA=0;DP=513 1 4462914 rs35786528;-/T,venter GTT GT 100 PASS AF=0.636288;HP=9;DB;NF=46;NR=44;NS=52;CA=0;DP=457 1 4464201 rs35933446;-/G AGC AC 100 PASS AF=0.0422945;HP=1;DB;NF=3;NR=5;NS=52;CA=0;DP=559 1 4465553 rs33984734;-/C,mills,venter GCC GC 100 PASS AF=0.832437;HP=3;DB;NF=43;NR=36;NS=52;CA=0;DP=507 1 4465878 rs55781312;-/GAACA,watson TACAGAA TA 100 PASS AF=0.547352;HP=1;DB;NF=48;NR=55;NS=52;CA=0;DP=612 1 4466414 rs34356738;-/T,venter AT ATT 100 PASS AF=0.0343632;HP=4;DB;NF=5;NR=2;NS=52;CA=0;DP=523 1 4468803 . CT CTTTTCTTTTCTTT 100 PASS AF=0.185641;HP=2;NF=2;NR=1;NS=51;CA=0;DP=271 1 4469024 . TT TTGTGT 26 PASS AF=0.65093;HP=2;NF=51;NR=54;NS=51;CA=0;DP=465 1 4470162 rs34280110;-/T,venter CT CTT 100 PASS AF=0.19103;HP=3;DB;NF=13;NR=16;NS=52;CA=0;DP=581 1 4472390 rs35540877;-/AAG TAAGA TA 100 PASS AF=0.0513799;HP=2;DB;NF=4;NR=3;NS=52;CA=0;DP=531 1 4481812 rs34806922;-/A,venter GAA GA 100 PASS AF=0.0356083;HP=3;DB;NF=4;NR=4;NS=52;CA=0;DP=576 1 4482705 . CA CATCTA 100 PASS AF=0.203301;HP=1;NF=34;NR=52;NS=50;CA=M;DP=382 1 4482808 . CTA CA 16 PASS AF=0.0550307;HP=1;NF=1;NR=1;NS=51;CA=M;DP=356 1 4482848 rs5772166;-/TCTCTCTC,mills ATCTCTCTCT AT 100 PASS AF=0.561639;HP=1;DB;NF=52;NR=17;NS=51;CA=M;DP=311 1 4484471 rs3059158;-/CT,mills,watson AG ACTG 100 PASS AF=0.497825;HP=1;DB;NF=31;NR=34;NS=52;CA=0;DP=538 1 4486660 rs34976033;-/CCCT,mills,venter,watson GCTCCC GC 100 PASS AF=0.593551;HP=1;DB;NF=42;NR=55;NS=52;CA=0;DP=566 1 4486840 rs35808993;-/A,venter GAT GT 100 PASS AF=0.0446408;HP=1;DB;NF=4;NR=4;NS=52;CA=0;DP=539 1 4495865 watson TGACCT TT 100 PASS AF=0.477912;HP=1;NF=15;NR=22;NS=52;CA=0;DP=386 1 4498895 . TAAACTCA TA 100 PASS AF=0.365307;HP=3;NF=30;NR=28;NS=52;CA=0;DP=561 1 4499763 . TT TTTTAGTTTAGTTTAGTTTAGTTTAGT 15 PASS AF=0.437504;HP=4;NF=5;NR=8;NS=51;CA=0;DP=440 1 4500994 rs57293099;-/A,venter GG GAG 19 PASS AF=0.533167;HP=5;DB;NF=26;NR=15;NS=51;CA=0;DP=466 1 4501978 rs34937816;-/T,mills,venter GT GTT 100 PASS AF=0.677682;HP=1;DB;NF=47;NR=42;NS=52;CA=0;DP=475 1 4504724 venter,watson TAGACA TA 100 PASS AF=0.381777;HP=1;NF=34;NR=33;NS=52;CA=0;DP=728 1 4504861 venter TACAGAGAGAGACAGAGAGA TA 100 PASS AF=0.208225;HP=1;NF=42;NR=31;NS=52;CA=0;DP=820 1 4506249 rs56013880;-/T,mills,venter GC GTC 100 PASS AF=0.652109;HP=2;DB;NF=41;NR=48;NS=52;CA=0;DP=522 1 4506287 venter TAG TG 100 PASS AF=0.348604;HP=1;NF=23;NR=27;NS=52;CA=0;DP=534 1 4510123 rs35963445;-/C,venter TC TCC 100 PASS AF=0.750939;HP=6;DB;NF=32;NR=50;NS=52;CA=0;DP=488 1 4511427 rs34235356;-/T,venter AT ATT 100 PASS AF=0.559297;HP=8;DB;NF=40;NR=27;NS=52;CA=0;DP=549 1 4512561 rs57315980;-/GAG TGGAG TG 100 PASS AF=0.0276885;HP=2;DB;NF=7;NR=4;NS=52;CA=0;DP=581 1 4512788 rs56318426;-/GGATAGTGTG TC TGTGTGGGATAC 100 PASS AF=0.145759;HP=1;DB;NF=7;NR=6;NS=52;CA=0;DP=570 1 4513234 rs5772168;-/ATCA,venter,watson TA TATCAA 100 PASS AF=0.761132;HP=1;DB;NF=45;NR=38;NS=52;CA=0;DP=478 1 4513552 rs34248962;-/G,venter CTC CC 100 PASS AF=0.397344;HP=1;DB;NF=19;NR=21;NS=52;CA=0;DP=502 1 4518079 . CTTTATGTCAAC CC 31 PASS AF=0.0537494;HP=3;NF=13;NR=6;NS=52;CA=0;DP=567 1 4519870 . CATAA CA 100 PASS AF=0.156873;HP=1;NF=25;NR=19;NS=52;CA=0;DP=518 1 4520552 venter,watson ATATT AT 100 PASS AF=0.0454741;HP=1;NF=13;NR=21;NS=52;CA=0;DP=523 1 4524683 rs60936673;-/A,venter GAC GC 100 PASS AF=0.0433734;HP=1;DB;NF=5;NR=1;NS=51;CA=0;DP=407 1 4531795 . CG CGAGCAGATAG 100 PASS AF=0.0529244;HP=1;NF=2;NR=3;NS=52;CA=0;DP=598 1 4533811 rs61232512;-/TCCCTCCTGGACAGCCAGG,watson TCCTCCTGGACAGCCAGGTCC TC 100 PASS AF=0.455665;HP=2;DB;NF=9;NR=12;NS=52;CA=0;DP=455 1 4535415 rs34971058;-/C,mills,venter GC GCC 100 PASS AF=0.872856;HP=1;DB;NF=71;NR=50;NS=52;CA=0;DP=585 1 4540778 rs5772169;-/T,mills CTG CG 100 PASS AF=0.129616;HP=1;DB;NF=9;NR=6;NS=52;CA=0;DP=518 1 4541031 . TT TTTTCT 100 PASS AF=0.0665496;HP=6;NF=18;NR=24;NS=51;CA=0;DP=371 1 4541492 rs5772170;-/G,mills,venter TG TGG 100 PASS AF=0.912727;HP=3;DB;NF=57;NR=39;NS=52;CA=0;DP=454 1 4542962 . CC CCTCTCTCTCTC 100 PASS AF=0.767807;HP=2;NF=57;NR=35;NS=52;CA=0;DP=481 1 4544333 rs3059964;-/CT,venter ACTC AC 100 PASS AF=0.941425;HP=1;DB;NF=54;NR=73;NS=52;CA=0;DP=591 1 4547027 rs34146010;-/C ACC AC 100 PASS AF=0.974502;HP=2;DB;NF=55;NR=74;NS=52;CA=0;DP=535 1 4547927 rs34056554;-/T,venter ATT AT 100 PASS AF=0.867021;HP=3;DB;NF=7;NR=12;NS=51;CA=0;DP=398 1 4551259 rs34018288;-/TG,venter,watson CT CTGT 100 PASS AF=0.964821;HP=1;DB;NF=25;NR=27;NS=52;CA=0;DP=445 1 4552887 . GT GTCT 100 PASS AF=0.155774;HP=1;NF=6;NR=7;NS=52;CA=0;DP=507 1 4556585 rs3833958;-/GGGCT,venter GA GAGCCCA 100 PASS AF=0.248571;HP=1;DB;NF=9;NR=9;NS=52;CA=0;DP=416 1 4558195 rs58248788;-/T,venter ATT AT 100 PASS AF=0.949748;HP=4;DB;NF=38;NR=18;NS=51;CA=0;DP=446 1 4558625 . AGA AA 100 PASS AF=0.105248;HP=1;NF=12;NR=4;NS=52;CA=0;DP=526 1 4570630 . GT GGGTTT 14 PASS AF=0.0570941;HP=1;NF=4;NR=2;NS=52;CA=0;DP=480 1 4574298 . GC GAC 41 PASS AF=0.0333335;HP=2;NF=1;NR=4;NS=52;CA=0;DP=497 1 4574507 . TT TTCCTCTAATGCT 100 PASS AF=0.406213;HP=2;NF=13;NR=8;NS=52;CA=0;DP=437 1 4577694 rs33988719;-/G,mills,venter TG TGG 100 PASS AF=0.999997;HP=1;DB;NF=52;NR=28;NS=52;CA=0;DP=381 1 4578235 . TAT TT 26 PASS AF=0.292482;HP=1;NF=8;NR=14;NS=51;CA=0;DP=330 1 4580634 . ATAAAATA AA 100 PASS AF=0.328083;HP=1;NF=11;NR=4;NS=51;CA=M;DP=372 1 4581760 . CTT CT 100 PASS AF=0.0551414;HP=2;NF=4;NR=7;NS=52;CA=0;DP=578 1 4583153 rs35427335;-/CA,venter,watson GCAC GC 100 PASS AF=0.0310016;HP=1;DB;NF=3;NR=4;NS=52;CA=0;DP=483 1 4586257 rs34899280;-/T GTC GC 100 PASS AF=0.311452;HP=1;DB;NF=16;NR=8;NS=51;CA=0;DP=441 1 4589959 venter,watson GG GGGCCTG 100 PASS AF=0.0494854;HP=3;NF=3;NR=4;NS=52;CA=0;DP=469 1 4590830 rs34057361;-/GCAAAGC,mills,venter,watson TGCAAAGCG TG 100 PASS AF=0.739178;HP=1;DB;NF=42;NR=52;NS=50;CA=0;DP=465 1 4595540 rs56784481;-/T TCT TT 53 PASS AF=0.154234;HP=1;DB;NF=7;NR=21;NS=52;CA=0;DP=439 1 4596270 . AC ACGCTGAGGCTGCAGCACCCCTCGTGGAGC 100 PASS AF=0.171201;HP=1;NF=6;NR=1;NS=52;CA=0;DP=498 1 4600396 rs36042545;-/AT,venter CATA CA 100 PASS AF=0.185579;HP=1;DB;NF=24;NR=23;NS=52;CA=0;DP=357 1 4603645 rs60786353;-/C,venter AC ACC 100 PASS AF=0.999998;HP=1;DB;NF=76;NR=57;NS=52;CA=0;DP=571 1 4607282 . GTGAT GT 100 PASS AF=0.287968;HP=1;NF=38;NR=26;NS=52;CA=0;DP=810 1 4607435 . GTGAT GT 100 PASS AF=0.347474;HP=1;NF=39;NR=53;NS=52;CA=0;DP=674 1 4611309 . CGTGTG CG 100 PASS AF=0.311775;HP=1;NF=38;NR=31;NS=52;CA=0;DP=486 1 4621966 rs35610947;-/GT TTGT TT 100 PASS AF=0.252136;HP=3;DB;NF=41;NR=42;NS=52;CA=0;DP=612 1 4623256 rs59174221;-/CTCCAGAAAGCAC GGAAAGCACCTCCAG GG 100 PASS AF=0.248792;HP=2;DB;NF=24;NR=28;NS=52;CA=0;DP=458 1 4623618 rs60584333;-/GTGTCGGGAGCAGAGACTG,venter GC GCTGGTGTCGGGAGCAGAGAC 100 PASS AF=0.624955;HP=1;DB;NF=8;NR=16;NS=51;CA=0;DP=518 1 4628242 rs56871532;-/TG,venter,watson CTGT CT 100 PASS AF=0.630417;HP=1;DB;NF=46;NR=41;NS=52;CA=0;DP=605 1 4631325 watson GAGGACATA GA 100 PASS AF=0.0694082;HP=1;NF=14;NR=10;NS=51;CA=0;DP=388 1 4633949 . TCC TC 100 PASS AF=0.223776;HP=7;NF=13;NR=4;NS=51;CA=0;DP=492 1 4637510 . TAAA TA 18 PASS AF=0.0428857;HP=9;NF=13;NR=6;NS=52;CA=0;DP=456 1 4639728 . GGTGTGTGTGTGTGTG GG 56 PASS AF=0.223403;HP=3;NF=39;NR=66;NS=51;CA=0;DP=466 1 4645583 rs59275910;-/G,venter AG AGG 100 PASS AF=0.999998;HP=1;DB;NF=41;NR=59;NS=51;CA=0;DP=416 1 4649824 . CTT CT 100 PASS AF=0.0615007;HP=2;NF=3;NR=3;NS=52;CA=0;DP=371 1 4653490 . GAG GG 19 PASS AF=0.016501;HP=1;NF=1;NR=2;NS=52;CA=0;DP=448 1 4654099 rs3086606;-/GTCTGCA,mills CC CCAGTCTGC 100 PASS AF=0.299705;HP=2;DB;NF=11;NR=10;NS=52;CA=0;DP=440 1 4655877 rs58828516;-/G TG TGG 100 PASS AF=0.083803;HP=6;DB;NF=13;NR=14;NS=52;CA=0;DP=553 1 4656096 rs34592768;-/G,mills TGG TG 100 PASS AF=0.0586852;HP=2;DB;NF=6;NR=4;NS=52;CA=0;DP=486 1 4656943 . GGTGTG GG 53 PASS AF=0.0156574;HP=2;NF=15;NR=18;NS=52;CA=0;DP=804 1 4668803 . CTT CT 39 PASS AF=0.0748695;HP=8;NF=8;NR=6;NS=52;CA=0;DP=401 1 4670089 rs34058244;-/AC,venter GA GACA 100 PASS AF=0.471432;HP=1;DB;NF=47;NR=39;NS=52;CA=0;DP=789 1 4670383 rs35737766;-/TCAC,watson ACACTC AC 100 PASS AF=0.331554;HP=1;DB;NF=20;NR=35;NS=52;CA=0;DP=609 1 4676654 . AGATG AG 10 PASS AF=0.011049;HP=1;NF=15;NR=18;NS=52;CA=0;DP=617 1 4684590 . TCCTGCACCTGCTGTGCCCCTGGCTCCCAGCACC TC 100 PASS AF=0.0368566;HP=2;NF=13;NR=7;NS=52;CA=0;DP=543 1 4689505 . TC TCTGTCCTCTCTCCTAGCTCTGGTGCCCTGAGATGC 100 PASS AF=0.355136;HP=1;NF=2;NR=3;NS=52;CA=0;DP=597 1 4693342 rs3835539;-/TTCA CC CCATTC 100 PASS AF=0.307703;HP=2;DB;NF=60;NR=61;NS=52;CA=0;DP=594 1 4695582 venter TGTGAGG TG 100 PASS AF=0.630317;HP=1;NF=17;NR=29;NS=52;CA=0;DP=408 1 4700273 . GCCT GT 51 PASS AF=0.154012;HP=2;NF=3;NR=3;NS=52;CA=0;DP=402 1 4700727 rs34897087;-/A,venter CG CGG 13 PASS AF=0.0702045;HP=8;DB;NF=22;NR=6;NS=51;CA=M;DP=305 1 4702014 rs34592315;-/AA,venter TAAA TA 100 PASS AF=0.183045;HP=3;DB;NF=9;NR=20;NS=52;CA=0;DP=551 1 4702135 . GCC GC 100 PASS AF=0.132917;HP=5;NF=18;NR=10;NS=52;CA=0;DP=561 1 4702842 rs3835540;-/GAC TGACG TG 100 PASS AF=0.333162;HP=1;DB;NF=25;NR=19;NS=52;CA=0;DP=517 1 4703849 rs35422518;-/TCTCCAGGC,mills,venter,watson AGCTCTCCAGG AG 100 PASS AF=0.461699;HP=1;DB;NF=52;NR=39;NS=52;CA=0;DP=558 1 4704242 . ATT AT 100 PASS AF=0.124811;HP=6;NF=16;NR=12;NS=52;CA=0;DP=518 1 4704545 . GCACAC GC 43 PASS AF=0.374122;HP=1;NF=68;NR=46;NS=52;CA=0;DP=586 1 4709952 rs55677440;-/GT TT TTGT 100 PASS AF=0.111566;HP=3;DB;NF=37;NR=55;NS=52;CA=0;DP=757 1 4712998 rs35177072;-/CTC,mills,venter,watson TCTCC TC 100 PASS AF=0.409205;HP=1;DB;NF=23;NR=30;NS=52;CA=0;DP=527 1 4714785 rs3835541;-/A,venter CAA CA 100 PASS AF=0.207747;HP=2;DB;NF=12;NR=9;NS=52;CA=0;DP=525 1 4715739 . GT GTT 100 PASS AF=0.0593871;HP=1;NF=4;NR=4;NS=52;CA=0;DP=486 1 4717874 rs33969697;-/C,mills,venter TCA TA 100 PASS AF=0.644689;HP=1;DB;NF=37;NR=47;NS=52;CA=0;DP=521 1 4720164 rs5772181;-/GA,mills,venter,watson TG TGAG 100 PASS AF=0.660601;HP=1;DB;NF=60;NR=61;NS=52;CA=0;DP=723 1 4725394 venter AG AGAGAGACATGAGTGAAGAAGG 100 PASS AF=0.486541;HP=1;NF=34;NR=40;NS=52;CA=0;DP=600 1 4726136 rs35816653;-/T,venter CT CTT 100 PASS AF=0.325542;HP=7;DB;NF=25;NR=33;NS=52;CA=0;DP=561 1 4728249 rs35594902;-/TGTT CT CTGTTT 100 PASS AF=0.236832;HP=1;DB;NF=16;NR=16;NS=52;CA=0;DP=595 1 4730619 rs56688128;-/AAGGC,venter,watson ACAAGGC AC 100 PASS AF=0.197783;HP=1;DB;NF=14;NR=10;NS=52;CA=0;DP=450 1 4738491 . ATCTCTCTCTCTCTCTCTCTCT AT 100 PASS AF=0.109332;HP=1;NF=34;NR=36;NS=52;CA=0;DP=556 1 4743143 rs34960969;-/T,venter ATT AT 100 PASS AF=0.443382;HP=2;DB;NF=27;NR=29;NS=51;CA=0;DP=521 1 4750482 . AC ACC 44 PASS AF=0.0773717;HP=1;NF=1;NR=10;NS=52;CA=0;DP=532 1 4751808 . CC CTC 100 PASS AF=0.287743;HP=6;NF=22;NR=19;NS=52;CA=0;DP=549 1 4753639 rs56735073;-/G AG AGG 100 PASS AF=0.354197;HP=6;DB;NF=26;NR=25;NS=52;CA=0;DP=499 1 4756338 . TGG TG 100 PASS AF=0.145276;HP=6;NF=12;NR=22;NS=52;CA=0;DP=505 1 4756654 . CTGT CT 100 PASS AF=0.0253358;HP=1;NF=2;NR=3;NS=52;CA=0;DP=502 1 4768227 rs34482713;-/A,venter CAC CC 100 PASS AF=0.624286;HP=1;DB;NF=16;NR=29;NS=52;CA=0;DP=382 1 4769408 rs3030792;-/CA,venter TC TCAC 100 PASS AF=0.564397;HP=1;DB;NF=37;NR=45;NS=51;CA=0;DP=550 1 4771107 rs59952959;-/TTATCGGTGGTTT ATTATCGGTGGTTTC AC 100 PASS AF=0.43732;HP=2;DB;NF=24;NR=26;NS=52;CA=0;DP=437 1 4771150 . AGGCAGAGGATTTAGGGGGCAGTGAAACTA AA 100 PASS AF=0.365014;HP=2;NF=25;NR=17;NS=51;CA=0;DP=446 1 4773228 . AACA AA 100 PASS AF=0.358433;HP=4;NF=49;NR=37;NS=51;CA=0;DP=403 1 4779293 rs35799766;-/A,venter GAA GA 100 PASS AF=0.620558;HP=4;DB;NF=40;NR=44;NS=52;CA=0;DP=539 1 4783405 . TACGTATATACATATACA TA 100 PASS AF=0.346752;HP=1;NF=20;NR=40;NS=52;CA=0;DP=331 1 4784171 . TA TAAGA 100 PASS AF=0.058761;HP=2;NF=4;NR=4;NS=52;CA=0;DP=522 1 4787548 rs35350740;-/CA,mills AACA AA 100 PASS AF=0.294238;HP=3;DB;NF=43;NR=40;NS=52;CA=0;DP=565 1 4790642 rs5772184;-/T,venter ATT AT 100 PASS AF=0.360239;HP=10;DB;NF=23;NR=25;NS=52;CA=0;DP=544 1 4794867 . AATA AA 59 PASS AF=0.0541594;HP=2;NF=6;NR=24;NS=52;CA=0;DP=316 1 4794934 . CT CTCTCTTT 21 PASS AF=0.322809;HP=1;NF=7;NR=9;NS=50;CA=M;DP=241 1 4800829 rs35005833;-/C,venter TC TCC 100 PASS AF=0.404199;HP=5;DB;NF=48;NR=15;NS=52;CA=0;DP=479 1 4806476 . GC GCC 100 PASS AF=0.0973173;HP=6;NF=8;NR=8;NS=52;CA=M;DP=398 1 4808450 rs34573971;-/A,venter GAA GA 100 PASS AF=0.332411;HP=9;DB;NF=26;NR=22;NS=52;CA=0;DP=474 1 4809140 rs60726929;-/TCCA,venter,watson TC TCATCC 100 PASS AF=0.348085;HP=1;DB;NF=49;NR=32;NS=52;CA=0;DP=579 1 4810276 rs3030822;-/TAGT,watson ATAGTT AT 100 PASS AF=0.242205;HP=1;DB;NF=27;NR=13;NS=52;CA=0;DP=582 1 4831434 . TA TACCACACACACA 100 PASS AF=0.49717;HP=1;NF=18;NR=17;NS=52;CA=0;DP=675 1 4831567 rs34042090;-/CA CCAC CC 100 PASS AF=0.535527;HP=4;DB;NF=52;NR=45;NS=52;CA=0;DP=738 1 4833596 rs35226825;-/T AT ATT 100 PASS AF=0.237481;HP=5;DB;NF=19;NR=19;NS=52;CA=0;DP=498 1 4839967 . TCCTGCCAGCCGGGGGC TC 100 PASS AF=0.0394386;HP=2;NF=5;NR=2;NS=52;CA=0;DP=565 1 4840948 rs59349393;-/AAACCACATCCCTTGAACT GACTAAACCACATCCCTTGAA GA 100 PASS AF=0.144437;HP=1;DB;NF=16;NR=17;NS=52;CA=0;DP=578 1 4846284 rs36118323;-/T,venter CT CTT 100 PASS AF=0.130437;HP=7;DB;NF=12;NR=15;NS=52;CA=0;DP=415 1 4855247 venter GA GACACA 100 PASS AF=0.301971;HP=1;NF=19;NR=3;NS=52;CA=0;DP=635 1 4864897 venter AT ATT 100 PASS AF=0.215684;HP=6;NF=17;NR=20;NS=52;CA=0;DP=450 1 4865373 rs34273857;-/A,venter CA CAA 100 PASS AF=0.169967;HP=6;DB;NF=17;NR=15;NS=52;CA=0;DP=533 pysam-0.7.7/tests/vcf-examples/10.vcf0000664000076400007650000032364111754437212017200 0ustar andreasandreas##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 676148 . A AC . 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A AAGAT . 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AGCC A . 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A AG . 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T TC . 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AT A . 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C CAA . 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T TC . 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GTC G . 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A AT . 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ATC A . 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A AGT . 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C CA . 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C CA . 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T TG . 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A AG . 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TATTA T . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 61531765 . AG A . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/vcf-examples/15.vcf0000664000076400007650000166544511754437212017221 0ustar andreasandreas##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 439104 . AG A . HighNoCallRate AC=0;AN=158;HW=0.00;HetPct=0.0;HomRefPct=20.6;HomVarPct=0.0;NoCallPct=79.4 GT . 0/0 . . . . 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . 0/0 0/0 . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . 0/0 . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . 0/0 0/0 . . . . . . . . . . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . . . . . . 0/0 . . . . . 0/0 0/0 0/0 0/0 . . . . . . . . . . 0/0 . . . . 0/0 . . 0/0 . . 0/0 0/0 0/0 . . 0/0 . . . . 0/0 . . . . . . . . . . . . . . . . 0/0 . . . . . 0/0 0/0 . 0/0 0/0 . . . . . . . . . 0/0 . 0/0 . . . . . 0/0 0/0 . 0/0 . . . . 0/0 . . . . 0/0 . . . . . . . . . . . . 0/0 . 0/0 . . . 0/0 . . . . 0/0 0/0 . 0/0 . . . . . 0/0 . . 0/0 . 0/0 . . . . . . 0/0 . . . 0/0 . 0/0 . . 0/0 . 0/0 . . 0/0 . . 0/0 . 0/0 0/0 0/0 0/0 . . . . . . 20 669442 . TG T . PASS AC=54;AN=766;HW=6.74;HetPct=12.0;HomRefPct=86.9;HomVarPct=1.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 676148 . A AC . 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C CT . 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C CAT . 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CT C . 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CT C . 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AAG A . PASS AC=334;AN=764;HW=9.47;HetPct=44.9;HomRefPct=33.7;HomVarPct=21.1;NoCallPct=0.3 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 20 1342549 . A AAGAT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1366475 . CT C . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1390810 . T TTC . HighNoCallRate AC=0;AN=566;HW=0.00;HetPct=0.0;HomRefPct=73.9;HomVarPct=0.0;NoCallPct=26.1 GT 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 20 1550416 . C CT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1655540 . AT A . PASS AC=4;AN=764;HW=0.00;HetPct=1.0;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2133769 . GA G . HardyWeinbergViolation AC=379;AN=766;HW=85.69;HetPct=34.7;HomRefPct=33.2;HomVarPct=32.1;NoCallPct=0.0 GT 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 20 2217137 . CT C . HighNoCallRate AC=0;AN=704;HW=0.00;HetPct=0.0;HomRefPct=91.9;HomVarPct=0.0;NoCallPct=8.1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 20 2263095 . TG T . HardyWeinbergViolation AC=358;AN=766;HW=812.29;HetPct=93.5;HomRefPct=6.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 20 2426886 . G GAATT . HighNoCallRate AC=11;AN=680;HW=0.00;HetPct=2.9;HomRefPct=85.9;HomVarPct=0.0;NoCallPct=11.2 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/1 . 0/1 . 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/1 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 20 2889034 . AAAAT A . PASS AC=6;AN=762;HW=0.00;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . CT C . PASS AC=4;AN=762;HW=0.00;HetPct=1.0;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3327993 . CAA C . HardyWeinbergViolation AC=3;AN=766;HW=21.06;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.3;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3700705 . CTTTGGG C . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 4037626 . TC T . 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G GA . 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CATT C . 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CAAAT C . 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CCTTGA C . 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C CATTTTAGG . 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GA G . PASS AC=377;AN=764;HW=5.70;HetPct=53.0;HomRefPct=24.0;HomVarPct=22.7;NoCallPct=0.3 GT 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 20 5416109 . CA C . PASS AC=2;AN=752;HW=0.00;HetPct=0.5;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5432262 . AGT A . PASS AC=4;AN=752;HW=0.00;HetPct=1.0;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5724449 . T TC . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5928403 . T TA . HardyWeinbergViolation AC=196;AN=762;HW=47.13;HetPct=29.2;HomRefPct=59.3;HomVarPct=11.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 6877907 . CA C . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 6969412 . CAAAGAAT C . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7035110 . CT C . HardyWeinbergViolation AC=340;AN=758;HW=1038.45;HetPct=1.0;HomRefPct=54.0;HomVarPct=43.9;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 . 0/0 . 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/0 1/1 . 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 20 7229260 . T TA . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7239075 . AG A . PASS AC=5;AN=766;HW=0.00;HetPct=1.3;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7942727 . A AC . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 7950562 . C CT . PASS AC=4;AN=760;HW=18.01;HetPct=0.5;HomRefPct=98.4;HomVarPct=0.3;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8195466 . C CT . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8233352 . TACTC T . PASS AC=56;AN=764;HW=1.84;HetPct=13.1;HomRefPct=85.9;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 8504000 . TAG T . PASS AC=5;AN=762;HW=0.00;HetPct=1.3;HomRefPct=98.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8779672 . TG T . HighNoCallRate AC=0;AN=86;HW=0.00;HetPct=0.0;HomRefPct=11.2;HomVarPct=0.0;NoCallPct=88.8 GT . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . . . . . . . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . 0/0 0/0 0/0 0/0 . . . 0/0 . . . . . 0/0 0/0 . . . . 0/0 . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . 0/0 . . . . . . . . . 0/0 . 0/0 . 0/0 0/0 . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . 0/0 . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . 0/0 0/0 . 0/0 . . 0/0 . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . 20 8794142 . AG A . HardyWeinbergViolation AC=52;AN=756;HW=57.86;HetPct=8.4;HomRefPct=87.7;HomVarPct=2.6;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 20 9231138 . AT A . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9900218 . C CT . HardyWeinbergViolation AC=3;AN=766;HW=21.06;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.3;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9921724 . AAAGT A . PASS AC=11;AN=758;HW=0.00;HetPct=2.9;HomRefPct=96.1;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9925738 . T TG . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 10090376 . T TG . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 10377174 . ATAAAAC A . HighNoCallRate AC=107;AN=514;HW=4.54;HetPct=20.6;HomRefPct=42.8;HomVarPct=3.7;NoCallPct=32.9 GT . . 0/0 0/0 . 0/0 . 0/1 . 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . . . . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 . 0/1 0/0 . . 0/0 . 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 . . 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 . . . . . . 0/0 . 1/1 . 0/0 . 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 . . . . 0/1 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 . . 0/0 . . . . . 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/1 . . . . . 0/0 . 0/1 0/1 . . 0/0 0/0 0/0 . 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/1 0/1 . 0/1 0/1 0/0 . 0/1 0/0 . . 0/0 . . . . . 0/0 0/1 0/1 0/0 0/1 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 . . . 0/0 0/0 0/0 0/1 . . 0/1 . . . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 . . 0/1 . . . . . . . . . . . 0/1 0/0 . 0/0 . 0/1 0/1 . . . . . . . . . . 0/0 0/1 . . 0/0 . 0/0 . . . 0/1 . . . 0/1 . . 0/1 . . . . 0/0 . 0/1 0/0 . 0/1 . 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 . . . 1/1 0/1 . . 0/0 . 0/0 0/0 0/0 0/0 0/1 . 0/1 0/1 . . 0/0 0/0 0/0 0/0 0/1 0/0 20 11229169 . T TA . PASS AC=3;AN=756;HW=0.00;HetPct=0.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 11511920 . AC A . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 11893900 . ATTAG A . 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A AG . 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TTATC T . 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GGGA G . PASS AC=3;AN=762;HW=0.00;HetPct=0.8;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13128894 . CT C . PASS AC=10;AN=764;HW=0.00;HetPct=2.6;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 20 13287841 . CAT C . PASS AC=134;AN=760;HW=0.21;HetPct=29.2;HomRefPct=67.1;HomVarPct=2.9;NoCallPct=0.8 GT 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 20 13365589 . T TG . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13566260 . AAATTG A . 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AT A . 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GAGAA G . 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TA T . 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TC T . 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T TA . 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AGT A . 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TTC T . 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AGCC A . 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T TC . 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GA G . 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TG T . 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TGA T . PASS AC=29;AN=764;HW=0.00;HetPct=7.6;HomRefPct=92.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15543319 . AG A . 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TG T . 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TG T . PASS AC=87;AN=750;HW=3.63;HetPct=19.1;HomRefPct=77.0;HomVarPct=1.8;NoCallPct=2.1 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 . 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15871330 . AG A . 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TA T . PASS AC=186;AN=764;HW=15.27;HetPct=32.4;HomRefPct=59.3;HomVarPct=8.1;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 20 16172883 . G GTAGC . HardyWeinbergViolation AC=79;AN=762;HW=42.59;HetPct=13.8;HomRefPct=82.2;HomVarPct=3.4;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16192114 . AT A . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16259934 . C CAA . PASS AC=0;AN=758;HW=0.00;HetPct=0.0;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16312599 . CTA C . 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GGTT G . PASS AC=6;AN=760;HW=0.00;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16747221 . CA C . PASS AC=291;AN=764;HW=3.13;HetPct=45.2;HomRefPct=39.2;HomVarPct=15.4;NoCallPct=0.3 GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 . 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 20 16769262 . TTTC T . HighNoCallRate AC=8;AN=600;HW=0.00;HetPct=2.1;HomRefPct=76.2;HomVarPct=0.0;NoCallPct=21.7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . 0/1 . . 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 0/1 . 0/1 . . 0/1 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/1 . . 0/0 0/0 . 0/0 0/0 . 0/0 . . . . . 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 . . . 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16813850 . C CA . 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T TC . 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TA T . 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TGC T . 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A AGT . 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C CA . 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AAG A . 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A ATT . 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TAA T . 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C CT . 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T TC . 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T TC . 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GGCCTGGGATGTAAA G . 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CCTT C . 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A AC . 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ATTACAGACT A . 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TA T . 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CA C . 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TG T . 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T TC . 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TC T . 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ACTT A . 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AG A . 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CA C . PASS AC=330;AN=762;HW=4.15;HetPct=46.5;HomRefPct=33.2;HomVarPct=19.8;NoCallPct=0.5 GT 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 . 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 . 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 20 21968507 . AC A . PASS AC=7;AN=762;HW=12.61;HetPct=1.3;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22411326 . CA C . HardyWeinbergViolation AC=321;AN=762;HW=136.49;HetPct=29.5;HomRefPct=42.8;HomVarPct=27.2;NoCallPct=0.5 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 . 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/1 20 22434333 . C CA . PASS AC=8;AN=766;HW=0.00;HetPct=2.1;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 22637424 . C CAGCCA . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22655862 . TATC T . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23169038 . TGTC T . HardyWeinbergViolation AC=380;AN=766;HW=1034.24;HetPct=98.7;HomRefPct=1.0;HomVarPct=0.3;NoCallPct=0.0 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 20 23200197 . ATT A . PASS AC=1;AN=766;HW=0.00;HetPct=0.3;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . CA C . PASS AC=8;AN=754;HW=11.33;HetPct=1.6;HomRefPct=96.6;HomVarPct=0.3;NoCallPct=1.6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23319459 . CAT C . HardyWeinbergViolation AC=10;AN=766;HW=26.72;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.5;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23813095 . CT C . PASS AC=26;AN=762;HW=1.46;HetPct=6.3;HomRefPct=93.0;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 23815381 . CT C . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23889003 . GA G . PASS AC=2;AN=766;HW=0.00;HetPct=0.5;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 24541328 . TA T . HighNoCallRate AC=0;AN=430;HW=0.00;HetPct=0.0;HomRefPct=56.1;HomVarPct=0.0;NoCallPct=43.9 GT . 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . . . . 0/0 0/0 . . . 0/0 . . . . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 . . . . . . 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . . . . . . 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . . . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . 0/0 . 0/0 . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 . . 0/0 . . . . . . 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . 0/0 . . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 0/0 . . . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 20 24710482 . GT G . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 24855121 . CT C . PASS AC=6;AN=760;HW=0.00;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25283938 . A AG . HardyWeinbergViolation AC=326;AN=762;HW=30.59;HetPct=40.2;HomRefPct=36.8;HomVarPct=22.5;NoCallPct=0.5 GT 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 . 0/1 . 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 20 25503211 . CATA C . 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GT G . 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CCTT C . 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C CCACAAGAAG . 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TATATC T . 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CG C . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 31881479 . AG A . HardyWeinbergViolation AC=40;AN=764;HW=34.05;HetPct=7.3;HomRefPct=90.9;HomVarPct=1.6;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32015223 . CT C . PASS AC=5;AN=764;HW=0.00;HetPct=1.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32158330 . CAG C . PASS AC=4;AN=760;HW=0.00;HetPct=1.0;HomRefPct=98.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 32456076 . GT G . 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CA C . 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A AG . 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GGCGTCTGA G . 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GTC G . 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A AAG . 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C CA . 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A AT . 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TAA T . 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CT C . 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ATC A . 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GA G . PASS AC=5;AN=764;HW=0.00;HetPct=1.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 35847597 . CTT C . PASS AC=1;AN=764;HW=0.00;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 36250348 . CG C . HighNoCallRate AC=0;AN=414;HW=0.00;HetPct=0.0;HomRefPct=54.0;HomVarPct=0.0;NoCallPct=46.0 GT 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 . . 0/0 . 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 . . 0/0 . . 0/0 . 0/0 . . . 0/0 . 0/0 . . . 0/0 0/0 0/0 . . 0/0 . . 0/0 . . . 0/0 0/0 . . . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . 0/0 0/0 . . . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . . . . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 . . . 0/0 0/0 . . 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 . 0/0 0/0 . . 0/0 0/0 . 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . . . . 0/0 . . 0/0 . 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . . . . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 . . 0/0 . . . . 20 36658020 . TG T . 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TC T . 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TAAAG T . 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ATAC A . 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CAG C . 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CAG C . 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TG T . 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CAT C . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37678954 . C CTGG . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37712193 . AAG A . PASS AC=29;AN=762;HW=0.00;HetPct=7.6;HomRefPct=91.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37836124 . AAAT A . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37954797 . A AGT . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37962643 . T TAA . 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TA T . 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T TA . 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GAAGA G . 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CCTT C . 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T TG . 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AG A . 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T TG . 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TGAG T . 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A AG . 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TG T . 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CTAAGGAGGGAAAAAGATATAAT C . 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TATC T . 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TG T . 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GC G . 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CACTT C . 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T TA . 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CT C . 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T TGGGTC . 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AG A . 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A AG . 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AG A . 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AG A . 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T TC . 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GC G . 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CA C . 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C CT . 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T TC . 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AACAG A . 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T TA . 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GAGTGTCGT G . 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GA G . 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T TTC . 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CTG C . PASS AC=86;AN=762;HW=16.06;HetPct=17.2;HomRefPct=79.6;HomVarPct=2.6;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 20 46011017 . GAT G . HighNoCallRate AC=4;AN=706;HW=0.00;HetPct=1.0;HomRefPct=91.1;HomVarPct=0.0;NoCallPct=7.8 GT . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46051811 . T TAAGC . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46353646 . A AG . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46413551 . TC T . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46569465 . CTG C . PASS AC=10;AN=762;HW=0.00;HetPct=2.6;HomRefPct=96.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 46720983 . ATACTTGG A . 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GC G . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47136092 . A AGTC . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47239432 . T TA . HardyWeinbergViolation AC=3;AN=762;HW=21.03;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 47335386 . GC G . 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C CA . 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CA C . 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CCTA C . 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G GT . 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T TG . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 49537420 . AG A . 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A AG . 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A AC . 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ACTTTT A . 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TTTTC T . 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A AT . 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T TC . 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G GAA . 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G GT . 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AC A . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51758677 . A ATT . HardyWeinbergViolation AC=87;AN=762;HW=72.50;HetPct=13.3;HomRefPct=81.5;HomVarPct=4.7;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 20 51838824 . GA G . PASS AC=4;AN=756;HW=17.99;HetPct=0.5;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51961394 . ATTTG A . PASS AC=8;AN=760;HW=0.00;HetPct=2.1;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 53081927 . CATGA C . 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T TG . 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T TA . 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T TC . 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CAG C . 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AC A . 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CAT C . 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A AC . 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TGAGC T . 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GT G . 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AG A . 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AAAC A . HardyWeinbergViolation AC=10;AN=764;HW=26.69;HetPct=1.6;HomRefPct=97.7;HomVarPct=0.5;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 55608811 . CT C . PASS AC=35;AN=762;HW=19.90;HetPct=7.0;HomRefPct=91.4;HomVarPct=1.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 55611547 . CAA C . 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GT G . 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CA C . 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T TGAGG . 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TG T . 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HardyWeinbergViolation AC=137;AN=764;HW=48.09;HetPct=22.2;HomRefPct=70.8;HomVarPct=6.8;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 20 57676578 . CCTTT C . PASS AC=7;AN=764;HW=0.00;HetPct=1.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 57693627 . AG A . HighNoCallRate AC=12;AN=292;HW=71.95;HetPct=0.5;HomRefPct=36.3;HomVarPct=1.3;NoCallPct=61.9 GT . . 0/0 . . . 0/0 . . . . 0/0 . 1/1 . . 0/0 . 0/0 . 0/0 . . . . . . . 0/0 0/0 . . . 0/0 . . . . . 0/0 . 0/0 . . 0/0 0/0 . . . . . . . . 0/0 . . . . 0/0 . . . 0/0 . 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 . 0/0 . . . 0/0 . . . . . . . . 0/0 . 0/0 . . 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 1/1 . . . . . . . 0/0 . . . 0/0 . . . . . . 0/0 1/1 . . . 0/0 . . . . . . . . 0/0 . 0/0 . . . 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 . . . . 0/0 . . 0/0 . . 1/1 . 0/0 0/0 . 0/0 0/0 0/1 . . 0/0 . 0/0 1/1 . . . . . . . 0/0 0/0 . . . . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . . . 0/0 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 . 0/0 . 0/0 0/0 . . . . . 0/0 . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . . . . . 0/0 . . 0/0 . . 0/0 . 0/0 0/0 . . 0/0 . . . 0/0 0/0 . . . . 0/0 . . . 0/0 . . . 0/0 . . . 0/0 . . 0/0 . 0/0 . . . . . . 0/0 . . . . . . . 0/0 . . 0/1 0/0 . . . . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 . . 0/0 . . . . 0/0 . . . . . 0/0 . 0/0 . . 0/0 . 0/0 . . . 0/0 20 57781799 . TGGG T . HardyWeinbergViolation AC=43;AN=764;HW=30.12;HetPct=8.1;HomRefPct=90.1;HomVarPct=1.6;NoCallPct=0.3 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 20 58288793 . TC T . PASS AC=44;AN=766;HW=12.53;HetPct=9.4;HomRefPct=89.6;HomVarPct=1.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 58790761 . TG T . HardyWeinbergViolation AC=232;AN=762;HW=35.81;HetPct=33.9;HomRefPct=52.2;HomVarPct=13.3;NoCallPct=0.5 GT 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 1/1 . 0/1 . 1/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 20 59072457 . AAGG A . HardyWeinbergViolation AC=12;AN=756;HW=41.94;HetPct=1.6;HomRefPct=96.3;HomVarPct=0.8;NoCallPct=1.3 GT . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 59153061 . CTG C . 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TATTA T . 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CCT C . 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TG T . 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C CT . 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TG T . HighNoCallRate AC=0;AN=712;HW=0.00;HetPct=0.0;HomRefPct=93.0;HomVarPct=0.0;NoCallPct=7.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60337932 . AC A . PASS AC=3;AN=764;HW=0.00;HetPct=0.8;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60925525 . GC G . PASS AC=2;AN=762;HW=0.00;HetPct=0.5;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 60961768 . GA G . HardyWeinbergViolation AC=365;AN=766;HW=84.86;HetPct=34.7;HomRefPct=35.0;HomVarPct=30.3;NoCallPct=0.0 GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 20 61000018 . GC G . PASS AC=203;AN=762;HW=0.38;HetPct=39.4;HomRefPct=53.3;HomVarPct=6.8;NoCallPct=0.5 GT 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 . 0/1 . 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 20 61531765 . AG A . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 61983510 . TCTGC T . PASS AC=75;AN=766;HW=0.03;HetPct=18.0;HomRefPct=81.2;HomVarPct=0.8;NoCallPct=0.0 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 20 62154368 . G GA . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62310426 . CTT C . PASS AC=1;AN=756;HW=0.00;HetPct=0.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62871860 . C CCCGCA . PASS AC=27;AN=764;HW=17.87;HetPct=5.5;HomRefPct=93.5;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/vcf-examples/23.vcf0000664000076400007650000042215712007611576017205 0ustar andreasandreas##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta ##source=Dindel2 ##source=SelectVariants ##source_20110031.1=/nfs/users/nfs_p/pd3/cvs/vcftools/perl/vcf-annotate -d /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.desc -a /nfs/users/nfs_p/pd3/sandbox/hapmap/dbSNP-b132/non-1kg-vld.tab.gz -c CHROM,FROM,INFO/VLD,INFO/KGPilot123,INFO/dbSNP ##vcfCTools=filter #CHROM POS ID REF ALT QUAL FILTER INFO 20 458502 . G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.2458;set=VQSR 20 766143 . C CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;SET_WGVQSR;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SET_WGVQSR;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SET_WGVQSR;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SET_WGVQSR;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SET_WGVQSR;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SET_WGVQSR;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SET_WGVQSR;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;SET_WGVQSR;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.3874;set=VQSR 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;SET_WGVQSR;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SET_WGVQSR;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SET_INTEGRATION;SET_WGVQSR;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SET_WGVQSR;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.9313;set=VQSR 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;SET_INTEGRATION;SET_WGVQSR;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;SET_INTEGRATION;SET_WGVQSR;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SET_INTEGRATION;SET_WGVQSR;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;SET_WGVQSR;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;SET_WGVQSR;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SET_WGVQSR;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;SET_WGVQSR;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SET_INTEGRATION;SET_WGVQSR;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SET_WGVQSR;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;SET_INTEGRATION;SET_WGVQSR;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SET_INTEGRATION;SET_WGVQSR;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SET_WGVQSR;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SET_WGVQSR;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;SET_INTEGRATION;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SET_WGVQSR;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SET_INTEGRATION;SET_WGVQSR;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SET_INTEGRATION;SET_WGVQSR;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SET_INTEGRATION;SET_WGVQSR;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SET_WGVQSR;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SET_INTEGRATION;SET_WGVQSR;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;SET_INTEGRATION;SET_WGVQSR;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SET_INTEGRATION;SET_WGVQSR;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;SET_WGVQSR;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SET_INTEGRATION;SET_WGVQSR;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SET_WGVQSR;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SET_INTEGRATION;SET_WGVQSR;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;SET_INTEGRATION;SET_WGVQSR;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;SET_WGVQSR;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SET_WGVQSR;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.8071;set=VQSR 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SET_INTEGRATION;SET_WGVQSR;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SET_INTEGRATION;SET_WGVQSR;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SET_WGVQSR;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SET_INTEGRATION;SET_WGVQSR;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SET_INTEGRATION;SET_WGVQSR;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SET_INTEGRATION;SET_WGVQSR;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SET_INTEGRATION;SET_WGVQSR;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SET_INTEGRATION;SET_WGVQSR;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SET_WGVQSR;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SET_INTEGRATION;SET_WGVQSR;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;SET_INTEGRATION;SET_WGVQSR;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SET_INTEGRATION;SET_WGVQSR;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;SET_INTEGRATION;SET_WGVQSR;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SET_INTEGRATION;SET_WGVQSR;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;SET_WGVQSR;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SET_INTEGRATION;SET_WGVQSR;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SET_WGVQSR;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SET_INTEGRATION;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;SET_WGVQSR;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;SET_INTEGRATION;SET_WGVQSR;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;SET_WGVQSR;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;SET_INTEGRATION;SET_WGVQSR;VQSLOD=6.1473;set=VQSR pysam-0.7.7/tests/vcf-examples/24.vcf0000664000076400007650000015205411754437212017203 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 256726 . T A . . Sample=HG00097;GT=0/1;PCR_454_AR=739;PCR_454_RR=885 20 256726 . T A . . Sample=HG00099;GT=0/1;PCR_454_AR=723;PCR_454_RR=714 20 256726 . T A . . Sample=HG00106;GT=0/1;PCR_454_AR=1092;PCR_454_RR=1102 20 256726 . T A . . Sample=HG00112;GT=0/1;PCR_454_AR=947;PCR_454_RR=1005 20 256726 . T A . . Sample=HG00104;GT=1/1;PCR_454_AR=1970;PCR_454_RR=52 20 257977 . G C . . Sample=NA19438;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1123 20 330407 . C G . . Sample=HG00134;GT=0/1;PCR_454_AR=1034;PCR_454_RR=1037 20 330407 . C G . . Sample=HG00148;GT=0/1;PCR_454_AR=840;PCR_454_RR=820 20 330407 . C G . . Sample=HG00151;GT=0/1;PCR_454_AR=952;PCR_454_RR=982 20 330407 . C G . . Sample=HG00358;GT=0/1;PCR_454_AR=880;PCR_454_RR=957 20 330407 . C G . . Sample=HG01277;GT=0/1;PCR_454_AR=914;PCR_454_RR=984 20 368826 . G A . . Sample=NA20346;GT=0/1;PCR_454_AR=632;PCR_454_RR=591 20 371957 . G A . . Sample=HG00150;GT=0/1;PCR_454_AR=403;PCR_454_RR=424 20 371957 . G A . . Sample=NA12287;GT=0/1;PCR_454_AR=401;PCR_454_RR=435 20 467031 . T A . . Sample=NA20510;GT=0/0;PCR_454_AR=5;PCR_454_RR=1763 20 741858 . G A . . Sample=NA18634;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1301 20 947853 . C T . . Sample=HG00578;GT=0/0;PCR_454_AR=0;PCR_454_RR=197 20 947853 . C T . . Sample=NA18861;GT=0/1;PCR_454_AR=40;PCR_454_RR=39 20 947853 . C T . . Sample=NA18868;GT=0/1;PCR_454_AR=88;PCR_454_RR=80 20 947853 . C T . . Sample=NA18870;GT=0/1;PCR_454_AR=66;PCR_454_RR=99 20 947853 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=96;PCR_454_RR=111 20 947908 . C T . . Sample=NA11993;GT=0/1;PCR_454_AR=598;PCR_454_RR=2114 20 947908 . C T . . Sample=NA18501;GT=0/1;PCR_454_AR=392;PCR_454_RR=1687 20 947908 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=635;PCR_454_RR=2218 20 947908 . C T . . Sample=NA18505;GT=0/1;PCR_454_AR=1312;PCR_454_RR=1429 20 947908 . C T . . Sample=NA18507;GT=0/1;PCR_454_AR=598;PCR_454_RR=2127 20 948715 . T G . . Sample=NA06989;GT=0/0;PCR_454_AR=4;PCR_454_RR=1252 20 1144999 . C T . . Sample=NA18510;GT=0/1;PCR_454_AR=450;PCR_454_RR=447 20 1144999 . C T . . Sample=NA19172;GT=0/1;PCR_454_AR=541;PCR_454_RR=531 20 1285858 . A C . . Sample=NA19311;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1315 20 1285932 . G A . . Sample=HG00097;GT=0/1;PCR_454_AR=868;PCR_454_RR=867 20 1285932 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=745;PCR_454_RR=680 20 1285932 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=780;PCR_454_RR=838 20 1285932 . G A . . Sample=HG00134;GT=0/1;PCR_454_AR=978;PCR_454_RR=944 20 1285932 . G A . . Sample=HG00128;GT=1/1;PCR_454_AR=1499;PCR_454_RR=14 20 1286090 . A G . . Sample=HG00235;GT=0/1;PCR_454_AR=1223;PCR_454_RR=1352 20 1286090 . A G . . Sample=HG00351;GT=0/1;PCR_454_AR=799;PCR_454_RR=823 20 1286090 . A G . . Sample=HG01125;GT=0/1;PCR_454_AR=1167;PCR_454_RR=1149 20 1286090 . A G . . Sample=NA19773;GT=0/1;PCR_454_AR=1070;PCR_454_RR=1130 20 1546804 . G A . . Sample=HG00141;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1231 20 1546804 . G A . . Sample=HG00149;GT=0/1;PCR_454_AR=1029;PCR_454_RR=1050 20 1546804 . G A . . Sample=HG00151;GT=0/1;PCR_454_AR=1135;PCR_454_RR=1034 20 1546804 . G A . . Sample=HG00177;GT=0/1;PCR_454_AR=1063;PCR_454_RR=1118 20 1546804 . G A . . Sample=HG00179;GT=0/1;PCR_454_AR=1118;PCR_454_RR=954 20 1551579 . T G . . Sample=NA20515;GT=0/0;PCR_454_AR=5;PCR_454_RR=1812 20 1551579 . T G . . Sample=NA19466;GT=0/1;PCR_454_AR=1011;PCR_454_RR=1042 20 1559334 . C T . . Sample=NA18941;GT=0/0;PCR_454_AR=1;PCR_454_RR=1193 20 1615980 . G A . . Sample=NA19914;GT=0/1;PCR_454_AR=441;PCR_454_RR=492 20 1616047 . C G . . Sample=NA07048;GT=0/1;PCR_454_AR=508;PCR_454_RR=813 20 1629751 . T C . . Sample=HG00156;GT=0/1;PCR_454_AR=285;PCR_454_RR=282 20 1896011 . C T . . Sample=NA18639;GT=0/0;PCR_454_AR=0;PCR_454_RR=29 20 1896011 . C T . . Sample=NA19314;GT=0/0;PCR_454_AR=0;PCR_454_RR=47 20 2291684 . T C . . Sample=NA19036;GT=0/1;PCR_454_AR=873;PCR_454_RR=1025 20 2291684 . T C . . Sample=NA19347;GT=0/1;PCR_454_AR=1116;PCR_454_RR=1217 20 2375127 . G A . . Sample=NA18615;GT=0/1;PCR_454_AR=1016;PCR_454_RR=1016 20 2777844 . T C . . Sample=NA20819;GT=0/1;PCR_454_AR=908;PCR_454_RR=970 20 2844678 . G A . . Sample=HG00360;GT=0/1;PCR_454_AR=1081;PCR_454_RR=1071 20 2944927 . A T . . Sample=NA12347;GT=0/1;PCR_454_AR=704;PCR_454_RR=752 20 2969014 . C G . . Sample=HG00151;GT=0/1;PCR_454_AR=684;PCR_454_RR=809 20 2969014 . C G . . Sample=NA18511;GT=0/1;PCR_454_AR=666;PCR_454_RR=704 20 2969014 . C G . . Sample=NA18523;GT=0/1;PCR_454_AR=767;PCR_454_RR=802 20 2969014 . C G . . Sample=NA18549;GT=0/1;PCR_454_AR=772;PCR_454_RR=838 20 2969014 . C G . . Sample=NA18858;GT=1/1;PCR_454_AR=1313;PCR_454_RR=8 20 3026344 . A C . . Sample=NA18640;GT=0/1;PCR_454_AR=1652;PCR_454_RR=1336 20 3128885 . G A . . Sample=NA19473;GT=0/1;PCR_454_AR=620;PCR_454_RR=669 20 3128950 . G A . . Sample=NA18624;GT=0/1;PCR_454_AR=570;PCR_454_RR=517 20 3128950 . G A . . Sample=NA18953;GT=0/1;PCR_454_AR=685;PCR_454_RR=700 20 3128950 . G A . . Sample=NA18998;GT=0/1;PCR_454_AR=606;PCR_454_RR=638 20 3128950 . G A . . Sample=NA19076;GT=0/1;PCR_454_AR=663;PCR_454_RR=643 20 3128950 . G A . . Sample=NA19088;GT=0/1;PCR_454_AR=492;PCR_454_RR=472 20 3171356 . T C . . Sample=NA12003;GT=0/0;PCR_454_AR=6;PCR_454_RR=1919 20 3171356 . T C . . Sample=NA12872;GT=0/0;PCR_454_AR=6;PCR_454_RR=2324 20 3193990 . G T . . Sample=NA12815;GT=0/0;PCR_454_AR=0;PCR_454_RR=1570 20 3193990 . G T . . Sample=NA18505;GT=0/0;PCR_454_AR=0;PCR_454_RR=1586 20 3204083 . G A . . Sample=HG00104;GT=0/1;PCR_454_AR=1059;PCR_454_RR=982 20 3204083 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1190;PCR_454_RR=1178 20 3204083 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=1156;PCR_454_RR=1277 20 3204083 . G A . . Sample=HG00099;GT=1/1;PCR_454_AR=2171;PCR_454_RR=12 20 3204083 . G A . . Sample=HG00106;GT=1/1;PCR_454_AR=2027;PCR_454_RR=19 20 3214580 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=852;PCR_454_RR=784 20 3214580 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=628;PCR_454_RR=682 20 3214580 . C T . . Sample=HG00129;GT=0/1;PCR_454_AR=869;PCR_454_RR=844 20 3214580 . C T . . Sample=HG00130;GT=0/1;PCR_454_AR=651;PCR_454_RR=767 20 3214580 . C T . . Sample=HG00128;GT=1/1;PCR_454_AR=1378;PCR_454_RR=3 20 3214802 . T C . . Sample=NA18526;GT=0/1;PCR_454_AR=969;PCR_454_RR=1018 20 3235915 . T C . . Sample=HG00560;GT=0/1;PCR_454_AR=795;PCR_454_RR=798 20 3235915 . T C . . Sample=HG00566;GT=0/1;PCR_454_AR=688;PCR_454_RR=650 20 3235915 . T C . . Sample=HG00596;GT=0/1;PCR_454_AR=863;PCR_454_RR=935 20 3235915 . T C . . Sample=HG01124;GT=0/1;PCR_454_AR=802;PCR_454_RR=836 20 3235915 . T C . . Sample=NA18487;GT=0/1;PCR_454_AR=942;PCR_454_RR=968 20 3274851 . C T . . Sample=NA19704;GT=0/1;PCR_454_AR=486;PCR_454_RR=479 20 3274851 . C T . . Sample=NA20334;GT=0/1;PCR_454_AR=512;PCR_454_RR=512 20 3274851 . C T . . Sample=NA20336;GT=0/1;PCR_454_AR=510;PCR_454_RR=440 20 3324372 . G C . . Sample=NA19003;GT=0/1;PCR_454_AR=1902;PCR_454_RR=1898 20 3362102 . T G . . Sample=NA06994;GT=0/0;PCR_454_AR=0;PCR_454_RR=526 20 3362102 . T G . . Sample=NA12249;GT=0/0;PCR_454_AR=0;PCR_454_RR=465 20 3515923 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=237;PCR_454_RR=261 20 3515923 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=299;PCR_454_RR=293 20 3515923 . G A . . Sample=HG00130;GT=0/1;PCR_454_AR=307;PCR_454_RR=279 20 3515923 . G A . . Sample=HG00128;GT=1/1;PCR_454_AR=633;PCR_454_RR=4 20 3515923 . G A . . Sample=HG00129;GT=1/1;PCR_454_AR=580;PCR_454_RR=2 20 3641233 . G T . . Sample=NA20773;GT=0/0;PCR_454_AR=3;PCR_454_RR=1477 20 3650204 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=737;PCR_454_RR=771 20 3650204 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=518;PCR_454_RR=552 20 3650204 . G A . . Sample=HG00141;GT=0/1;PCR_454_AR=643;PCR_454_RR=668 20 3650204 . G A . . Sample=HG00143;GT=0/1;PCR_454_AR=549;PCR_454_RR=613 20 3650204 . G A . . Sample=HG00148;GT=0/1;PCR_454_AR=708;PCR_454_RR=830 20 3652397 . G A . . Sample=NA18635;GT=0/1;PCR_454_AR=1604;PCR_454_RR=1658 20 3672827 . A T . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=941 20 3672827 . A T . . Sample=HG00349;GT=0/0;PCR_454_AR=2;PCR_454_RR=943 20 3675119 . G T . . Sample=NA20544;GT=0/1;PCR_454_AR=577;PCR_454_RR=657 20 3687329 . T C . . Sample=NA18532;GT=0/1;PCR_454_AR=702;PCR_454_RR=746 20 3842125 . C G . . Sample=NA12155;GT=0/1;PCR_454_AR=1193;PCR_454_RR=1178 20 4680289 . G A . . Sample=NA18856;GT=0/1;PCR_454_AR=1335;PCR_454_RR=1278 20 4680289 . G A . . Sample=NA19130;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1286 20 4680289 . G A . . Sample=NA19213;GT=0/1;PCR_454_AR=1305;PCR_454_RR=1241 20 4680289 . G A . . Sample=NA19311;GT=0/1;PCR_454_AR=1332;PCR_454_RR=1400 20 4680289 . G A . . Sample=NA19332;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1275 20 4848511 . G A . . Sample=NA19440;GT=0/0;PCR_454_AR=8;PCR_454_RR=2951 20 4848511 . G A . . Sample=NA19448;GT=0/1;PCR_454_AR=1278;PCR_454_RR=1434 20 4848511 . G A . . Sample=NA19461;GT=0/1;PCR_454_AR=1412;PCR_454_RR=1478 20 5099300 . A G . . Sample=NA19138;GT=0/1;PCR_454_AR=511;PCR_454_RR=496 20 5903387 . A C . . Sample=HG00566;GT=0/1;PCR_454_AR=1400;PCR_454_RR=1384 20 5903387 . A C . . Sample=HG01124;GT=0/1;PCR_454_AR=856;PCR_454_RR=1007 20 5903387 . A C . . Sample=HG01125;GT=0/1;PCR_454_AR=891;PCR_454_RR=816 20 5903387 . A C . . Sample=HG01149;GT=0/1;PCR_454_AR=1011;PCR_454_RR=959 20 5903387 . A C . . Sample=HG01278;GT=0/1;PCR_454_AR=1077;PCR_454_RR=1049 20 5923222 . C T . . Sample=HG00592;GT=0/1;PCR_454_AR=968;PCR_454_RR=950 20 5923222 . C T . . Sample=NA18567;GT=0/1;PCR_454_AR=678;PCR_454_RR=728 20 5923222 . C T . . Sample=NA18602;GT=0/1;PCR_454_AR=926;PCR_454_RR=988 20 5923222 . C T . . Sample=NA18624;GT=0/1;PCR_454_AR=991;PCR_454_RR=963 20 5923222 . C T . . Sample=NA18632;GT=0/1;PCR_454_AR=892;PCR_454_RR=906 20 5943955 . G C . . Sample=HG00565;GT=0/1;PCR_454_AR=259;PCR_454_RR=227 20 5943955 . G C . . Sample=HG00566;GT=0/1;PCR_454_AR=245;PCR_454_RR=235 20 5943955 . G C . . Sample=HG00577;GT=0/1;PCR_454_AR=264;PCR_454_RR=305 20 5943955 . G C . . Sample=HG00578;GT=0/1;PCR_454_AR=210;PCR_454_RR=261 20 5943955 . G C . . Sample=HG00593;GT=0/1;PCR_454_AR=261;PCR_454_RR=238 20 6015109 . G A . . Sample=NA20796;GT=0/1;PCR_454_AR=440;PCR_454_RR=500 20 6060150 . C T . . Sample=NA18961;GT=0/1;PCR_454_AR=384;PCR_454_RR=464 20 7967973 . G A . . Sample=NA19371;GT=0/1;PCR_454_AR=281;PCR_454_RR=506 20 7967973 . G A . . Sample=NA19390;GT=0/1;PCR_454_AR=410;PCR_454_RR=538 20 8665657 . G A . . Sample=NA19740;GT=0/1;PCR_454_AR=724;PCR_454_RR=703 20 9453955 . C A . . Sample=NA20314;GT=0/1;PCR_454_AR=1048;PCR_454_RR=1147 20 9520132 . G A . . Sample=HG00143;GT=0/1;PCR_454_AR=472;PCR_454_RR=583 20 9520132 . G A . . Sample=HG01624;GT=0/1;PCR_454_AR=589;PCR_454_RR=589 20 9520132 . G A . . Sample=NA12046;GT=0/1;PCR_454_AR=688;PCR_454_RR=708 20 9520132 . G A . . Sample=NA18517;GT=0/1;PCR_454_AR=566;PCR_454_RR=585 20 9520132 . G A . . Sample=NA18858;GT=0/1;PCR_454_AR=550;PCR_454_RR=561 20 9543621 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=499;PCR_454_RR=480 20 9543621 . C T . . Sample=HG00104;GT=0/1;PCR_454_AR=524;PCR_454_RR=480 20 9543621 . C T . . Sample=HG00112;GT=0/1;PCR_454_AR=467;PCR_454_RR=406 20 9543621 . C T . . Sample=HG00099;GT=1/1;PCR_454_AR=1321;PCR_454_RR=9 20 9543621 . C T . . Sample=HG00106;GT=1/1;PCR_454_AR=802;PCR_454_RR=6 20 9547022 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=853;PCR_454_RR=944 20 9560813 . T C . . Sample=NA12761;GT=0/1;PCR_454_AR=692;PCR_454_RR=734 20 10030206 . C T . . Sample=NA19175;GT=0/1;PCR_454_AR=784;PCR_454_RR=759 20 10030206 . C T . . Sample=NA19380;GT=0/1;PCR_454_AR=781;PCR_454_RR=739 20 10030206 . C T . . Sample=NA19446;GT=0/1;PCR_454_AR=533;PCR_454_RR=540 20 13098183 . A C . . Sample=NA19453;GT=0/1;PCR_454_AR=857;PCR_454_RR=1146 20 16253907 . C A . . Sample=NA19087;GT=0/1;PCR_454_AR=868;PCR_454_RR=854 20 16254032 . G A . . Sample=NA19651;GT=0/1;PCR_454_AR=299;PCR_454_RR=263 20 16485159 . T G . . Sample=NA18625;GT=0/1;PCR_454_AR=160;PCR_454_RR=1004 20 17474781 . G A . . Sample=NA18870;GT=0/1;PCR_454_AR=496;PCR_454_RR=536 20 17585255 . C G . . Sample=NA18528;GT=0/1;PCR_454_AR=370;PCR_454_RR=390 20 17923814 . C T . . Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1854 20 17923814 . C T . . Sample=HG00126;GT=0/0;PCR_454_AR=1;PCR_454_RR=1724 20 17928182 . T G . . Sample=NA18522;GT=0/1;PCR_454_AR=222;PCR_454_RR=1564 20 17931030 . C G . . Sample=NA20508;GT=0/1;PCR_454_AR=495;PCR_454_RR=446 20 17933265 . G A . . Sample=NA19137;GT=0/1;PCR_454_AR=300;PCR_454_RR=315 20 17968811 . C G . . Sample=NA19222;GT=0/1;PCR_454_AR=150;PCR_454_RR=189 20 18123396 . A G . . Sample=NA20507;GT=0/0;PCR_454_AR=5;PCR_454_RR=2239 20 18125941 . T C . . Sample=NA12006;GT=0/0;PCR_454_AR=2;PCR_454_RR=2354 20 18125941 . T C . . Sample=NA12762;GT=0/0;PCR_454_AR=4;PCR_454_RR=1116 20 18374912 . T A . . Sample=NA19189;GT=0/1;PCR_454_AR=896;PCR_454_RR=888 20 18440904 . G C . . Sample=NA19058;GT=0/1;PCR_454_AR=685;PCR_454_RR=881 20 19698200 . C T . . Sample=NA18574;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1086 20 20020489 . T C . . Sample=NA19000;GT=0/1;PCR_454_AR=459;PCR_454_RR=436 20 20028425 . C T . . Sample=NA20787;GT=0/1;PCR_454_AR=687;PCR_454_RR=739 20 20033171 . G A . . Sample=NA19468;GT=0/0;PCR_454_AR=109;PCR_454_RR=1866 20 20051634 . A G . . Sample=NA19711;GT=0/1;PCR_454_AR=659;PCR_454_RR=2324 20 20051634 . A G . . Sample=NA20126;GT=0/1;PCR_454_AR=687;PCR_454_RR=2379 20 20177371 . T C . . Sample=NA19713;GT=0/1;PCR_454_AR=882;PCR_454_RR=785 20 21346240 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=707;PCR_454_RR=711 20 21346240 . C T . . Sample=NA18489;GT=0/1;PCR_454_AR=670;PCR_454_RR=648 20 21346240 . C T . . Sample=NA18498;GT=0/1;PCR_454_AR=706;PCR_454_RR=667 20 21346240 . C T . . Sample=NA18502;GT=0/1;PCR_454_AR=698;PCR_454_RR=678 20 21346240 . C T . . Sample=NA18505;GT=1/1;PCR_454_AR=1096;PCR_454_RR=2 20 21494183 . C T . . Sample=HG00128;GT=0/1;PCR_454_AR=556;PCR_454_RR=605 20 21494183 . C T . . Sample=HG00151;GT=0/1;PCR_454_AR=465;PCR_454_RR=425 20 21494183 . C T . . Sample=HG00234;GT=0/1;PCR_454_AR=583;PCR_454_RR=487 20 21494183 . C T . . Sample=HG00355;GT=0/1;PCR_454_AR=608;PCR_454_RR=521 20 21494183 . C T . . Sample=HG00362;GT=0/1;PCR_454_AR=518;PCR_454_RR=577 20 21687304 . C T . . Sample=NA19657;GT=0/1;PCR_454_AR=804;PCR_454_RR=862 20 23028428 . C T . . Sample=NA18970;GT=0/1;PCR_454_AR=360;PCR_454_RR=418 20 23028637 . C G . . Sample=NA18517;GT=0/1;PCR_454_AR=358;PCR_454_RR=374 20 23028637 . C G . . Sample=NA19118;GT=0/1;PCR_454_AR=502;PCR_454_RR=432 20 23420987 . G T . . Sample=NA19076;GT=0/0;PCR_454_AR=20;PCR_454_RR=1732 20 23420993 . C G . . Sample=NA19076;GT=0/0;PCR_454_AR=40;PCR_454_RR=3495 20 23424637 . C T . . Sample=HG00126;GT=0/1;PCR_454_AR=766;PCR_454_RR=721 20 23424637 . C T . . Sample=HG00150;GT=0/1;PCR_454_AR=444;PCR_454_RR=435 20 23424637 . C T . . Sample=HG00247;GT=0/1;PCR_454_AR=510;PCR_454_RR=486 20 23424637 . C T . . Sample=HG00565;GT=0/1;PCR_454_AR=684;PCR_454_RR=609 20 23424637 . C T . . Sample=HG00593;GT=0/1;PCR_454_AR=640;PCR_454_RR=676 20 23545657 . A C . . Sample=NA18924;GT=0/1;PCR_454_AR=767;PCR_454_RR=780 20 23548918 . T C . . Sample=NA18501;GT=0/1;PCR_454_AR=1397;PCR_454_RR=1168 20 23548918 . T C . . Sample=NA18502;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1383 20 23548918 . T C . . Sample=NA18856;GT=0/1;PCR_454_AR=1376;PCR_454_RR=1446 20 23548918 . T C . . Sample=NA18907;GT=0/1;PCR_454_AR=1522;PCR_454_RR=1533 20 23548918 . T C . . Sample=NA19036;GT=0/1;PCR_454_AR=1549;PCR_454_RR=1624 20 23667793 . G T . . Sample=NA11994;GT=0/0;PCR_454_AR=135;PCR_454_RR=1637 20 23667793 . G T . . Sample=NA12400;GT=0/1;PCR_454_AR=651;PCR_454_RR=619 20 23667793 . G T . . Sample=NA18527;GT=0/1;PCR_454_AR=816;PCR_454_RR=732 20 23667793 . G T . . Sample=NA18566;GT=0/1;PCR_454_AR=928;PCR_454_RR=2446 20 23667793 . G T . . Sample=NA19064;GT=0/1;PCR_454_AR=892;PCR_454_RR=2346 20 23667834 . A C . . Sample=NA18510;GT=0/0;PCR_454_AR=27;PCR_454_RR=622 20 23667834 . A C . . Sample=NA18858;GT=0/0;PCR_454_AR=32;PCR_454_RR=615 20 23731469 . G T . . Sample=NA20544;GT=0/1;PCR_454_AR=292;PCR_454_RR=376 20 23804690 . A C . . Sample=NA19749;GT=0/1;PCR_454_AR=1141;PCR_454_RR=1145 20 23807156 . G C . . Sample=HG00129;GT=0/0;PCR_454_AR=0;PCR_454_RR=1447 20 23807156 . G C . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=1603 20 23860201 . C T . . Sample=NA18553;GT=0/1;PCR_454_AR=722;PCR_454_RR=657 20 23965921 . G A . . Sample=NA18549;GT=0/0;PCR_454_AR=21;PCR_454_RR=582 20 23965921 . G A . . Sample=NA19000;GT=0/0;PCR_454_AR=19;PCR_454_RR=337 20 24523782 . G A . . Sample=NA19921;GT=0/1;PCR_454_AR=933;PCR_454_RR=1005 20 24523986 . C A . . Sample=HG00104;GT=0/1;PCR_454_AR=1056;PCR_454_RR=1346 20 24954343 . G A . . Sample=NA19146;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1132 20 25058490 . T G . . Sample=NA11830;GT=0/0;PCR_454_AR=5;PCR_454_RR=1757 20 25187224 . A G . . Sample=NA19137;GT=0/1;PCR_454_AR=69;PCR_454_RR=566 20 25203611 . T C . . Sample=NA12006;GT=0/1;PCR_454_AR=1326;PCR_454_RR=1209 20 25252066 . A G . . Sample=NA18637;GT=0/1;PCR_454_AR=1208;PCR_454_RR=1230 20 25262768 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=920;PCR_454_RR=727 20 25262768 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=733;PCR_454_RR=613 20 25262768 . G A . . Sample=HG00112;GT=0/1;PCR_454_AR=756;PCR_454_RR=723 20 25262768 . G A . . Sample=HG00130;GT=0/1;PCR_454_AR=854;PCR_454_RR=827 20 25262768 . G A . . Sample=HG00152;GT=0/1;PCR_454_AR=798;PCR_454_RR=764 20 25277132 . C T . . Sample=NA18861;GT=0/1;PCR_454_AR=415;PCR_454_RR=446 20 25434162 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=566;PCR_454_RR=613 20 25434162 . C T . . Sample=NA19395;GT=0/1;PCR_454_AR=504;PCR_454_RR=531 20 25439088 . C T . . Sample=NA19095;GT=0/0;PCR_454_AR=1;PCR_454_RR=1220 20 25439088 . C T . . Sample=NA19923;GT=0/1;PCR_454_AR=575;PCR_454_RR=834 20 25457145 . G A . . Sample=NA12842;GT=0/1;PCR_454_AR=333;PCR_454_RR=438 20 25457559 . G A . . Sample=NA19159;GT=0/1;PCR_454_AR=1225;PCR_454_RR=1285 20 25457665 . C T . . Sample=NA20341;GT=0/1;PCR_454_AR=627;PCR_454_RR=1348 20 25459659 . T C . . Sample=NA18647;GT=0/0;PCR_454_AR=5;PCR_454_RR=2809 20 25459659 . T C . . Sample=NA18748;GT=0/0;PCR_454_AR=5;PCR_454_RR=2184 20 25459659 . T C . . Sample=HG01274;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1375 20 25459659 . T C . . Sample=NA12275;GT=0/1;PCR_454_AR=1183;PCR_454_RR=1148 20 25459659 . T C . . Sample=NA12718;GT=0/1;PCR_454_AR=1017;PCR_454_RR=1225 20 25478961 . G A . . Sample=HG00104;GT=0/0;PCR_454_AR=1;PCR_454_RR=1933 20 25478961 . G A . . Sample=HG00234;GT=0/0;PCR_454_AR=0;PCR_454_RR=1964 20 25478961 . G A . . Sample=HG00364;GT=0/0;PCR_454_AR=2;PCR_454_RR=1909 20 25478961 . G A . . Sample=HG00593;GT=0/0;PCR_454_AR=2;PCR_454_RR=2173 20 25478961 . G A . . Sample=HG01271;GT=0/0;PCR_454_AR=0;PCR_454_RR=2082 20 30407977 . A G . . Sample=NA12287;GT=0/1;PCR_454_AR=1313;PCR_454_RR=1488 20 30432438 . C T . . Sample=NA19352;GT=0/1;PCR_454_AR=1043;PCR_454_RR=964 20 30432438 . C T . . Sample=NA19654;GT=0/1;PCR_454_AR=937;PCR_454_RR=1465 20 30432570 . T C . . Sample=NA18510;GT=0/1;PCR_454_AR=1224;PCR_454_RR=1413 20 30432570 . T C . . Sample=NA18858;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1052 20 30432570 . T C . . Sample=NA18868;GT=0/1;PCR_454_AR=1087;PCR_454_RR=966 20 30432570 . T C . . Sample=NA18871;GT=0/1;PCR_454_AR=1178;PCR_454_RR=1344 20 30432570 . T C . . Sample=NA18522;GT=1/1;PCR_454_AR=1873;PCR_454_RR=7 20 30602754 . C T . . Sample=NA19749;GT=0/1;PCR_454_AR=63;PCR_454_RR=409 20 30729618 . G A . . Sample=NA11994;GT=0/0;PCR_454_AR=0;PCR_454_RR=1866 20 30729618 . G A . . Sample=NA07037;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1435 20 30729618 . G A . . Sample=NA12058;GT=0/1;PCR_454_AR=963;PCR_454_RR=990 20 30729618 . G A . . Sample=NA12144;GT=0/1;PCR_454_AR=1419;PCR_454_RR=1136 20 30729618 . G A . . Sample=NA12282;GT=0/1;PCR_454_AR=1353;PCR_454_RR=1148 20 30789767 . G A . . Sample=HG00350;GT=0/0;PCR_454_AR=36;PCR_454_RR=553 20 30897726 . G A . . Sample=NA20507;GT=0/0;PCR_454_AR=239;PCR_454_RR=2404 20 30918043 . C T . . Sample=NA19707;GT=0/1;PCR_454_AR=1147;PCR_454_RR=1123 20 30918043 . C T . . Sample=NA20775;GT=0/1;PCR_454_AR=1234;PCR_454_RR=1140 20 31021429 . G C . . Sample=NA18870;GT=0/1;PCR_454_AR=747;PCR_454_RR=929 20 31021429 . G C . . Sample=NA19319;GT=0/1;PCR_454_AR=585;PCR_454_RR=657 20 31021429 . G C . . Sample=NA19445;GT=0/1;PCR_454_AR=531;PCR_454_RR=553 20 31021429 . G C . . Sample=NA20127;GT=0/1;PCR_454_AR=661;PCR_454_RR=679 20 31021429 . G C . . Sample=NA20317;GT=0/1;PCR_454_AR=874;PCR_454_RR=917 20 31022764 . C T . . Sample=NA18498;GT=0/1;PCR_454_AR=1455;PCR_454_RR=1259 20 31022764 . C T . . Sample=NA18507;GT=0/1;PCR_454_AR=1020;PCR_454_RR=972 20 31022764 . C T . . Sample=NA18511;GT=0/1;PCR_454_AR=1339;PCR_454_RR=1297 20 31022764 . C T . . Sample=NA18856;GT=0/1;PCR_454_AR=1582;PCR_454_RR=1572 20 31022764 . C T . . Sample=NA18870;GT=0/1;PCR_454_AR=1642;PCR_454_RR=1613 20 31024033 . G A . . Sample=HG01356;GT=0/1;PCR_454_AR=1045;PCR_454_RR=1002 20 31024033 . G A . . Sample=NA18537;GT=0/1;PCR_454_AR=794;PCR_454_RR=788 20 31024033 . G A . . Sample=NA18557;GT=0/1;PCR_454_AR=830;PCR_454_RR=795 20 31024033 . G A . . Sample=NA18558;GT=0/1;PCR_454_AR=833;PCR_454_RR=878 20 31024033 . G A . . Sample=NA18637;GT=1/1;PCR_454_AR=1528;PCR_454_RR=6 20 31040782 . G A . . Sample=HG00097;GT=0/1;PCR_454_AR=978;PCR_454_RR=1231 20 31040782 . G A . . Sample=HG00179;GT=0/1;PCR_454_AR=1054;PCR_454_RR=993 20 31040782 . G A . . Sample=HG01620;GT=0/1;PCR_454_AR=1091;PCR_454_RR=1111 20 31040782 . G A . . Sample=NA12273;GT=0/1;PCR_454_AR=1073;PCR_454_RR=1182 20 31040782 . G A . . Sample=NA12341;GT=0/1;PCR_454_AR=1102;PCR_454_RR=1318 20 31375167 . G A . . Sample=NA18486;GT=0/1;PCR_454_AR=563;PCR_454_RR=523 20 31375167 . G A . . Sample=NA19113;GT=0/1;PCR_454_AR=628;PCR_454_RR=620 20 31388076 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=809;PCR_454_RR=773 20 31388076 . C T . . Sample=NA18519;GT=0/1;PCR_454_AR=683;PCR_454_RR=752 20 31388076 . C T . . Sample=NA18856;GT=0/1;PCR_454_AR=1012;PCR_454_RR=1073 20 31388076 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=888;PCR_454_RR=931 20 31388076 . C T . . Sample=NA18522;GT=1/1;PCR_454_AR=1422;PCR_454_RR=2 20 31424592 . C T . . Sample=NA19146;GT=0/1;PCR_454_AR=237;PCR_454_RR=257 20 31434427 . A G . . Sample=NA11995;GT=0/1;PCR_454_AR=325;PCR_454_RR=325 20 31604884 . A G . . Sample=NA12748;GT=0/1;PCR_454_AR=1098;PCR_454_RR=1153 20 31606483 . G C . . Sample=NA18740;GT=0/1;PCR_454_AR=595;PCR_454_RR=964 20 31606907 . G A . . Sample=NA19753;GT=0/0;PCR_454_AR=0;PCR_454_RR=1627 20 31606907 . G A . . Sample=NA19747;GT=0/1;PCR_454_AR=952;PCR_454_RR=884 20 31622899 . A G . . Sample=NA19038;GT=0/1;PCR_454_AR=196;PCR_454_RR=111 20 31626754 . G A . . Sample=NA18579;GT=0/1;PCR_454_AR=941;PCR_454_RR=902 20 31643241 . A C . . Sample=NA18622;GT=0/1;PCR_454_AR=832;PCR_454_RR=877 20 31659074 . G A . . Sample=NA19449;GT=0/1;PCR_454_AR=915;PCR_454_RR=863 20 31672711 . A G . . Sample=NA20754;GT=0/1;PCR_454_AR=762;PCR_454_RR=820 20 31680333 . C T . . Sample=HG00156;GT=0/1;PCR_454_AR=446;PCR_454_RR=438 20 31680333 . C T . . Sample=HG00235;GT=0/1;PCR_454_AR=525;PCR_454_RR=435 20 31680333 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=433;PCR_454_RR=415 20 31680333 . C T . . Sample=NA12043;GT=0/1;PCR_454_AR=559;PCR_454_RR=477 20 31680333 . C T . . Sample=NA12046;GT=0/1;PCR_454_AR=364;PCR_454_RR=330 20 31695565 . C T . . Sample=NA19054;GT=0/1;PCR_454_AR=988;PCR_454_RR=944 20 31889182 . T C . . Sample=HG01277;GT=0/1;PCR_454_AR=594;PCR_454_RR=639 20 31889182 . T C . . Sample=HG01278;GT=0/1;PCR_454_AR=533;PCR_454_RR=540 20 31889182 . T C . . Sample=HG01623;GT=0/1;PCR_454_AR=703;PCR_454_RR=668 20 31889182 . T C . . Sample=NA18487;GT=0/1;PCR_454_AR=644;PCR_454_RR=647 20 31889182 . T C . . Sample=NA18486;GT=1/1;PCR_454_AR=1419;PCR_454_RR=15 20 31890796 . G A . . Sample=NA18595;GT=0/1;PCR_454_AR=36;PCR_454_RR=49 20 31967485 . T C . . Sample=NA18757;GT=0/0;PCR_454_AR=4;PCR_454_RR=1506 20 32162066 . G C . . Sample=HG00099;GT=0/1;PCR_454_AR=98;PCR_454_RR=92 20 32162066 . G C . . Sample=NA12282;GT=0/1;PCR_454_AR=72;PCR_454_RR=74 20 32162066 . G C . . Sample=NA12342;GT=0/1;PCR_454_AR=105;PCR_454_RR=134 20 32162066 . G C . . Sample=NA12778;GT=0/1;PCR_454_AR=94;PCR_454_RR=122 20 32162066 . G C . . Sample=NA19773;GT=0/1;PCR_454_AR=84;PCR_454_RR=115 20 32295637 . A G . . Sample=NA19204;GT=0/1;PCR_454_AR=1263;PCR_454_RR=1230 20 32298533 . G A . . Sample=HG01125;GT=0/1;PCR_454_AR=1577;PCR_454_RR=1574 20 32298533 . G A . . Sample=NA18510;GT=0/1;PCR_454_AR=1537;PCR_454_RR=1597 20 32298533 . G A . . Sample=NA18520;GT=0/1;PCR_454_AR=1689;PCR_454_RR=1754 20 32298533 . G A . . Sample=NA19099;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1940 20 32298533 . G A . . Sample=NA19129;GT=0/1;PCR_454_AR=1900;PCR_454_RR=1840 20 32336754 . G A . . Sample=HG00358;GT=0/1;PCR_454_AR=1185;PCR_454_RR=1161 20 32336754 . G A . . Sample=HG00565;GT=0/1;PCR_454_AR=1018;PCR_454_RR=958 20 32336754 . G A . . Sample=HG00595;GT=0/1;PCR_454_AR=1201;PCR_454_RR=1222 20 32336754 . G A . . Sample=NA18532;GT=0/1;PCR_454_AR=1204;PCR_454_RR=1235 20 32336754 . G A . . Sample=NA18542;GT=1/1;PCR_454_AR=2997;PCR_454_RR=11 20 32358043 . A T . . Sample=NA18955;GT=0/1;PCR_454_AR=1050;PCR_454_RR=1022 20 32881901 . T C . . Sample=NA19257;GT=0/1;PCR_454_AR=1007;PCR_454_RR=966 20 33328321 . C T . . Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=629 20 33328321 . C T . . Sample=NA18516;GT=0/1;PCR_454_AR=613;PCR_454_RR=605 20 33328321 . C T . . Sample=NA19044;GT=0/1;PCR_454_AR=629;PCR_454_RR=661 20 33328321 . C T . . Sample=NA19102;GT=0/1;PCR_454_AR=680;PCR_454_RR=625 20 33328321 . C T . . Sample=NA19175;GT=0/1;PCR_454_AR=652;PCR_454_RR=703 20 33330691 . C G . . Sample=NA19189;GT=0/1;PCR_454_AR=604;PCR_454_RR=575 20 33433247 . G A . . Sample=NA11919;GT=0/1;PCR_454_AR=196;PCR_454_RR=195 20 33447313 . C T . . Sample=HG01125;GT=0/1;PCR_454_AR=260;PCR_454_RR=285 20 33447313 . C T . . Sample=NA18504;GT=0/1;PCR_454_AR=231;PCR_454_RR=217 20 33447313 . C T . . Sample=NA18517;GT=0/1;PCR_454_AR=298;PCR_454_RR=311 20 33447313 . C T . . Sample=NA18520;GT=0/1;PCR_454_AR=254;PCR_454_RR=256 20 33447313 . C T . . Sample=NA18522;GT=0/1;PCR_454_AR=286;PCR_454_RR=277 20 33517251 . C T . . Sample=HG00126;GT=0/1;PCR_454_AR=685;PCR_454_RR=676 20 33517301 . G A . . Sample=NA20282;GT=0/1;PCR_454_AR=1082;PCR_454_RR=1076 20 33523396 . A C . . Sample=NA18910;GT=0/1;PCR_454_AR=879;PCR_454_RR=933 20 33572880 . C T . . Sample=NA20516;GT=0/1;PCR_454_AR=935;PCR_454_RR=847 20 33575007 . C T . . Sample=NA19118;GT=0/1;PCR_454_AR=793;PCR_454_RR=659 20 33575043 . C T . . Sample=NA19036;GT=0/1;PCR_454_AR=972;PCR_454_RR=919 20 33575043 . C T . . Sample=NA19308;GT=0/1;PCR_454_AR=801;PCR_454_RR=728 20 33575043 . C T . . Sample=NA19434;GT=0/1;PCR_454_AR=825;PCR_454_RR=915 20 33575043 . C T . . Sample=NA19439;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1073 20 33575043 . C T . . Sample=NA19466;GT=0/1;PCR_454_AR=936;PCR_454_RR=931 20 33583330 . A G . . Sample=HG00097;GT=1/1;PCR_454_AR=651;PCR_454_RR=5 20 33583330 . A G . . Sample=HG00099;GT=1/1;PCR_454_AR=326;PCR_454_RR=0 20 33583330 . A G . . Sample=HG00104;GT=1/1;PCR_454_AR=430;PCR_454_RR=2 20 33583330 . A G . . Sample=HG00106;GT=1/1;PCR_454_AR=613;PCR_454_RR=3 20 33583330 . A G . . Sample=HG00112;GT=1/1;PCR_454_AR=632;PCR_454_RR=6 20 33584196 . C T . . Sample=NA12286;GT=0/1;PCR_454_AR=989;PCR_454_RR=1638 20 33584196 . C T . . Sample=NA12750;GT=0/1;PCR_454_AR=886;PCR_454_RR=1206 20 33584196 . C T . . Sample=NA19750;GT=0/1;PCR_454_AR=1179;PCR_454_RR=1155 20 33584196 . C T . . Sample=NA20807;GT=0/1;PCR_454_AR=1089;PCR_454_RR=1724 20 33584196 . C T . . Sample=NA20826;GT=0/1;PCR_454_AR=1373;PCR_454_RR=1259 20 33587399 . G A . . Sample=NA19328;GT=0/1;PCR_454_AR=893;PCR_454_RR=754 20 33711732 . T A . . Sample=NA19347;GT=0/1;PCR_454_AR=887;PCR_454_RR=946 20 33874473 . C A . . Sample=NA18626;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1012 20 33874719 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=585;PCR_454_RR=542 20 33874719 . C T . . Sample=HG00141;GT=0/1;PCR_454_AR=499;PCR_454_RR=508 20 33874719 . C T . . Sample=HG00142;GT=0/1;PCR_454_AR=541;PCR_454_RR=540 20 33874719 . C T . . Sample=HG00143;GT=0/1;PCR_454_AR=699;PCR_454_RR=604 20 33874719 . C T . . Sample=HG00156;GT=0/1;PCR_454_AR=722;PCR_454_RR=617 20 34092317 . C A . . Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=1205 20 34092317 . C A . . Sample=HG00266;GT=0/0;PCR_454_AR=3;PCR_454_RR=3354 20 34218898 . A G . . Sample=NA12763;GT=0/1;PCR_454_AR=295;PCR_454_RR=291 20 34292440 . T C . . Sample=NA18639;GT=0/1;PCR_454_AR=481;PCR_454_RR=572 20 34317286 . G A . . Sample=NA19204;GT=0/1;PCR_454_AR=665;PCR_454_RR=705 20 34611604 . C T . . Sample=NA11893;GT=0/1;PCR_454_AR=1180;PCR_454_RR=1243 20 35060852 . G A . . Sample=NA12283;GT=0/1;PCR_454_AR=433;PCR_454_RR=444 20 35060852 . G A . . Sample=NA19676;GT=0/1;PCR_454_AR=368;PCR_454_RR=421 20 35068262 . A C . . Sample=NA20759;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1190 20 35075140 . C T . . Sample=NA19444;GT=0/1;PCR_454_AR=1174;PCR_454_RR=605 20 35075140 . C T . . Sample=NA19448;GT=0/1;PCR_454_AR=1574;PCR_454_RR=932 20 35075309 . G A . . Sample=NA18549;GT=0/1;PCR_454_AR=923;PCR_454_RR=1559 20 35075309 . G A . . Sample=NA19391;GT=0/1;PCR_454_AR=1114;PCR_454_RR=1064 20 35075309 . G A . . Sample=NA19397;GT=0/1;PCR_454_AR=1198;PCR_454_RR=1233 20 35176551 . A G . . Sample=NA20289;GT=0/1;PCR_454_AR=532;PCR_454_RR=1682 20 35207263 . G A . . Sample=HG00234;GT=0/1;PCR_454_AR=235;PCR_454_RR=221 20 35219406 . G C . . Sample=HG00105;GT=0/0;PCR_454_AR=57;PCR_454_RR=585 20 35219406 . G C . . Sample=HG00130;GT=0/0;PCR_454_AR=58;PCR_454_RR=574 20 35438474 . G A . . Sample=NA18642;GT=0/1;PCR_454_AR=1030;PCR_454_RR=1093 20 35507540 . G A . . Sample=NA19740;GT=0/1;PCR_454_AR=466;PCR_454_RR=584 20 35539699 . T C . . Sample=NA12717;GT=0/1;PCR_454_AR=336;PCR_454_RR=421 20 35812756 . C T . . Sample=NA19726;GT=0/1;PCR_454_AR=1085;PCR_454_RR=1070 20 35944759 . A C . . Sample=NA11831;GT=0/0;PCR_454_AR=1;PCR_454_RR=1726 20 35944759 . A C . . Sample=NA11832;GT=0/0;PCR_454_AR=3;PCR_454_RR=1809 20 36024598 . C T . . Sample=NA19682;GT=0/1;PCR_454_AR=677;PCR_454_RR=797 20 36024598 . C T . . Sample=NA20528;GT=0/1;PCR_454_AR=691;PCR_454_RR=703 20 36030944 . T C . . Sample=NA18618;GT=0/0;PCR_454_AR=0;PCR_454_RR=985 20 36030944 . T C . . Sample=NA18626;GT=0/0;PCR_454_AR=2;PCR_454_RR=778 20 36030944 . T C . . Sample=NA18916;GT=0/1;PCR_454_AR=454;PCR_454_RR=444 20 36030944 . T C . . Sample=NA19150;GT=0/1;PCR_454_AR=471;PCR_454_RR=509 20 36488331 . A G . . Sample=NA20340;GT=0/1;PCR_454_AR=1388;PCR_454_RR=1472 20 36640610 . C G . . Sample=NA18508;GT=0/1;PCR_454_AR=985;PCR_454_RR=1026 20 36641870 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1095 20 36641870 . G A . . Sample=NA11893;GT=0/1;PCR_454_AR=976;PCR_454_RR=1033 20 36641870 . G A . . Sample=NA12399;GT=0/1;PCR_454_AR=971;PCR_454_RR=973 20 36641870 . G A . . Sample=NA12489;GT=0/1;PCR_454_AR=1107;PCR_454_RR=1037 20 36641870 . G A . . Sample=NA12749;GT=0/1;PCR_454_AR=947;PCR_454_RR=885 20 36775155 . A G . . Sample=NA19067;GT=0/1;PCR_454_AR=771;PCR_454_RR=772 20 36775233 . G A . . Sample=NA19352;GT=0/1;PCR_454_AR=732;PCR_454_RR=723 20 36784261 . G A . . Sample=NA19171;GT=0/1;PCR_454_AR=1197;PCR_454_RR=1200 20 36841848 . C T . . Sample=NA19449;GT=0/1;PCR_454_AR=402;PCR_454_RR=394 20 36869075 . G A . . Sample=NA19185;GT=0/1;PCR_454_AR=1430;PCR_454_RR=1382 20 36869206 . C T . . Sample=NA20287;GT=0/1;PCR_454_AR=584;PCR_454_RR=626 20 36979308 . T A . . Sample=NA11894;GT=0/1;PCR_454_AR=973;PCR_454_RR=1087 20 37001736 . C T . . Sample=NA18987;GT=0/1;PCR_454_AR=122;PCR_454_RR=88 20 39798902 . C T . . Sample=NA18994;GT=0/1;PCR_454_AR=1212;PCR_454_RR=1202 20 39981307 . G T . . Sample=NA18595;GT=0/1;PCR_454_AR=1273;PCR_454_RR=1102 20 39981307 . G T . . Sample=NA18622;GT=0/1;PCR_454_AR=635;PCR_454_RR=623 20 39981307 . G T . . Sample=NA18977;GT=0/1;PCR_454_AR=1251;PCR_454_RR=1141 20 39981307 . G T . . Sample=NA18978;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1331 20 39981307 . G T . . Sample=NA18998;GT=0/1;PCR_454_AR=1174;PCR_454_RR=1225 20 39986913 . G A . . Sample=NA20317;GT=0/1;PCR_454_AR=627;PCR_454_RR=535 20 39987386 . G A . . Sample=NA19437;GT=0/1;PCR_454_AR=989;PCR_454_RR=971 20 39992390 . G A . . Sample=NA18636;GT=0/1;PCR_454_AR=925;PCR_454_RR=969 20 39993723 . C T . . Sample=NA18489;GT=0/1;PCR_454_AR=677;PCR_454_RR=819 20 39993723 . C T . . Sample=NA18505;GT=0/1;PCR_454_AR=603;PCR_454_RR=578 20 39993723 . C T . . Sample=NA18517;GT=0/1;PCR_454_AR=791;PCR_454_RR=747 20 39993723 . C T . . Sample=NA19380;GT=0/1;PCR_454_AR=869;PCR_454_RR=972 20 39993790 . G A . . Sample=NA18871;GT=0/1;PCR_454_AR=2297;PCR_454_RR=2512 20 40033848 . A G . . Sample=HG00559;GT=0/0;PCR_454_AR=6;PCR_454_RR=2130 20 40050233 . T G . . Sample=HG01133;GT=0/0;PCR_454_AR=2;PCR_454_RR=1613 20 40050233 . T G . . Sample=NA18502;GT=0/0;PCR_454_AR=4;PCR_454_RR=1967 20 40162202 . T C . . Sample=NA12874;GT=0/1;PCR_454_AR=171;PCR_454_RR=157 20 42143783 . A G . . Sample=NA20334;GT=0/1;PCR_454_AR=1011;PCR_454_RR=632 20 42143783 . A G . . Sample=NA20336;GT=0/1;PCR_454_AR=1556;PCR_454_RR=492 20 42196587 . G A . . Sample=NA19312;GT=0/1;PCR_454_AR=522;PCR_454_RR=486 20 42196587 . G A . . Sample=NA19383;GT=0/1;PCR_454_AR=693;PCR_454_RR=821 20 42333997 . C T . . Sample=NA19058;GT=0/1;PCR_454_AR=994;PCR_454_RR=994 20 42680115 . G A . . Sample=NA18611;GT=0/1;PCR_454_AR=1042;PCR_454_RR=1086 20 42747246 . C T . . Sample=HG00097;GT=0/1;PCR_454_AR=1132;PCR_454_RR=1174 20 42747246 . C T . . Sample=HG00106;GT=0/1;PCR_454_AR=899;PCR_454_RR=983 20 42747246 . C T . . Sample=HG00112;GT=0/1;PCR_454_AR=901;PCR_454_RR=960 20 42747246 . C T . . Sample=HG00135;GT=0/1;PCR_454_AR=677;PCR_454_RR=680 20 42747246 . C T . . Sample=HG00142;GT=0/1;PCR_454_AR=928;PCR_454_RR=956 20 42939738 . C T . . Sample=NA18611;GT=0/1;PCR_454_AR=1131;PCR_454_RR=984 20 43243299 . G C . . Sample=NA18633;GT=0/1;PCR_454_AR=1194;PCR_454_RR=1277 20 43255152 . G A . . Sample=HG00130;GT=0/0;PCR_454_AR=0;PCR_454_RR=2287 20 43255152 . G A . . Sample=HG00234;GT=0/0;PCR_454_AR=1;PCR_454_RR=2172 20 43255152 . G A . . Sample=NA18618;GT=0/0;PCR_454_AR=2;PCR_454_RR=2266 20 43255152 . G A . . Sample=NA18956;GT=0/0;PCR_454_AR=0;PCR_454_RR=2152 20 43255152 . G A . . Sample=NA19083;GT=0/1;PCR_454_AR=986;PCR_454_RR=974 20 43723672 . G A . . Sample=NA18530;GT=0/1;PCR_454_AR=356;PCR_454_RR=401 20 43723672 . G A . . Sample=NA18622;GT=0/1;PCR_454_AR=449;PCR_454_RR=391 20 43739354 . G A . . Sample=NA18504;GT=0/1;PCR_454_AR=455;PCR_454_RR=1477 20 43934213 . G T . . Sample=HG01345;GT=0/1;PCR_454_AR=1327;PCR_454_RR=1169 20 44190750 . T G . . Sample=HG00143;GT=0/1;PCR_454_AR=898;PCR_454_RR=938 20 44190750 . T G . . Sample=NA12340;GT=0/1;PCR_454_AR=882;PCR_454_RR=872 20 44424037 . G A . . Sample=HG00152;GT=0/1;PCR_454_AR=603;PCR_454_RR=593 20 44469565 . C T . . Sample=NA18549;GT=0/1;PCR_454_AR=999;PCR_454_RR=246 20 44485866 . T A . . Sample=NA12890;GT=0/1;PCR_454_AR=536;PCR_454_RR=596 20 44506417 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=1320;PCR_454_RR=1305 20 44506417 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1559;PCR_454_RR=1533 20 44506417 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=3211;PCR_454_RR=20 20 44506417 . G A . . Sample=HG00112;GT=1/1;PCR_454_AR=2632;PCR_454_RR=20 20 44506417 . G A . . Sample=HG00122;GT=1/1;PCR_454_AR=2875;PCR_454_RR=6 20 44506987 . G C . . Sample=NA19117;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1532 20 44511253 . C T . . Sample=NA20799;GT=0/1;PCR_454_AR=1286;PCR_454_RR=1280 20 44519372 . G A . . Sample=NA19437;GT=0/0;PCR_454_AR=0;PCR_454_RR=2075 20 44519372 . G A . . Sample=NA19917;GT=0/1;PCR_454_AR=1243;PCR_454_RR=1234 20 44576246 . G A . . Sample=NA18912;GT=0/1;PCR_454_AR=458;PCR_454_RR=2154 20 44576246 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=1131;PCR_454_RR=1078 20 44576246 . G A . . Sample=NA20276;GT=0/1;PCR_454_AR=860;PCR_454_RR=852 20 44576246 . G A . . Sample=NA20289;GT=0/1;PCR_454_AR=492;PCR_454_RR=2174 20 44580998 . T C . . Sample=NA18566;GT=0/1;PCR_454_AR=877;PCR_454_RR=925 20 44680318 . C G . . Sample=HG00592;GT=0/0;PCR_454_AR=0;PCR_454_RR=3602 20 44680318 . C G . . Sample=HG01139;GT=0/0;PCR_454_AR=1;PCR_454_RR=3510 20 44856207 . G A . . Sample=NA11995;GT=0/1;PCR_454_AR=127;PCR_454_RR=17 20 44980779 . G A . . Sample=NA18553;GT=0/1;PCR_454_AR=993;PCR_454_RR=1022 20 45919012 . C T . . Sample=NA19445;GT=0/1;PCR_454_AR=265;PCR_454_RR=525 20 46271051 . C G . . Sample=NA18486;GT=0/1;PCR_454_AR=754;PCR_454_RR=749 20 47262594 . C A . . Sample=NA20291;GT=0/1;PCR_454_AR=1210;PCR_454_RR=1153 20 47558430 . C T . . Sample=NA20296;GT=0/1;PCR_454_AR=699;PCR_454_RR=682 20 47733688 . T C . . Sample=NA18630;GT=0/0;PCR_454_AR=0;PCR_454_RR=806 20 47739668 . G A . . Sample=NA19036;GT=0/0;PCR_454_AR=1;PCR_454_RR=2292 20 47886859 . C T . . Sample=NA18956;GT=0/0;PCR_454_AR=1;PCR_454_RR=2153 20 47990798 . C G . . Sample=HG00105;GT=0/0;PCR_454_AR=0;PCR_454_RR=387 20 47990798 . C G . . Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=534 20 48124475 . C T . . Sample=NA19257;GT=0/1;PCR_454_AR=628;PCR_454_RR=644 20 48273201 . A C . . Sample=NA19914;GT=0/1;PCR_454_AR=338;PCR_454_RR=323 20 48713355 . T C . . Sample=NA12155;GT=0/0;PCR_454_AR=8;PCR_454_RR=1686 20 48713355 . T C . . Sample=NA12815;GT=0/0;PCR_454_AR=10;PCR_454_RR=1607 20 49218698 . C T . . Sample=NA19338;GT=0/1;PCR_454_AR=776;PCR_454_RR=682 20 49218698 . C T . . Sample=NA19457;GT=0/1;PCR_454_AR=803;PCR_454_RR=759 20 49219065 . C T . . Sample=NA18599;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1080 20 49354597 . A G . . Sample=HG00177;GT=0/1;PCR_454_AR=580;PCR_454_RR=617 20 49354597 . A G . . Sample=NA11829;GT=0/1;PCR_454_AR=778;PCR_454_RR=869 20 49354597 . A G . . Sample=NA20510;GT=0/1;PCR_454_AR=518;PCR_454_RR=631 20 49354597 . A G . . Sample=NA20512;GT=0/1;PCR_454_AR=238;PCR_454_RR=333 20 49354597 . A G . . Sample=NA20586;GT=0/1;PCR_454_AR=562;PCR_454_RR=642 20 50048925 . G C . . Sample=NA20507;GT=0/1;PCR_454_AR=774;PCR_454_RR=809 20 50051804 . C T . . Sample=NA19102;GT=0/1;PCR_454_AR=136;PCR_454_RR=155 20 50071136 . C T . . Sample=NA18637;GT=0/1;PCR_454_AR=334;PCR_454_RR=349 20 50140178 . G A . . Sample=NA18924;GT=0/1;PCR_454_AR=540;PCR_454_RR=481 20 50140178 . G A . . Sample=NA19321;GT=0/1;PCR_454_AR=481;PCR_454_RR=652 20 50235576 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=982;PCR_454_RR=886 20 50235576 . G A . . Sample=HG00122;GT=0/1;PCR_454_AR=838;PCR_454_RR=717 20 50235576 . G A . . Sample=HG00126;GT=0/1;PCR_454_AR=795;PCR_454_RR=769 20 50235576 . G A . . Sample=HG00135;GT=0/1;PCR_454_AR=972;PCR_454_RR=930 20 50235576 . G A . . Sample=HG00148;GT=0/1;PCR_454_AR=933;PCR_454_RR=931 20 50310567 . C T . . Sample=NA19152;GT=0/1;PCR_454_AR=689;PCR_454_RR=773 20 50310567 . C T . . Sample=NA19377;GT=0/1;PCR_454_AR=736;PCR_454_RR=683 20 50406859 . G A . . Sample=NA19921;GT=0/1;PCR_454_AR=1045;PCR_454_RR=930 20 50407501 . A C . . Sample=HG00118;GT=0/1;PCR_454_AR=569;PCR_454_RR=608 20 50407508 . C T . . Sample=NA20534;GT=0/1;PCR_454_AR=753;PCR_454_RR=2120 20 50408613 . A G . . Sample=NA18487;GT=0/1;PCR_454_AR=637;PCR_454_RR=634 20 50408613 . A G . . Sample=NA18502;GT=0/1;PCR_454_AR=561;PCR_454_RR=553 20 50408613 . A G . . Sample=NA18519;GT=0/1;PCR_454_AR=571;PCR_454_RR=554 20 50408613 . A G . . Sample=NA18908;GT=0/1;PCR_454_AR=731;PCR_454_RR=791 20 50408613 . A G . . Sample=NA18909;GT=0/1;PCR_454_AR=683;PCR_454_RR=634 20 50803476 . G A . . Sample=NA19046;GT=0/1;PCR_454_AR=692;PCR_454_RR=685 20 50803476 . G A . . Sample=NA19375;GT=0/1;PCR_454_AR=735;PCR_454_RR=803 20 50803476 . G A . . Sample=NA19376;GT=0/1;PCR_454_AR=892;PCR_454_RR=831 20 51872037 . G A . . Sample=NA18502;GT=0/1;PCR_454_AR=602;PCR_454_RR=654 20 51872037 . G A . . Sample=NA18504;GT=0/1;PCR_454_AR=717;PCR_454_RR=760 20 51872037 . G A . . Sample=NA18507;GT=0/1;PCR_454_AR=790;PCR_454_RR=822 20 51872037 . G A . . Sample=NA18508;GT=0/1;PCR_454_AR=868;PCR_454_RR=914 20 51872037 . G A . . Sample=NA18501;GT=1/1;PCR_454_AR=1687;PCR_454_RR=5 20 52192483 . T C . . Sample=HG00266;GT=0/1;PCR_454_AR=1044;PCR_454_RR=1029 20 52198279 . G A . . Sample=NA19065;GT=0/1;PCR_454_AR=1001;PCR_454_RR=1070 20 52561468 . A G . . Sample=HG00118;GT=0/1;PCR_454_AR=398;PCR_454_RR=501 20 52561468 . A G . . Sample=HG00126;GT=0/1;PCR_454_AR=228;PCR_454_RR=250 20 52561468 . A G . . Sample=HG00130;GT=0/1;PCR_454_AR=472;PCR_454_RR=535 20 52561468 . A G . . Sample=HG00134;GT=0/1;PCR_454_AR=462;PCR_454_RR=543 20 52561468 . A G . . Sample=HG00143;GT=0/1;PCR_454_AR=355;PCR_454_RR=404 20 52779394 . G T . . Sample=NA20540;GT=0/1;PCR_454_AR=470;PCR_454_RR=557 20 53205268 . T C . . Sample=NA19038;GT=0/1;PCR_454_AR=447;PCR_454_RR=421 20 53226967 . G A . . Sample=NA19462;GT=0/1;PCR_454_AR=770;PCR_454_RR=792 20 54961540 . A T . . Sample=HG00106;GT=0/1;PCR_454_AR=457;PCR_454_RR=411 20 54961540 . A T . . Sample=HG00112;GT=0/1;PCR_454_AR=466;PCR_454_RR=483 20 54961540 . A T . . Sample=HG00134;GT=0/1;PCR_454_AR=480;PCR_454_RR=467 20 54961540 . A T . . Sample=HG00143;GT=0/1;PCR_454_AR=522;PCR_454_RR=458 20 54961540 . A T . . Sample=HG00097;GT=1/1;PCR_454_AR=937;PCR_454_RR=4 20 54970682 . C T . . Sample=NA18912;GT=0/1;PCR_454_AR=683;PCR_454_RR=745 20 54970682 . C T . . Sample=NA19171;GT=0/1;PCR_454_AR=819;PCR_454_RR=792 20 55021021 . G A . . Sample=NA19087;GT=0/1;PCR_454_AR=1018;PCR_454_RR=1144 20 55108414 . G A . . Sample=NA20756;GT=1/1;PCR_454_AR=1220;PCR_454_RR=3 20 55206884 . C T . . Sample=NA19726;GT=0/1;PCR_454_AR=806;PCR_454_RR=864 20 55206884 . C T . . Sample=NA19738;GT=0/1;PCR_454_AR=988;PCR_454_RR=1033 20 56087684 . C T . . Sample=NA18599;GT=0/1;PCR_454_AR=1158;PCR_454_RR=1234 20 56089789 . C T . . Sample=HG01277;GT=0/1;PCR_454_AR=737;PCR_454_RR=779 20 56137833 . A G . . Sample=HG00099;GT=0/1;PCR_454_AR=794;PCR_454_RR=777 20 56137833 . A G . . Sample=HG00106;GT=0/1;PCR_454_AR=1272;PCR_454_RR=1196 20 56137833 . A G . . Sample=HG00097;GT=1/1;PCR_454_AR=1763;PCR_454_RR=4 20 56137833 . A G . . Sample=HG00104;GT=1/1;PCR_454_AR=1726;PCR_454_RR=5 20 56137833 . A G . . Sample=HG00112;GT=1/1;PCR_454_AR=1821;PCR_454_RR=3 20 57036354 . C T . . Sample=NA19080;GT=0/1;PCR_454_AR=1722;PCR_454_RR=1581 20 57036538 . C T . . Sample=NA19248;GT=0/1;PCR_454_AR=1224;PCR_454_RR=902 20 57415535 . C T . . Sample=NA19722;GT=0/1;PCR_454_AR=291;PCR_454_RR=1503 20 57415601 . G A . . Sample=NA20296;GT=0/1;PCR_454_AR=1262;PCR_454_RR=350 20 57428947 . G T . . Sample=NA19311;GT=0/1;PCR_454_AR=1304;PCR_454_RR=553 20 57572729 . C T . . Sample=NA19707;GT=0/1;PCR_454_AR=840;PCR_454_RR=1015 20 57576684 . T G . . Sample=NA18747;GT=0/0;PCR_454_AR=3;PCR_454_RR=1578 20 57597952 . C T . . Sample=NA20529;GT=0/1;PCR_454_AR=816;PCR_454_RR=883 20 57768304 . G A . . Sample=NA20818;GT=0/1;PCR_454_AR=710;PCR_454_RR=535 20 57769546 . C T . . Sample=NA18917;GT=0/0;PCR_454_AR=61;PCR_454_RR=810 20 57769738 . A G . . Sample=NA18527;GT=0/1;PCR_454_AR=799;PCR_454_RR=792 20 57769738 . A G . . Sample=NA18530;GT=0/1;PCR_454_AR=558;PCR_454_RR=527 20 57769738 . A G . . Sample=NA18532;GT=0/1;PCR_454_AR=734;PCR_454_RR=719 20 57769738 . A G . . Sample=NA18545;GT=0/1;PCR_454_AR=524;PCR_454_RR=502 20 57769738 . A G . . Sample=NA18593;GT=0/1;PCR_454_AR=809;PCR_454_RR=835 20 58444902 . C T . . Sample=NA19095;GT=0/1;PCR_454_AR=164;PCR_454_RR=144 20 58467100 . C T . . Sample=NA19324;GT=0/1;PCR_454_AR=312;PCR_454_RR=301 20 58560056 . C T . . Sample=HG00593;GT=0/1;PCR_454_AR=1491;PCR_454_RR=1378 20 58560056 . C T . . Sample=NA18553;GT=0/1;PCR_454_AR=1226;PCR_454_RR=1216 20 58564005 . G A . . Sample=NA19355;GT=0/0;PCR_454_AR=0;PCR_454_RR=2602 20 58567458 . A C . . Sample=HG00143;GT=0/0;PCR_454_AR=1;PCR_454_RR=878 20 58567458 . A C . . Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=883 20 58571705 . C T . . Sample=NA19319;GT=0/1;PCR_454_AR=342;PCR_454_RR=265 20 60504808 . C T . . Sample=NA18639;GT=0/1;PCR_454_AR=1079;PCR_454_RR=1027 20 60504808 . C T . . Sample=NA19921;GT=0/1;PCR_454_AR=914;PCR_454_RR=890 20 60701482 . T A . . Sample=NA19651;GT=0/1;PCR_454_AR=540;PCR_454_RR=612 20 60708462 . T C . . Sample=NA18962;GT=0/1;PCR_454_AR=891;PCR_454_RR=784 20 60738559 . G A . . Sample=NA18965;GT=0/1;PCR_454_AR=1072;PCR_454_RR=896 20 60838713 . C T . . Sample=NA20506;GT=0/1;PCR_454_AR=618;PCR_454_RR=642 20 60866830 . A C . . Sample=NA18923;GT=0/0;PCR_454_AR=0;PCR_454_RR=211 20 60868936 . C T . . Sample=NA19119;GT=0/1;PCR_454_AR=1424;PCR_454_RR=1554 20 60878814 . G A . . Sample=NA18638;GT=0/1;PCR_454_AR=223;PCR_454_RR=1299 20 60884465 . G A . . Sample=NA19681;GT=0/1;PCR_454_AR=928;PCR_454_RR=1002 20 60885810 . C T . . Sample=HG00134;GT=0/0;PCR_454_AR=2;PCR_454_RR=2017 20 60885810 . C T . . Sample=HG00350;GT=0/0;PCR_454_AR=4;PCR_454_RR=1963 20 60886712 . T C . . Sample=NA19438;GT=0/1;PCR_454_AR=929;PCR_454_RR=721 20 60891010 . C T . . Sample=NA19700;GT=0/1;PCR_454_AR=334;PCR_454_RR=389 20 60893610 . C T . . Sample=HG00359;GT=0/0;PCR_454_AR=2;PCR_454_RR=2041 20 60893610 . C T . . Sample=NA19758;GT=0/1;PCR_454_AR=1173;PCR_454_RR=1158 20 60893636 . C T . . Sample=NA20520;GT=0/1;PCR_454_AR=847;PCR_454_RR=1197 20 60893636 . C T . . Sample=NA20540;GT=0/1;PCR_454_AR=776;PCR_454_RR=1355 20 60893960 . C T . . Sample=NA19236;GT=0/1;PCR_454_AR=1310;PCR_454_RR=1388 20 60897486 . C T . . Sample=HG00099;GT=0/1;PCR_454_AR=454;PCR_454_RR=403 20 60897486 . C T . . Sample=HG00122;GT=0/1;PCR_454_AR=465;PCR_454_RR=352 20 60897486 . C T . . Sample=HG00097;GT=1/1;PCR_454_AR=849;PCR_454_RR=3 20 60897486 . C T . . Sample=HG00104;GT=1/1;PCR_454_AR=925;PCR_454_RR=4 20 60897486 . C T . . Sample=HG00118;GT=1/1;PCR_454_AR=799;PCR_454_RR=7 20 60907674 . G A . . Sample=HG00104;GT=0/1;PCR_454_AR=279;PCR_454_RR=228 20 60907674 . G A . . Sample=HG00106;GT=0/1;PCR_454_AR=334;PCR_454_RR=295 20 60907674 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=739;PCR_454_RR=4 20 60907674 . G A . . Sample=HG00099;GT=1/1;PCR_454_AR=395;PCR_454_RR=3 20 60907674 . G A . . Sample=HG00112;GT=1/1;PCR_454_AR=980;PCR_454_RR=6 20 60911433 . A C . . Sample=NA11920;GT=0/1;PCR_454_AR=341;PCR_454_RR=380 20 60911433 . A C . . Sample=NA20278;GT=0/1;PCR_454_AR=398;PCR_454_RR=444 20 60913173 . C T . . Sample=NA18522;GT=0/1;PCR_454_AR=1062;PCR_454_RR=1032 20 60920914 . T C . . Sample=NA18530;GT=0/1;PCR_454_AR=937;PCR_454_RR=877 20 60920914 . T C . . Sample=NA18873;GT=0/1;PCR_454_AR=791;PCR_454_RR=836 20 60920914 . T C . . Sample=NA19038;GT=0/1;PCR_454_AR=895;PCR_454_RR=857 20 60920914 . T C . . Sample=NA19099;GT=0/1;PCR_454_AR=1115;PCR_454_RR=1150 20 60920914 . T C . . Sample=NA19317;GT=0/1;PCR_454_AR=1165;PCR_454_RR=1206 20 60927411 . G A . . Sample=HG00099;GT=0/1;PCR_454_AR=330;PCR_454_RR=345 20 60927411 . G A . . Sample=HG00112;GT=0/1;PCR_454_AR=389;PCR_454_RR=468 20 60927411 . G A . . Sample=HG00118;GT=0/1;PCR_454_AR=1434;PCR_454_RR=538 20 60927411 . G A . . Sample=HG00097;GT=1/1;PCR_454_AR=993;PCR_454_RR=7 20 60927411 . G A . . Sample=HG00104;GT=1/1;PCR_454_AR=837;PCR_454_RR=8 20 60937543 . A G . . Sample=HG00115;GT=0/0;PCR_454_AR=2;PCR_454_RR=3444 20 60963387 . C T . . Sample=NA18992;GT=0/1;PCR_454_AR=689;PCR_454_RR=728 20 60986026 . T C . . Sample=NA18511;GT=0/1;PCR_454_AR=510;PCR_454_RR=522 20 60986026 . T C . . Sample=NA18520;GT=0/1;PCR_454_AR=384;PCR_454_RR=403 20 60986026 . T C . . Sample=NA18861;GT=0/1;PCR_454_AR=372;PCR_454_RR=432 20 60986026 . T C . . Sample=NA18908;GT=0/1;PCR_454_AR=428;PCR_454_RR=386 20 60989186 . G T . . Sample=HG00351;GT=0/0;PCR_454_AR=0;PCR_454_RR=299 20 60989186 . G T . . Sample=HG00099;GT=0/1;PCR_454_AR=1182;PCR_454_RR=966 20 60989186 . G T . . Sample=HG01344;GT=0/1;PCR_454_AR=654;PCR_454_RR=302 20 60989186 . G T . . Sample=NA12045;GT=0/1;PCR_454_AR=504;PCR_454_RR=534 20 60989186 . G T . . Sample=HG00130;GT=1/1;PCR_454_AR=76;PCR_454_RR=2 20 60992370 . C T . . Sample=NA18917;GT=0/1;PCR_454_AR=598;PCR_454_RR=363 20 60992370 . C T . . Sample=NA19453;GT=0/1;PCR_454_AR=541;PCR_454_RR=677 20 61288592 . G A . . Sample=HG01625;GT=0/1;PCR_454_AR=852;PCR_454_RR=871 20 61288592 . G A . . Sample=NA12383;GT=0/1;PCR_454_AR=794;PCR_454_RR=737 20 61288592 . G A . . Sample=NA19780;GT=0/1;PCR_454_AR=1012;PCR_454_RR=880 20 61288592 . G A . . Sample=NA20508;GT=0/1;PCR_454_AR=913;PCR_454_RR=773 20 61512157 . C T . . Sample=NA18933;GT=0/1;PCR_454_AR=1227;PCR_454_RR=1206 20 61512157 . C T . . Sample=NA18934;GT=0/1;PCR_454_AR=1110;PCR_454_RR=1182 20 61512157 . C T . . Sample=NA19771;GT=0/1;PCR_454_AR=1250;PCR_454_RR=1148 20 61512982 . T A . . Sample=NA18559;GT=0/1;PCR_454_AR=1255;PCR_454_RR=1117 20 61513433 . T C . . Sample=NA20810;GT=0/0;PCR_454_AR=1;PCR_454_RR=550 20 61525226 . G A . . Sample=NA19428;GT=0/1;PCR_454_AR=719;PCR_454_RR=719 20 61542496 . G C . . Sample=NA19648;GT=0/1;PCR_454_AR=237;PCR_454_RR=1305 20 61574860 . C T . . Sample=NA19762;GT=0/1;PCR_454_AR=703;PCR_454_RR=488 20 61591950 . T G . . Sample=HG00106;GT=0/0;PCR_454_AR=2;PCR_454_RR=1219 20 61591950 . T G . . Sample=HG00122;GT=0/0;PCR_454_AR=0;PCR_454_RR=1227 20 61833992 . G A . . Sample=NA18489;GT=0/1;PCR_454_AR=738;PCR_454_RR=786 20 61833992 . G A . . Sample=NA19093;GT=0/1;PCR_454_AR=839;PCR_454_RR=739 20 61834856 . G A . . Sample=NA19041;GT=0/1;PCR_454_AR=389;PCR_454_RR=374 20 61834856 . G A . . Sample=NA19095;GT=0/1;PCR_454_AR=383;PCR_454_RR=364 20 61834856 . G A . . Sample=NA19113;GT=0/1;PCR_454_AR=322;PCR_454_RR=325 20 61834856 . G A . . Sample=NA19318;GT=0/1;PCR_454_AR=434;PCR_454_RR=399 20 61834856 . G A . . Sample=NA19334;GT=0/1;PCR_454_AR=380;PCR_454_RR=343 20 61943307 . G C . . Sample=NA19201;GT=0/1;PCR_454_AR=920;PCR_454_RR=890 20 61943346 . G A . . Sample=NA19758;GT=0/1;PCR_454_AR=683;PCR_454_RR=705 20 62187372 . C G . . Sample=NA19117;GT=0/0;PCR_454_AR=0;PCR_454_RR=963 20 62187668 . C T . . Sample=NA12154;GT=0/1;PCR_454_AR=905;PCR_454_RR=664 20 62194106 . C T . . Sample=NA18910;GT=0/1;PCR_454_AR=1083;PCR_454_RR=1040 20 62194106 . C T . . Sample=NA19338;GT=0/1;PCR_454_AR=784;PCR_454_RR=854 20 62194106 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=757;PCR_454_RR=817 20 62194106 . C T . . Sample=NA19376;GT=0/1;PCR_454_AR=1152;PCR_454_RR=962 20 62194106 . C T . . Sample=NA19439;GT=0/1;PCR_454_AR=1387;PCR_454_RR=1456 20 62194211 . C A . . Sample=HG00156;GT=0/1;PCR_454_AR=1116;PCR_454_RR=536 20 62194211 . C A . . Sample=NA07051;GT=0/1;PCR_454_AR=2089;PCR_454_RR=259 20 62194211 . C A . . Sample=NA12003;GT=0/1;PCR_454_AR=1330;PCR_454_RR=796 20 62194290 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=1000;PCR_454_RR=751 20 62194290 . C T . . Sample=NA19351;GT=0/1;PCR_454_AR=901;PCR_454_RR=771 20 62198552 . G C . . Sample=NA20542;GT=0/1;PCR_454_AR=1527;PCR_454_RR=1010 20 62198883 . C T . . Sample=NA19346;GT=0/1;PCR_454_AR=1447;PCR_454_RR=1455 20 62198883 . C T . . Sample=NA19351;GT=0/1;PCR_454_AR=903;PCR_454_RR=1401 20 62198883 . C T . . Sample=NA20340;GT=0/1;PCR_454_AR=843;PCR_454_RR=892 20 62198960 . G A . . Sample=NA20534;GT=0/1;PCR_454_AR=1223;PCR_454_RR=864 20 62200240 . G A . . Sample=NA18910;GT=0/1;PCR_454_AR=1221;PCR_454_RR=1347 20 62226984 . G C . . Sample=HG00559;GT=0/0;PCR_454_AR=2;PCR_454_RR=1774 20 62226984 . G C . . Sample=NA12003;GT=0/0;PCR_454_AR=1;PCR_454_RR=1871 20 62250734 . C T . . Sample=NA19473;GT=0/1;PCR_454_AR=607;PCR_454_RR=722 20 62297382 . A T . . Sample=NA11993;GT=0/0;PCR_454_AR=3;PCR_454_RR=2573 20 62297382 . A T . . Sample=NA19117;GT=0/0;PCR_454_AR=5;PCR_454_RR=1753 20 62305427 . G A . . Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=803 20 62305427 . G A . . Sample=HG00122;GT=0/0;PCR_454_AR=28;PCR_454_RR=1300 20 62319912 . G T . . Sample=HG00128;GT=0/0;PCR_454_AR=1;PCR_454_RR=1911 20 62319912 . G T . . Sample=HG00560;GT=0/0;PCR_454_AR=0;PCR_454_RR=2111 20 62324258 . C G . . Sample=NA18562;GT=0/1;PCR_454_AR=1126;PCR_454_RR=1126 20 62324622 . C G . . Sample=NA18574;GT=0/1;PCR_454_AR=1153;PCR_454_RR=1158 20 62325731 . G A . . Sample=NA18548;GT=0/1;PCR_454_AR=779;PCR_454_RR=2199 20 62325821 . G A . . Sample=NA20278;GT=0/1;PCR_454_AR=819;PCR_454_RR=764 20 62325821 . G A . . Sample=NA20507;GT=0/1;PCR_454_AR=1163;PCR_454_RR=1060 20 62326150 . G A . . Sample=NA18870;GT=0/1;PCR_454_AR=1080;PCR_454_RR=892 20 62326234 . C T . . Sample=HG00128;GT=0/0;PCR_454_AR=0;PCR_454_RR=761 20 62326234 . C T . . Sample=HG00179;GT=0/0;PCR_454_AR=1;PCR_454_RR=1158 20 62326811 . G T . . Sample=HG00149;GT=0/0;PCR_454_AR=0;PCR_454_RR=1467 20 62326811 . G T . . Sample=HG00151;GT=0/0;PCR_454_AR=1;PCR_454_RR=1492 20 62407154 . C T . . Sample=NA18987;GT=0/0;PCR_454_AR=181;PCR_454_RR=2041 20 62421536 . C T . . Sample=NA20521;GT=0/1;PCR_454_AR=856;PCR_454_RR=910 20 62421536 . C T . . Sample=NA20543;GT=0/1;PCR_454_AR=865;PCR_454_RR=854 20 62593676 . C T . . Sample=NA20291;GT=0/1;PCR_454_AR=1038;PCR_454_RR=995 20 62594479 . C T . . Sample=NA19746;GT=0/1;PCR_454_AR=349;PCR_454_RR=347 20 62595981 . C T . . Sample=NA19172;GT=0/1;PCR_454_AR=440;PCR_454_RR=415 20 62630426 . C T . . Sample=NA19428;GT=0/1;PCR_454_AR=1246;PCR_454_RR=1277 20 62632542 . C T . . Sample=NA18501;GT=0/1;PCR_454_AR=1203;PCR_454_RR=1150 20 62657404 . C T . . Sample=NA18612;GT=0/1;PCR_454_AR=1480;PCR_454_RR=1071 20 62700725 . G A . . Sample=NA19020;GT=0/1;PCR_454_AR=832;PCR_454_RR=815 20 62700725 . G A . . Sample=NA19036;GT=0/1;PCR_454_AR=1024;PCR_454_RR=966 20 62729481 . C T . . Sample=NA20276;GT=0/1;PCR_454_AR=401;PCR_454_RR=408 20 62899302 . T C . . Sample=HG00104;GT=0/0;PCR_454_AR=10;PCR_454_RR=871 20 62899302 . T C . . Sample=HG00128;GT=0/0;PCR_454_AR=2;PCR_454_RR=950 pysam-0.7.7/tests/vcf-examples/12.vcf0000664000076400007650000027233611754437212017206 0ustar andreasandreas##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.7.7/tests/vcf-examples/21.vcf0000664000076400007650000006760711754437212017211 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 207414 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 792106 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 894031 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 1508892 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 1686745 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 1818886 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2062981 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2773229 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2817761 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 2994966 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3126723 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 3523369 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3635082 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3714080 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 3905791 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 3907250 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4171994 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4246375 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 4375206 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4434727 . A T 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;Sanger=Mono;pcr454_ss=NoCall;pcr454_ps=Poly 20 4495199 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4835415 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 4915769 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 4983198 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 5441171 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 5978029 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 6061317 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly 20 6328925 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 6675461 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 6976115 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7013349 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 7039302 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7638704 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7688381 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7726350 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 7733957 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 7850516 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8095059 . G A 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 8232012 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8415290 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 8438535 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 8815233 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 8953629 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Poly 20 9237267 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 9744549 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 9780416 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10252552 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10314038 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 10757416 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11087688 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11094107 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 11098680 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11353163 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11510559 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11787224 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11821024 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 11932295 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 11965311 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12023599 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12505523 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12570054 . A C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12667452 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 12678271 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly 20 12704885 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12733996 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 12737269 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 12788981 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12828594 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 12999157 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13083804 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13197077 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 13217896 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13276778 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13375116 . G A 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 13648056 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 13672895 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14160159 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14266815 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14865143 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 14882868 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15244725 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15277072 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 15390867 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15785205 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15833020 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15847620 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 15953253 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 15964434 . G C 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 16183922 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16190824 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16557779 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 16730061 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 16794015 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17048741 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17299827 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17299845 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17390323 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17624973 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17666040 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17735813 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17794990 . A G 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall 20 17809418 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17860794 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 17881936 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 17893097 . C G 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 18188883 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 18199319 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18233699 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18536869 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 18637785 . T C 0 . Consensus=Mono;PacBio=NoCall;Sqnm=Mono;Sanger=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 18763166 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19102715 . A G 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 19244609 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19573719 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 19815613 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 20511479 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;Sanger=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 20639358 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21278490 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21297718 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 21418269 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21560553 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 21618451 . G A 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 21705723 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22076189 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22118677 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22320721 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 22368918 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23020003 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23214163 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23273877 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23335790 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Mono 20 23790659 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23830388 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 23837678 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23901081 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23946361 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 23949242 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 24539119 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 24986457 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25183729 . G A 0 . Consensus=Mono;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Mono;pcr454_ps=Mono 20 25277133 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25292464 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 25528915 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 25851836 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 25970163 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 29920798 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 30007713 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30051768 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30183598 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30604408 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 30759940 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 30881454 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 31356560 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 31450036 . A G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Mono;pcr454_ss=Poly;pcr454_ps=Poly 20 31589920 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 31922121 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 32801430 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 32943975 . G T 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;pcr454_ss=NoCall;pcr454_ps=NoCall 20 33155812 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34090682 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34254080 . C T 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 34312126 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 34481504 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 34694577 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 35026572 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 35472344 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 35882698 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36044719 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36047623 . C A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36204890 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 36469514 . G C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 36840217 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 37460945 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 37665246 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 37732397 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37874645 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37958191 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 37996273 . C T 0 . Consensus=Mono;PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 38016547 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38435682 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 38505534 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38803278 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38963803 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 38971986 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 39269586 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 39289390 . C A 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=NoCall;pcr454_ps=NoCall 20 39318956 . T A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 39736197 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 40241339 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 41473555 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 41878576 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42022716 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 42033671 . A C 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 42270334 . C T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 42449590 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 42521157 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42624300 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 42984548 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43200148 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43425384 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43521990 . C G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43565804 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43591237 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43805929 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43866692 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 43902088 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 44478507 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 44768810 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 45151582 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 45414003 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 45776825 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 46454905 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 46823642 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47001376 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47079360 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 47248953 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47480655 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47529099 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47703355 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 47919541 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48126120 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48157380 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48233077 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 48488571 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48534468 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 48631385 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48654970 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 48708007 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 48979827 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49100106 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49509102 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 49631170 . G A 0 . Consensus=Mono;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;pcr454_ss=Mono;pcr454_ps=Mono 20 50210361 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50309600 . C A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50681296 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 50750138 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 51639257 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 51814664 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 51891088 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52299250 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52363435 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 52583941 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 52787584 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 53256945 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54155398 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54172374 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=Poly 20 54209446 . A G 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 54317862 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 54852735 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 54889864 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55208711 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55220477 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55224856 . G T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 55441530 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 55585710 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 55630163 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56031994 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56316071 . T G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 56366198 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56703987 . G A 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 56794829 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56797026 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 56922427 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57025102 . A T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57104529 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57360225 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 57630386 . T A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 57754033 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 57956631 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 57997801 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 58046279 . C G 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 58186723 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58214460 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58317759 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58491642 . A C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58560045 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58629232 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58805192 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 58869523 . A G 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59337535 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59441596 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59445223 . G A 0 . Consensus=Poly;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=Poly;pcr454_ps=Poly 20 59605846 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 59864395 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=NoCall;pcr454_ps=NoCall 20 60099821 . G T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60290551 . A G 0 . Consensus=Poly;PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 60362527 . G C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60516358 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60559594 . C T 0 . Consensus=Poly;PacBio=NoCall;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60745115 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60831300 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 60907675 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61458191 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61717607 . C T 0 . Consensus=Poly;PacBio=Mono;Sqnm=Poly;pcr454_ss=Mono;pcr454_ps=Mono 20 61771154 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 61950497 . G A 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62000091 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62550780 . C T 0 . Consensus=NoCall;PacBio=NoCall;Sqnm=NoCall;pcr454_ss=NoCall;pcr454_ps=NoCall 20 62558259 . T C 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly 20 62727205 . C T 0 . Consensus=Poly;PacBio=Poly;Sqnm=Poly;pcr454_ss=Poly;pcr454_ps=Poly pysam-0.7.7/tests/vcf-examples/16.vcf0000664000076400007650000067501512007614264017207 0ustar andreasandreas##fileformat=VCFv4.0 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01455', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01456', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01461', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01462', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01465', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01491', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01492', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01494', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01495', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01497', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01515', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01518', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01521', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01551'], 'minReads': 2, 'refFile': '/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 64, 'maxSize': 100, 'ploidy': 2, 'maxRegionSize': 10000, 'nCPU': 1, 'minFlank': 3, 'logFileName': 'LogsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.log', 'regions': ['20:1-100001'], 'maxVariants': 6, 'genIndels': 1, 'labels': None, 'dataType': 'population', 'minMapQual': 20, 'rlen': 100, 'nInd': 994, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'minReadQual': 20, 'maxCoverage': 1000000.0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 1, 'output': 'VariantCallsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.vcf'} ##reference=/lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta 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freebayes.20:57800000-57900000.baq.20110328.vcf, freebayes.20:57900000-58000000.baq.20110328.vcf, freebayes.20:58000000-58100000.baq.20110328.vcf, freebayes.20:58100000-58200000.baq.20110328.vcf, freebayes.20:58200000-58300000.baq.20110328.vcf, freebayes.20:58300000-58400000.baq.20110328.vcf, freebayes.20:58400000-58500000.baq.20110328.vcf, freebayes.20:58500000-58600000.baq.20110328.vcf, freebayes.20:58600000-58700000.baq.20110328.vcf, freebayes.20:58700000-58800000.baq.20110328.vcf, freebayes.20:58800000-58900000.baq.20110328.vcf, freebayes.20:58900000-59000000.baq.20110328.vcf, freebayes.20:59000000-59100000.baq.20110328.vcf, freebayes.20:59100000-59200000.baq.20110328.vcf, freebayes.20:59200000-59300000.baq.20110328.vcf, freebayes.20:59300000-59400000.baq.20110328.vcf, freebayes.20:59400000-59500000.baq.20110328.vcf, freebayes.20:59500000-59600000.baq.20110328.vcf, freebayes.20:59600000-59700000.baq.20110328.vcf, freebayes.20:59700000-59800000.baq.20110328.vcf, freebayes.20:59800000-59900000.baq.20110328.vcf, freebayes.20:59900000-60000000.baq.20110328.vcf, freebayes.20:60000000-60100000.baq.20110328.vcf, freebayes.20:60100000-60200000.baq.20110328.vcf, freebayes.20:60200000-60300000.baq.20110328.vcf, freebayes.20:60300000-60400000.baq.20110328.vcf, freebayes.20:60400000-60500000.baq.20110328.vcf, freebayes.20:60500000-60600000.baq.20110328.vcf, freebayes.20:60600000-60700000.baq.20110328.vcf, freebayes.20:60700000-60800000.baq.20110328.vcf, freebayes.20:60800000-60900000.baq.20110328.vcf, freebayes.20:60900000-61000000.baq.20110328.vcf, freebayes.20:61000000-61100000.baq.20110328.vcf, freebayes.20:61100000-61200000.baq.20110328.vcf, freebayes.20:61200000-61300000.baq.20110328.vcf, freebayes.20:61300000-61400000.baq.20110328.vcf, freebayes.20:61400000-61500000.baq.20110328.vcf, freebayes.20:61500000-61600000.baq.20110328.vcf, freebayes.20:61600000-61700000.baq.20110328.vcf, freebayes.20:61700000-61800000.baq.20110328.vcf, freebayes.20:61800000-61900000.baq.20110328.vcf, freebayes.20:61900000-62000000.baq.20110328.vcf, freebayes.20:62000000-62100000.baq.20110328.vcf, freebayes.20:62100000-62200000.baq.20110328.vcf, freebayes.20:62200000-62300000.baq.20110328.vcf, freebayes.20:62300000-62400000.baq.20110328.vcf, freebayes.20:62400000-62500000.baq.20110328.vcf, freebayes.20:62500000-62600000.baq.20110328.vcf, freebayes.20:62600000-62700000.baq.20110328.vcf, freebayes.20:62700000-62800000.baq.20110328.vcf, freebayes.20:62800000-62900000.baq.20110328.vcf, freebayes.20:62900000-63000000.baq.20110328.vcf, freebayes.20:63000000-63025520.baq.20110328.vcf #CHROM POS ID REF ALT QUAL FILTER INFO 20 458502 . G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 539571 . TG T 18546 PASS AA=71;AB=0.92482;ABA=63;ABP=1316.6;ABR=775;AC=42;AF=0.03512;AN=1196;BL=3915;BR=252;BVAR;BaseQRankSum=0.556;DEL;DP=10073;Dels=0.01;EL=47;EPP=19.189;ER=24;FS=2.124;HETAR=290;HOMA=156;HOMR=570;HRun=1;InbreedingCoeff=0.0620;LEN=1;LRB=0.87905;LRBP=6995.1;MQ0=0;MQ0Fraction=0.0000;MQM=127.99;MQRankSum=0.410;NS=1016;RA=3090;RL=71;RPP=157.18;RR=0;RUN=1;ReadPosRankSum=-11.038;SAB=0.66197;SAF=47;SAP=19.189;SAR=24;SRB=0.55016;SRF=1700;SRP=70.544;SRR=1390;VQSLOD=2.6772;set=filterInVQSR-2of5;sumGLbyD=4.71 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR 20 766143 . C A,CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1948787 . GTC G,GTCTC 78.70 PASS AC=18,18;AF=0.01466,0.01466;AN=1228;BaseQRankSum=3.894;DP=19030;DP4=1874,1916,21,20;FR;FS=0.767;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=16.5619;INDEL;InbreedingCoeff=0.2332;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.080;NF;NR;PP;PV4=0.88,1,0.094,0.47;QD=0.28;ReadPosRankSum=0.822;SB=-172.46;SC=CTCGACCCCTGTCTCTCTCTC;TC;TR=13;TU=CT;VQSLOD=3.7405;set=filterInVQSR-2of5 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2512346 . A AC 11046.11 PASS AC=673;AF=0.57034;AN=1180;BaseQRankSum=19.890;DP=2717;FS=26.809;HRun=0;HaplotypeScore=19.0575;InbreedingCoeff=0.3068;MQ=61.07;MQ0=25;MQ0Fraction=0.0092;MQRankSum=2.745;QD=5.80;ReadPosRankSum=3.139;SB=-4564.39;VQSLOD=4.3252;set=VQSR 20 2597210 rs71329387 TAAAG T 32206.62 PASS AA=689;AB=0.5805;ABA=542;ABP=75.724;ABR=750;AC=253;AF=0.20738;BL=29921;BR=30215;BVAR;BaseQRankSum=20.638;DB;DEL;DP=29293;DP4=1750,1070,405,274;Dels=0.18;EL=345;EPP=3.0135;ER=344;FQ=999;FR;FS=1.827;HETAR=225;HOMA=55;HOMR=783;HP=7;HPLen=4;HR=3;HRun=0;HU=A;INDEL;InbreedingCoeff=0.1419;LEN=4;LRB=0.0048889;LRBP=6.1314;MQ=66.96;MQ0=0;MQ0Fraction=0.0000;MQM=42.925;MQRankSum=-7.105;NF;NR;NS=1063;PP;PV4=0.25,1,9e-20,1;RA=4619;RL=345;RPP=3.0135;RR=344;RUN=1;ReadPosRankSum=2.719;SAB=0.53556;SAF=369;SAP=10.577;SAR=320;SC=GAAAGGAAAATAAAGAAGGAG;SRB=0.52414;SRF=2421;SRP=26.389;SRR=2198;TC;TR=3;TU=A;VQSLOD=9.7974;dbSNP=130;set=Intersection;sumGLbyD=33.30 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3635363 . T TG 999 PASS AA=16;AB=0.61905;ABA=16;ABP=8.1805;ABR=26;AF=0.0141;AF1=0.01726;AN=708;BL=614;BR=523;BVAR;BaseQRankSum=2.337;CI95=0.01106,0.02434;DP=14594;DP4=2128,2038,6,10;Dels=0.00;EL=7;EPP=3.5532;ER=9;FQ=999;FR;FS=5.579;HETAR=8;HOMA=0;HOMR=1055;HP=3;HPLen=3;HR=3;HRun=3;HU=G;INDEL;INS;InbreedingCoeff=0.0633;LEN=1;LRB=0.080035;LRBP=18.826;MQ=100.74;MQ0=0;MQ0Fraction=0.0000;MQM=51.312;MQRankSum=2.569;NF;NR;NS=1063;PP;PV4=0.32,1,1,1;RA=5628;RL=9;RPP=3.5532;RR=7;RUN=1;ReadPosRankSum=-1.941;SAB=0.375;SAF=6;SAP=5.1818;SAR=10;SC=AAGGTTCGCTTGGGTGTGGAG;SRB=0.4984;SRF=2805;SRP=3.1353;SRR=2823;TC;TR=3;TU=G;VQSLOD=9.3275;set=Intersection;sumGLbyD=11.68 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA AA,T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5071386 . AT A 45200.27 PASS AC=685;AF=0.7495;AN=914;BaseQRankSum=11.006;DP=2725;FS=8.133;HRun=3;HaplotypeScore=50.5496;InbreedingCoeff=0.2364;MQ=81.40;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.411;QD=18.51;ReadPosRankSum=3.429;SB=-22405.85;VQSLOD=4.2872;set=VQSR 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 5992611 . G GT 799.56 PASS AA=39;AB=0.8301;ABA=35;ABP=197.98;ABR=171;AC=13;AF=0.0183;AN=712;BL=1164;BR=1566;BVAR;BaseQRankSum=1.914;DP=9561;Dels=0.01;EL=16;EPP=5.7386;ER=23;FS=0.739;HETAR=32;HOMA=0;HOMR=1024;HRun=9;INS;InbreedingCoeff=0.0339;LEN=1;LRB=0.14725;LRBP=131.55;MQ0=0;MQ0Fraction=0.0000;MQM=97.231;MQRankSum=0.764;NS=1056;RA=5204;RL=16;RPP=5.7386;RR=23;RUN=1;ReadPosRankSum=-1.169;SAB=0.69231;SAF=27;SAP=15.538;SAR=12;SRB=0.56399;SRF=2935;SRP=188.09;SRR=2269;VQSLOD=4.6516;set=Intersection;sumGLbyD=5.96 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 6903392 . TC CC,T 999 PASS AF=0.0000;AF1=0.01192;CI95=0.008547,0.01709;DP=10440;DP4=2544,2062,9,11;Dels=0.01;FQ=999;FR;HP=2;HPLen=3;HR=3;HRun=2;HU=T;INDEL;InbreedingCoeff=0.0324;MQ=62.78;MQ0=2;MQ0Fraction=0.0009;NF;NR;PP;PV4=0.38,0.0069,0.36,0.41;QD=8.05;SB=-320.13;SC=TTATTTTCTTTCCAATTTTTA;TC;TR=8;TU=CTTT;set=filterInVQSR-2of5;sumGLbyD=13.22 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10640876 . TA T 42819 PASS AA=86;AB=0.92316;ABA=75;ABP=1521;ABR=901;AC=40;AF=0.0447;AN=894;BL=6265;BR=415;BVAR;BaseQRankSum=-0.850;DEL;DP=8223;Dels=0.00;EL=41;EPP=3.4143;ER=45;FS=3.190;HETAR=336;HOMA=384;HOMR=290;HRun=1;InbreedingCoeff=0.0173;LEN=1;LRB=0.87575;LRBP=11128;MQ0=0;MQ0Fraction=0.0000;MQM=76.163;MQRankSum=1.314;NS=1034;RA=2046;RL=83;RPP=164.61;RR=3;RUN=1;ReadPosRankSum=-12.060;SAB=0.46512;SAF=40;SAP=3.9193;SAR=46;SRB=0.5523;SRF=1130;SRP=51.615;SRR=916;VQSLOD=3.9183;set=filterInVQSR-2of5;sumGLbyD=4.00 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 11767787 . CA C 1382.10 PASS AA=24;AB=0.56667;ABA=13;ABP=4.1684;ABR=17;AC=10;AF=0.00810;AN=1234;BL=967;BR=819;BVAR;BaseQRankSum=1.629;DEL;DP=22318;DP4=2190,2491,8,14;Dels=0.01;EL=16;EPP=8.8009;ER=8;FQ=999;FR;FS=2.536;HETAR=6;HOMA=3;HOMR=1051;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0823;LEN=1;LRB=0.082867;LRBP=29.642;MQ=65.44;MQ0Fraction=0.0032;MQM=50.583;MQRankSum=0.931;NF;NR;NS=1060;PP;PV4=0.39,0.018,1,0.37;RA=5568;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-0.694;SAB=0.375;SAF=9;SAP=6.2675;SAR=15;SC=TGAACATGTACAGACTTGGTT;SRB=0.44325;SRF=2468;SRP=158.78;SRR=3100;TC;TR=1;TU=A;VQSLOD=9.9622;set=Intersection;sumGLbyD=15.42 20 12021825 . A AG 1063.30 PASS AA=26;AB=0.53704;ABA=25;ABP=3.6537;ABR=29;AC=12;AF=0.0214;AN=562;BL=1077;BR=815;BVAR;BaseQRankSum=-3.787;DP=22049;DP4=2650,2464,13,12;Dels=0.00;EL=18;EPP=11.362;ER=8;FR;FS=0.735;HETAR=12;HOMA=1;HOMR=1064;HP=1;HR=1;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0876;LEN=1;LRB=0.13848;LRBP=81.794;MQ=102.78;MQ0=0;MQ0Fraction=0.0000;MQM=85.538;MQRankSum=-0.126;NF;NR;NS=1077;PP;PV4=1,1,0.19,0.2;RA=6457;RL=17;RPP=8.3555;RR=9;RUN=1;ReadPosRankSum=-1.941;SAB=0.57692;SAF=15;SAP=4.3466;SAR=11;SC=GTAGTTTAACAGTTTATCAGG;SRB=0.5182;SRF=3346;SRP=21.582;SRR=3111;TC;TR=1;TU=G;VQSLOD=8.0483;set=Intersection;sumGLbyD=13.94 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR 20 14033345 . A AT 2718.30 PASS AA=91;AB=0.80899;ABA=85;ABP=372.04;ABR=360;AC=43;AF=0.03895;AN=1104;BL=3916;BR=4753;BVAR;BaseQRankSum=-6.609;DP=8350;Dels=0.02;EL=46;EPP=3.0342;ER=45;FR;FS=0.498;HETAR=70;HOMA=1;HOMR=871;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.096551;LRBP=178.49;MQ0=0;MQ0Fraction=0.0000;MQM=54.879;MQRankSum=2.164;NF;NR;NS=942;PP;RA=3717;RL=37;RPP=9.9065;RR=54;RUN=1;ReadPosRankSum=-1.447;SAB=0.48352;SAF=44;SAP=3.2251;SAR=47;SC=TTGCAAACAGATTTTTTTTTT;SRB=0.45252;SRF=1682;SRP=75.807;SRR=2035;TC;TR=11;TU=T;VQSLOD=3.8299;set=filterInVQSR-2of5;sumGLbyD=3.88 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16073315 rs111824749 GA G,GAA,GAAA 6400.63 PASS AC=138,47,20;AF=0.11577,0.03943,0.01678;AN=1192;BVAR;BaseQRankSum=11.377;DB;DEL;DP=35284;DP4=1695,1547,60,56;Dels=0.08;FR;FS=9.576;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2137;MQ=106.87;MQ0=1;MQ0Fraction=0.0003;MQRankSum=0.773;NF;NR;PP;PV4=0.92,1,0.024,0.45;RUN=1;ReadPosRankSum=-2.224;SC=TATTTGAGGAGAAAAAAAAAA;TC;TR=10;TU=A;VQSLOD=9.3264;set=Intersection;sumGLbyD=8.64 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR 20 19149501 . A AG 17.85 PASS AC=1;AF=0.0015;AN=670;BaseQRankSum=0.769;DP=1635;FS=9.858;HRun=0;HaplotypeScore=12.1949;InbreedingCoeff=-0.0381;MQ=102.63;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.200;QD=3.23;ReadPosRankSum=0.292;SB=-7.06;VQSLOD=4.4695;set=VQSR 20 19540281 . AC A 19710 PASS AA=145;AB=0.81843;ABA=134;ABP=652.98;ABR=604;AC=115;AF=0.09583;AN=1200;BL=9637;BR=817;BVAR;BaseQRankSum=-13.669;DEL;DP=10963;Dels=0.01;EL=66;EPP=5.5412;ER=79;FS=1.252;HETAR=305;HOMA=681;HOMR=59;HRun=1;InbreedingCoeff=0.0298;LEN=1;LRB=0.8437;LRBP=16162;MQ0=0;MQ0Fraction=0.0000;MQM=118.51;MQRankSum=-2.194;NS=1046;RA=823;RL=141;RPP=284.09;RR=4;RUN=1;ReadPosRankSum=-20.775;SAB=0.45517;SAF=66;SAP=5.5412;SAR=79;SRB=0.452;SRF=372;SRP=19.477;SRR=451;VQSLOD=3.9584;set=filterInVQSR-2of5;sumGLbyD=3.29 20 20015051 . TGAGGGTGG T 1820.73 PASS AF=0.0112;AF1=0.01638;AN=714;BaseQRankSum=6.652;CI95=0.01106,0.02212;DP=9910;DP4=2812,1912,6,11;Dels=0.01;FQ=999;FR;FS=6.147;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0077;MQ=129.13;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.195;NF;NR;PP;PV4=0.049,1,5.5e-05,0.006;ReadPosRankSum=-1.989;SC=TTGGTGGAGTTGAGGGTGGGA;TC;TR=2;TU=T;VQSLOD=6.5963;set=Intersection;sumGLbyD=33.49 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26075169 . CTTCATT C 34603 PASS AA=311;AB=0.88905;ABA=298;ABP=3534.4;ABR=2388;AC=235;AF=0.18921;AN=1242;BL=17537;BR=5525;BVAR;BaseQRankSum=33.761;DEL;DP=20706;DS;Dels=0.01;EL=206;EPP=74.236;ER=105;FR;FS=94.549;HETAR=596;HOMA=99;HOMR=336;HP=3;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2083;LEN=6;LRB=0.52086;LRBP=13589;MQ0Fraction=0.0426;MQM=14.524;MQRankSum=-37.199;NF;NR;NS=1038;PP;RA=3600;RL=311;RPP=678.34;RR=0;RUN=1;ReadPosRankSum=-27.333;SAB=0.66238;SAF=206;SAP=74.236;SAR=105;SC=TCACCATCATCTTCATTATCA;SRB=0.55833;SRF=2010;SRP=109.41;SRR=1590;TC;TR=7;TU=ATC;VQSLOD=1.4394;set=filterInVQSR-2of5;sumGLbyD=4.96 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26136208 . A AT 17172.04 PASS AA=252;AB=0.73593;ABA=183;ABP=338.07;ABR=510;AC=381;AF=0.30775;AN=1238;BL=8304;BR=14158;BVAR;BaseQRankSum=41.520;DP=40036;DP4=2448,2564,317,366;Dels=0.00;EL=163;EPP=50.197;ER=89;FQ=999;FS=6.531;HETAR=149;HOMA=52;HOMR=708;HRun=1;INDEL;INS;InbreedingCoeff=-0.3996;LEN=1;LRB=0.26062;LRBP=3315.9;MQ=64.20;MQ0=22;MQ0Fraction=0.0048;MQM=25.706;MQRankSum=-29.318;NS=909;PV4=0.24,1.1e-119,3.2e-281,1;RA=2939;RL=58;RPP=162.39;RR=194;RUN=1;ReadPosRankSum=0.592;SAB=0.24206;SAF=61;SAP=148.64;SAR=191;SRB=0.4852;SRF=1426;SRP=8.6026;SRR=1513;VQSLOD=0.5981;set=filterInVQSR-2of5;sumGLbyD=5.77 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34358698 . A AAAAAAT 583.61 PASS AC=27;AF=0.02542;AN=1062;BaseQRankSum=5.228;DP=1997;FS=3.765;HRun=0;HaplotypeScore=27.7123;InbreedingCoeff=0.0566;MQ=55.50;MQ0=14;MQ0Fraction=0.0070;MQRankSum=-3.961;QD=5.21;ReadPosRankSum=0.862;SB=-399.69;VQSLOD=4.3826;set=VQSR 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35086229 rs112534255 G GAT 6109.24 PASS AA=14;AB=0.71795;ABA=11;ABP=19.101;ABR=28;AC=35;AF=0.0509;AN=688;BL=846;BR=517;BVAR;BaseQRankSum=-7.153;DB;DP=15775;DP4=2064,2212,31,22;Dels=0.00;EL=7;EPP=3.0103;ER=7;FR;FS=0.000;HETAR=10;HOMA=2;HOMR=914;HP=3;HPLen=4;HR=4;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.1170;LEN=2;LRB=0.24138;LRBP=175.46;MQ=54.65;MQ0Fraction=0.0118;MQM=45.643;MQRankSum=1.614;NF;NR;NS=926;PP;PV4=0.17,1,1,1;RA=2867;RL=11;RPP=12.937;RR=3;RUN=1;ReadPosRankSum=-0.520;SAB=0.71429;SAF=10;SAP=8.5941;SAR=4;SC=TTTTAGTAAAGGGGATTTCAC;SRB=0.58249;SRF=1670;SRP=172.46;SRR=1197;TC;TR=4;TU=G;VQSLOD=10.3126;set=Intersection;sumGLbyD=42.13 20 35575895 rs67189278 AGTGT A,AGT,AGTGTGT,TGTGT 43809.26 PASS AC=593,3,481;AF=0.53327,0.00270,0.43255;AN=1112;BVAR;BaseQRankSum=-8.327;DB;DEL;DP=8989;Dels=0.04;FR;FS=9.400;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INS;InbreedingCoeff=0.7735;LEN=2;MQ0Fraction=0.0400;MQRankSum=-2.719;NF;NR;PP;RUN=1;ReadPosRankSum=-9.301;SC=TGTGTGTGTGAGTGTGTGTGT;TC;TR=22;TU=GT;VQSLOD=8.6440;set=Intersection;sumGLbyD=6.01 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38122459 . T TG,TGG 1346.40 PASS ABR=339;AC=37,26;AF=0.02989,0.02100;BVAR;BaseQRankSum=10.222;DP=16425;FS=601.551;HOMA=0;HOMR=1008;HaplotypeScore=20.6522;INS;InbreedingCoeff=0.0829;MQ=105.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-4.295;NS=1079;QD=0.40;RA=6208;RUN=1;ReadPosRankSum=-14.427;SAB=1;SAR=0;SB=-368.88;SRB=0.34907;SRF=2167;SRP=1231.4;SRR=4041;VQSLOD=-3.3455;set=filterInVQSR-2of5 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 38882632 rs72004513 AGTGTGTGTGT A,AGT,AGTGT,AGTGTGT,AGTGTGTGT,AGTGTGTGTGTGT 12304.47 PASS AC=57,24,51,78,89,186;AF=0.04664,0.01964,0.04173,0.06383,0.07283,0.15221;AN=1222;BVAR;BaseQRankSum=3.183;DB;DEL;DP=49261;DP4=144,106,104,101;Dels=0.05;FQ=999;FR;FS=5.209;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.9090;MQ=87.48;MQ0Fraction=0.0071;MQRankSum=-0.897;NF;NR;PP;PV4=0.16,1,0.19,1;RUN=1;ReadPosRankSum=3.551;SC=TAACTCCTCAAGTGTGTGTGT;TC;TR=47;TU=GT;VQSLOD=9.9069;set=Intersection;sumGLbyD=5.30 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41453533 rs112736557 T TA 1734.60 PASS AA=44;AB=0.58025;ABA=34;ABP=7.5409;ABR=47;AC=23;AF=0.0345;AN=666;BL=2061;BR=2408;BVAR;BaseQRankSum=5.768;DB;DP=7437;Dels=0.00;EL=25;EPP=4.787;ER=19;FR;FS=3.680;HETAR=17;HOMA=5;HOMR=975;HP=7;HPLen=6;HR=6;HRun=6;HU=A;INS;InbreedingCoeff=0.1712;LEN=1;LRB=0.077646;LRBP=61.517;MQ0=0;MQ0Fraction=0.0000;MQM=75.614;MQRankSum=-4.976;NF;NR;NS=997;PP;RA=4229;RL=21;RPP=3.2077;RR=23;RUN=1;ReadPosRankSum=-0.039;SAB=0.5;SAF=22;SAP=3.0103;SAR=22;SC=CCTTTCTCCATAAAAAAGCTT;SRB=0.46299;SRF=1958;SRP=53.315;SRR=2271;TC;TR=6;TU=A;VQSLOD=7.8972;set=Intersection;sumGLbyD=13.16 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41687456 . A AT 19682 PASS AA=446;AB=0.61202;ABA=426;ABP=122.69;ABR=672;AC=162;AF=0.13214;AN=1226;BL=15293;BR=20484;BVAR;BaseQRankSum=2.364;DP=29324;DP4=1993,1785,261,252;Dels=0.01;EL=214;EPP=4.5878;ER=232;FQ=999;FR;FS=1.923;HETAR=170;HOMA=7;HOMR=897;HP=11;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0769;LEN=1;LRB=0.14509;LRBP=1638.5;MQ=91.55;MQ0=0;MQ0Fraction=0.0000;MQM=57.168;MQRankSum=-0.764;NF;NR;NS=1074;PP;PV4=0.45,1,3.5e-08,1;RA=5437;RL=179;RPP=40.714;RR=267;RUN=1;ReadPosRankSum=0.356;SAB=0.51794;SAF=231;SAP=4.2567;SAR=215;SC=AGAAAACCTTATTTTTTTTTC;SRB=0.51094;SRF=2778;SRP=8.666;SRR=2659;TC;TR=9;TU=T;VQSLOD=9.6786;set=Intersection;sumGLbyD=10.93 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46384744 . CT C 17791 PASS AA=51;AB=0.94826;ABA=49;ABP=1655.8;ABR=898;AC=23;AF=0.01867;AN=1232;BL=120;BR=3678;BVAR;BaseQRankSum=-0.185;DEL;DP=13879;Dels=0.00;EL=23;EPP=4.0747;ER=28;FS=2.864;HETAR=262;HOMA=78;HOMR=722;HRun=2;InbreedingCoeff=0.0193;LEN=1;LRB=0.93681;LRBP=7240.9;MQ0=0;MQ0Fraction=0.0000;MQM=66.667;MQRankSum=1.031;NS=1079;RA=5295;RL=0;RPP=113.76;RR=51;RUN=1;ReadPosRankSum=-12.934;SAB=0.54902;SAF=28;SAP=4.0747;SAR=23;SRB=0.54674;SRF=2895;SRP=103.49;SRR=2400;VQSLOD=3.0419;set=filterInVQSR-2of5;sumGLbyD=3.47 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 48519434 rs56747320 TA T,TAA 26754 PASS AC=91,355;AF=0.07738,0.30187;AN=1176;BVAR;BaseQRankSum=-5.499;DB;DEL;DP=24872;DP4=726,883,443,502;Dels=0.04;FR;FS=1.430;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.2576;LEN=1;MQ=71.86;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-0.526;NF;NR;PP;PV4=0.41,1,0.00077,1;RUN=1;ReadPosRankSum=-4.130;SC=CGTCTTAAACTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=7.3200;set=Intersection;sumGLbyD=10.43 20 49086519 rs111404890 CA C,CAA 1379.10 PASS AA=43;AB=0.672;ABA=41;ABP=35.131;ABR=84;AC=7,14;AF=0.0100,0.0201;AN=698;BL=1097;BR=2286;BVAR;BaseQRankSum=-2.656;DB;DP=9319;Dels=0.00;EL=22;EPP=3.0608;ER=21;FR;FS=1.147;HETAR=20;HOMA=0;HOMR=1029;HP=11;HPLen=8;HR=8;HRun=8;HU=A;INS;InbreedingCoeff=0.0760;LEN=1;LRB=0.35146;LRBP=910.45;MQ0=0;MQ0Fraction=0.0000;MQM=47.674;MQRankSum=2.682;NF;NR;NS=1049;PP;RA=5237;RL=10;RPP=29.724;RR=33;RUN=1;ReadPosRankSum=-2.367;SAB=0.48837;SAF=21;SAP=3.0608;SAR=22;SC=GTAAAACAAACAAAAAAAATG;SRB=0.48635;SRF=2547;SRP=11.489;SRR=2690;TC;TR=11;TU=AAAC;VQSLOD=7.3084;set=Intersection;sumGLbyD=9.84 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49681276 . TC T 40042 PASS AA=72;AB=0.93908;ABA=70;ABP=1927.1;ABR=1079;AC=18;AF=0.0196;AN=918;BL=514;BR=4340;BVAR;BaseQRankSum=0.869;DEL;DP=10368;Dels=0.00;EL=33;EPP=4.096;ER=39;FS=17.302;HETAR=389;HOMA=269;HOMR=405;HRun=1;InbreedingCoeff=0.0626;LEN=1;LRB=0.78822;LRBP=6551.6;MQ0=0;MQ0Fraction=0.0000;MQM=123.06;MQRankSum=-1.047;NS=1064;RA=3095;RL=3;RPP=134.38;RR=69;RUN=1;ReadPosRankSum=-10.928;SAB=0.58333;SAF=42;SAP=7.3532;SAR=30;SRB=0.57738;SRF=1787;SRP=163.99;SRR=1308;VQSLOD=2.8517;set=filterInVQSR-2of5;sumGLbyD=3.69 20 49690436 . GT G 473.74 PASS AF=0.0263;AF1=0.02287;BaseQRankSum=3.830;CI95=0.01327,0.03319;DP=7473;DP4=2241,1740,14,12;Dels=0.01;FQ=129;FR;FS=0.000;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;InbreedingCoeff=0.1310;MQ=51.71;MQ0Fraction=0.0407;MQRankSum=1.792;NF;NR;PP;PV4=0.84,5.7e-10,0.22,1;ReadPosRankSum=0.973;SC=GTAGGACGGGGTTTTACCATG;TC;TR=4;TU=T;VQSLOD=7.4809;set=Intersection;sumGLbyD=10.96 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50059710 . C CCA 4175.86 PASS AA=28;AB=0.62963;ABA=20;ABP=10.892;ABR=34;AC=36;AF=0.0738;AN=488;BL=1050;BR=1273;BVAR;BaseQRankSum=3.198;DP=9138;Dels=0.00;EL=10;EPP=7.9737;ER=18;FR;FS=19.190;HETAR=10;HOMA=2;HOMR=1053;HP=6;HPLen=7;HR=7;HRun=0;HU=C;INS;InbreedingCoeff=0.1390;LEN=2;LRB=0.095997;LRBP=49.496;MQ0=0;MQ0Fraction=0.0000;MQM=57.464;MQRankSum=-1.875;NF;NR;NS=1065;PP;RA=5745;RL=12;RPP=4.2511;RR=16;RUN=1;ReadPosRankSum=-2.894;SAB=0.5;SAF=14;SAP=3.0103;SAR=14;SC=GGAGACCCCCCCTTCATCCTA;SRB=0.48129;SRF=2765;SRP=20.482;SRR=2980;TC;TR=7;TU=C;VQSLOD=5.1567;set=Intersection;sumGLbyD=11.49 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR 20 53960980 . GC G 588.40 PASS AA=32;AB=0.78632;ABA=25;ABP=86.324;ABR=92;AF=0.0275;AF1=0.01689;AN=690;BL=1047;BR=1108;BVAR;BaseQRankSum=3.049;CI95=0.006637,0.02876;DEL;DP=11389;DP4=1514,1481,16,12;Dels=0.02;EL=27;EPP=35.854;ER=5;FQ=17.6;FS=0.652;HETAR=27;HOMA=3;HOMR=1006;HRun=1;INDEL;InbreedingCoeff=0.0473;LEN=1;LRB=0.028306;LRBP=6.7597;MQ=106.54;MQ0=0;MQ0Fraction=0.0000;MQM=115.53;MQRankSum=1.395;NS=1036;PV4=0.57,0.0057,0.46,0.22;RA=4207;RL=14;RPP=4.096;RR=18;RUN=1;ReadPosRankSum=-5.581;SAB=0.40625;SAF=13;SAP=5.4532;SAR=19;SRB=0.48586;SRF=2044;SRP=10.32;SRR=2163;VQSLOD=6.0155;set=Intersection;sumGLbyD=7.94 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57529209 . TA AA,T 1285.20 PASS AA=52;AB=0.89572;ABA=39;ABP=511.72;ABR=335;AC=0;AF=0.0000;AN=694;BL=1317;BR=3667;BVAR;BaseQRankSum=1.788;DEL;DP=8008;Dels=0.00;EL=30;EPP=5.6829;ER=22;FR;HETAR=151;HOMA=83;HOMR=752;HP=7;HR=7;HU=A;InbreedingCoeff=0.1368;LEN=1;LRB=0.47151;LRBP=2409.1;MQ0=0;MQ0Fraction=0.0000;MQM=58.288;MQRankSum=-0.490;NF;NR;NS=987;PP;QD=2.29;RA=2909;RL=4;RPP=83.856;RR=48;RUN=1;ReadPosRankSum=0.513;SAB=0.46154;SAF=24;SAP=3.6784;SAR=28;SB=-361.38;SC=CATAATTTTTTAAAAAAATAG;SRB=0.46855;SRF=1363;SRP=28.009;SRR=1546;TC;TR=7;TU=A;set=filterInVQSR-2of5;sumGLbyD=5.59 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58287008 . T TC 23.57 PASS AC=1;AF=0.0015;AN=678;BaseQRankSum=1.500;DP=1783;FS=0.000;HRun=1;HaplotypeScore=13.0585;InbreedingCoeff=0.0243;MQ=98.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.259;QD=5.43;ReadPosRankSum=1.115;SB=-40.33;VQSLOD=4.9523;set=VQSR 20 58418087 . TAC T 1908.26 PASS AA=64;AB=0.58667;ABA=62;ABP=12.796;ABR=88;AC=24;AF=0.0337;AN=712;BL=2841;BR=2706;BVAR;BaseQRankSum=12.276;DEL;DP=21427;DP4=2243,2398,22,31;Dels=0.03;EL=29;EPP=4.2318;ER=35;FQ=999;FR;FS=0.961;HETAR=21;HOMA=1;HOMR=1050;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0008;LEN=2;LRB=0.024337;LRBP=10.145;MQ=93.02;MQ0=0;MQ0Fraction=0.0000;MQM=51.109;MQRankSum=-3.746;NF;NR;NS=1072;PP;PV4=0.34,1.8e-11,2.3e-08,1;RA=6247;RL=37;RPP=6.4032;RR=27;RUN=1;ReadPosRankSum=0.418;SAB=0.4375;SAF=28;SAP=5.1818;SAR=36;SC=AGCCATAGGATACACAAAATC;SRB=0.47911;SRF=2993;SRP=26.689;SRR=3254;TC;TR=5;TU=AC;VQSLOD=10.5463;set=Intersection;sumGLbyD=12.25 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62067246 . T TCGA 60869.60 PASS AC=1024;AF=0.88889;AN=1152;BaseQRankSum=17.328;DP=2144;FS=2.378;HRun=0;HaplotypeScore=22.0069;InbreedingCoeff=0.1400;MQ=86.75;MQ0=6;MQ0Fraction=0.0028;MQRankSum=-5.536;QD=29.45;ReadPosRankSum=1.266;SB=-24220.18;VQSLOD=6.4647;set=VQSR 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR 20 62952465 . G GT 9149.70 PASS AA=156;AB=0.66667;ABA=110;ABP=82.631;ABR=220;AC=8;AF=0.00768;AN=1042;BL=6618;BR=3296;BVAR;BaseQRankSum=-0.466;DP=6244;Dels=0.00;EL=70;EPP=6.5737;ER=86;FS=2.927;HETAR=88;HOMA=34;HOMR=664;HRun=0;INS;InbreedingCoeff=0.0711;LEN=1;LRB=0.33508;LRBP=2420.2;MQ0Fraction=0.0431;MQM=29.506;MQRankSum=-3.251;NS=786;RA=1722;RL=146;RPP=260.47;RR=10;RUN=1;ReadPosRankSum=-2.554;SAB=0.47436;SAF=74;SAP=3.9012;SAR=82;SRB=0.50523;SRF=870;SRP=3.4189;SRR=852;VQSLOD=6.1217;set=Intersection;sumGLbyD=16.58 pysam-0.7.7/tests/vcf-examples/20.vcf0000664000076400007650000003434311754437212017177 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO 20 207414 . G A . . PacBio=NoCall;Sqnm=NoCall 20 792106 . C G . . PacBio=Poly;Sqnm=NoCall 20 894031 . G A . . PacBio=Poly;Sqnm=Poly 20 1508892 . A G . . PacBio=Poly;Sqnm=Poly 20 1686745 . G A . . PacBio=Poly;Sqnm=NoCall 20 1818886 . C T . . PacBio=Poly;Sqnm=Poly 20 2062981 . A G . . PacBio=Poly;Sqnm=Poly 20 2773229 . A G . . PacBio=Poly;Sqnm=Poly 20 2817761 . T C . . PacBio=Poly;Sqnm=Poly 20 2994966 . G T . . PacBio=Poly;Sqnm=Poly 20 3126723 . C T . . PacBio=Poly;Sqnm=Poly 20 3523369 . G A . . PacBio=Poly;Sqnm=Poly 20 3635082 . A G . . PacBio=Poly;Sqnm=Poly 20 3714080 . C G . . PacBio=Poly;Sqnm=Poly 20 3905791 . G A . . PacBio=Poly;Sqnm=NoCall 20 3907250 . A G . . PacBio=Poly;Sqnm=Poly 20 4171994 . C T . . PacBio=Poly;Sqnm=Poly 20 4246375 . T C . . PacBio=Poly;Sqnm=NoCall 20 4375206 . C T . . PacBio=Poly;Sqnm=Poly 20 4434727 . A T . . PacBio=NoCall;Sqnm=Mono;Sanger=Mono 20 4495199 . G C . . PacBio=Poly;Sqnm=Poly 20 4835415 . C T . . PacBio=Poly;Sqnm=Poly 20 4915769 . T C . . PacBio=Poly;Sqnm=NoCall 20 4983198 . T C . . PacBio=Poly;Sqnm=Poly 20 5441171 . C T . . PacBio=Poly;Sqnm=NoCall 20 5978029 . T C . . PacBio=Poly;Sqnm=Poly 20 6061317 . C A . . PacBio=Poly;Sqnm=Poly 20 6328925 . C A . . PacBio=Poly;Sqnm=Poly 20 6675461 . C T . . PacBio=Poly;Sqnm=NoCall 20 6976115 . C T . . PacBio=Poly;Sqnm=Poly 20 7013349 . G A . . PacBio=NoCall;Sqnm=NoCall 20 7039302 . C T . . PacBio=Poly;Sqnm=Poly 20 7638704 . C A . . PacBio=Poly;Sqnm=Poly 20 7688381 . G A . . PacBio=Poly;Sqnm=Poly 20 7726350 . G T . . PacBio=Poly;Sqnm=Poly 20 7733957 . C T . . PacBio=Poly;Sqnm=Poly 20 7850516 . T C . . PacBio=Poly;Sqnm=Poly 20 8095059 . G A . . PacBio=NoCall;Sqnm=NoCall 20 8232012 . T A . . PacBio=Poly;Sqnm=Poly 20 8415290 . A C . . PacBio=Poly;Sqnm=Poly 20 8438535 . T C . . PacBio=Poly;Sqnm=NoCall 20 8815233 . G A . . PacBio=Mono;Sqnm=NoCall 20 8953629 . C G . . PacBio=Poly;Sqnm=Poly 20 9237267 . T A . . PacBio=Poly;Sqnm=Poly 20 9744549 . T C . . PacBio=Poly;Sqnm=Poly 20 9780416 . C A . . PacBio=Poly;Sqnm=Poly 20 10252552 . T C . . PacBio=Poly;Sqnm=Poly 20 10314038 . C G . . PacBio=Poly;Sqnm=Poly 20 10757416 . T C . . PacBio=Poly;Sqnm=Poly 20 11087688 . A G . . PacBio=Poly;Sqnm=Poly 20 11094107 . G A . . PacBio=NoCall;Sqnm=NoCall 20 11098680 . G A . . PacBio=Poly;Sqnm=Poly 20 11353163 . G C . . PacBio=Poly;Sqnm=Poly 20 11510559 . A G . . PacBio=Poly;Sqnm=Poly 20 11787224 . C T . . PacBio=Poly;Sqnm=Poly 20 11821024 . T C . . PacBio=Poly;Sqnm=Poly 20 11932295 . A G . . PacBio=Poly;Sqnm=Poly 20 11965311 . G T . . PacBio=Poly;Sqnm=Poly 20 12023599 . C T . . PacBio=Poly;Sqnm=Poly 20 12505523 . G T . . PacBio=Poly;Sqnm=Poly 20 12570054 . A C . . PacBio=NoCall;Sqnm=Poly 20 12667452 . A G . . PacBio=Poly;Sqnm=Poly 20 12678271 . G A . . PacBio=Poly;Sqnm=Mono 20 12704885 . T C . . PacBio=Poly;Sqnm=Poly 20 12733996 . C T . . PacBio=Poly;Sqnm=NoCall 20 12737269 . C T . . PacBio=NoCall;Sqnm=NoCall 20 12788981 . G A . . PacBio=Poly;Sqnm=Poly 20 12828594 . T C . . PacBio=Poly;Sqnm=Poly 20 12999157 . T C . . PacBio=Poly;Sqnm=Poly 20 13083804 . C G . . PacBio=Poly;Sqnm=Poly 20 13197077 . G T . . PacBio=Poly;Sqnm=NoCall 20 13217896 . A G . . PacBio=NoCall;Sqnm=Poly 20 13276778 . G A . . PacBio=Poly;Sqnm=Poly 20 13375116 . G A . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 13648056 . T C . . PacBio=Poly;Sqnm=Poly 20 13672895 . C T . . PacBio=Poly;Sqnm=Poly 20 14160159 . C G . . PacBio=Poly;Sqnm=Poly 20 14266815 . T A . . PacBio=Poly;Sqnm=Poly 20 14865143 . C T . . PacBio=Poly;Sqnm=Poly 20 14882868 . T G . . PacBio=Poly;Sqnm=Poly 20 15244725 . C A . . PacBio=Poly;Sqnm=Poly 20 15277072 . G A . . PacBio=Poly;Sqnm=Poly 20 15390867 . C T . . PacBio=Poly;Sqnm=Poly 20 15785205 . T C . . PacBio=Poly;Sqnm=Poly 20 15833020 . A G . . PacBio=Poly;Sqnm=Poly 20 15847620 . C T . . PacBio=Poly;Sqnm=Poly 20 15953253 . G A . . PacBio=Poly;Sqnm=NoCall 20 15964434 . G C . . PacBio=NoCall;Sqnm=NoCall 20 16183922 . G A . . PacBio=Poly;Sqnm=Poly 20 16190824 . A G . . PacBio=Poly;Sqnm=Poly 20 16557779 . A G . . PacBio=Poly;Sqnm=Poly 20 16730061 . C T . . PacBio=Poly;Sqnm=Poly 20 16794015 . T C . . PacBio=Poly;Sqnm=Poly 20 17048741 . G A . . PacBio=Poly;Sqnm=Poly 20 17299827 . G A . . PacBio=Poly;Sqnm=Poly 20 17299845 . C T . . PacBio=Poly;Sqnm=Poly 20 17390323 . G A . . PacBio=Poly;Sqnm=Poly 20 17624973 . C G . . PacBio=Poly;Sqnm=Poly 20 17666040 . G A . . PacBio=Poly;Sqnm=Poly 20 17735813 . T C . . PacBio=Poly;Sqnm=Poly 20 17794990 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 17809418 . G A . . PacBio=Poly;Sqnm=Poly 20 17860794 . C T . . PacBio=Mono;Sqnm=NoCall 20 17881936 . A G . . PacBio=Poly;Sqnm=Poly 20 17893097 . C G . . PacBio=NoCall;Sqnm=NoCall 20 18188883 . A G . . PacBio=Poly;Sqnm=Poly 20 18199319 . G A . . PacBio=Poly;Sqnm=Poly 20 18233699 . C T . . PacBio=Poly;Sqnm=Poly 20 18536869 . G A . . PacBio=Poly;Sqnm=Poly 20 18637785 . T C . . PacBio=NoCall;Sqnm=Mono;Sanger=Mono;NotCalledInValidationSamples 20 18763166 . G A . . PacBio=Poly;Sqnm=Poly 20 19102715 . A G . . PacBio=NoCall;Sqnm=NoCall 20 19244609 . C T . . PacBio=Poly;Sqnm=Poly 20 19573719 . C T . . PacBio=Poly;Sqnm=Poly 20 19815613 . A G . . PacBio=NoCall;Sqnm=Poly 20 20511479 . C T . . PacBio=Poly;Sqnm=Poly;Sanger=Poly 20 20639358 . T C . . PacBio=Poly;Sqnm=Poly 20 21278490 . T C . . PacBio=Poly;Sqnm=Poly 20 21297718 . C G . . PacBio=Poly;Sqnm=Poly 20 21418269 . A T . . PacBio=Poly;Sqnm=Poly 20 21560553 . A T . . PacBio=Poly;Sqnm=Poly 20 21618451 . G A . . PacBio=NoCall;Sqnm=NoCall 20 21705723 . C A . . PacBio=Poly;Sqnm=Poly 20 22076189 . A G . . PacBio=Poly;Sqnm=Poly 20 22118677 . T A . . PacBio=Poly;Sqnm=Poly 20 22320721 . C T . . PacBio=Poly;Sqnm=Poly 20 22368918 . C A . . PacBio=Poly;Sqnm=Poly 20 23020003 . A G . . PacBio=Poly;Sqnm=Poly 20 23214163 . G A . . PacBio=Poly;Sqnm=Poly 20 23273877 . T C . . PacBio=Poly;Sqnm=Poly 20 23335790 . C T . . PacBio=Poly;Sqnm=NoCall 20 23790659 . C T . . PacBio=Poly;Sqnm=Poly 20 23830388 . T C . . PacBio=Poly;Sqnm=NoCall 20 23837678 . C G . . PacBio=Poly;Sqnm=Poly 20 23901081 . A C . . PacBio=Poly;Sqnm=Poly 20 23946361 . C T . . PacBio=Poly;Sqnm=Poly 20 23949242 . A G . . PacBio=Poly;Sqnm=Poly 20 24539119 . A G . . PacBio=Poly;Sqnm=Poly 20 24986457 . C T . . PacBio=Poly;Sqnm=Poly 20 25183729 . G A . . PacBio=NoCall;Sqnm=NoCall 20 25277133 . C T . . PacBio=Poly;Sqnm=Poly 20 25292464 . C T . . PacBio=Poly;Sqnm=NoCall 20 25528915 . G C . . PacBio=Poly;Sqnm=Poly 20 25851836 . A G . . PacBio=NoCall;Sqnm=NoCall 20 25970163 . C T . . PacBio=Poly;Sqnm=Poly 20 29920798 . C T . . PacBio=NoCall;Sqnm=NoCall 20 30007713 . T C . . PacBio=Poly;Sqnm=Poly 20 30051768 . T C . . PacBio=Poly;Sqnm=Poly 20 30183598 . T C . . PacBio=Poly;Sqnm=Poly 20 30604408 . G A . . PacBio=NoCall;Sqnm=NoCall 20 30759940 . G T . . PacBio=Poly;Sqnm=Poly 20 30881454 . G T . . PacBio=Poly;Sqnm=Poly 20 31356560 . C T . . PacBio=Poly;Sqnm=Poly 20 31450036 . A G . . PacBio=NoCall;Sqnm=Mono 20 31589920 . A T . . PacBio=Poly;Sqnm=Poly 20 31922121 . C T . . PacBio=NoCall;Sqnm=NoCall 20 32801430 . G C . . PacBio=Poly;Sqnm=Poly 20 32943975 . G T . . PacBio=Mono;Sqnm=Mono 20 33155812 . C A . . PacBio=Poly;Sqnm=Poly 20 34090682 . C T . . PacBio=Poly;Sqnm=Poly 20 34254080 . C T . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 34312126 . C T . . PacBio=Poly;Sqnm=NoCall 20 34481504 . G A . . PacBio=Poly;Sqnm=Poly 20 34694577 . G A . . PacBio=Poly;Sqnm=Poly 20 35026572 . T C . . PacBio=Poly;Sqnm=Poly 20 35472344 . T G . . PacBio=Poly;Sqnm=Poly 20 35882698 . G A . . PacBio=Poly;Sqnm=NoCall 20 36044719 . G A . . PacBio=Poly;Sqnm=NoCall 20 36047623 . C A . . PacBio=NoCall;Sqnm=NoCall 20 36204890 . C T . . PacBio=Poly;Sqnm=NoCall 20 36469514 . G C . . PacBio=NoCall;Sqnm=Poly 20 36840217 . T C . . PacBio=Poly;Sqnm=Poly 20 37460945 . C T . . PacBio=Mono;Sqnm=Poly 20 37665246 . G A . . PacBio=Poly;Sqnm=NoCall 20 37732397 . A G . . PacBio=Poly;Sqnm=Poly 20 37874645 . G T . . PacBio=Poly;Sqnm=Poly 20 37958191 . T C . . PacBio=Poly;Sqnm=Poly 20 37996273 . C T . . PacBio=Mono;Sqnm=NoCall;NotCalledInValidationSamples 20 38016547 . C T . . PacBio=Poly;Sqnm=Poly 20 38435682 . A G . . PacBio=Poly;Sqnm=Poly 20 38505534 . A T . . PacBio=Poly;Sqnm=Poly 20 38803278 . A G . . PacBio=Poly;Sqnm=Poly 20 38963803 . G C . . PacBio=Poly;Sqnm=Poly 20 38971986 . A G . . PacBio=Poly;Sqnm=Poly 20 39269586 . G A . . PacBio=Poly;Sqnm=Poly 20 39289390 . C A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 39318956 . T A . . PacBio=Poly;Sqnm=Poly 20 39736197 . A G . . PacBio=Poly;Sqnm=Poly 20 40241339 . T C . . PacBio=Poly;Sqnm=Poly 20 41473555 . G A . . PacBio=Poly;Sqnm=Poly 20 41878576 . T G . . PacBio=Poly;Sqnm=Poly 20 42022716 . A G . . PacBio=Poly;Sqnm=Poly 20 42033671 . A C . . PacBio=NoCall;Sqnm=NoCall 20 42270334 . C T . . PacBio=NoCall;Sqnm=NoCall 20 42449590 . C T . . PacBio=Poly;Sqnm=NoCall 20 42521157 . T G . . PacBio=Poly;Sqnm=Poly 20 42624300 . C A . . PacBio=Poly;Sqnm=Poly 20 42984548 . G A . . PacBio=Poly;Sqnm=Poly 20 43200148 . G C . . PacBio=Poly;Sqnm=Poly 20 43425384 . T G . . PacBio=Poly;Sqnm=Poly 20 43521990 . C G . . PacBio=Poly;Sqnm=Poly 20 43565804 . G A . . PacBio=Poly;Sqnm=Poly 20 43591237 . T C . . PacBio=Poly;Sqnm=Poly 20 43805929 . C T . . PacBio=Poly;Sqnm=Poly 20 43866692 . A G . . PacBio=Poly;Sqnm=Poly 20 43902088 . C T . . PacBio=Poly;Sqnm=Poly 20 44478507 . C A . . PacBio=Poly;Sqnm=Poly 20 44768810 . C T . . PacBio=Poly;Sqnm=Poly 20 45151582 . G A . . PacBio=Poly;Sqnm=Poly 20 45414003 . G A . . PacBio=Poly;Sqnm=Poly 20 45776825 . G C . . PacBio=Poly;Sqnm=Poly 20 46454905 . G A . . PacBio=Poly;Sqnm=NoCall 20 46823642 . C T . . PacBio=Poly;Sqnm=Poly 20 47001376 . C T . . PacBio=Poly;Sqnm=Poly 20 47079360 . G C . . PacBio=Poly;Sqnm=NoCall 20 47248953 . G A . . PacBio=Poly;Sqnm=Poly 20 47480655 . C T . . PacBio=Poly;Sqnm=Poly 20 47529099 . T C . . PacBio=Poly;Sqnm=Poly 20 47703355 . A C . . PacBio=Poly;Sqnm=Poly 20 47919541 . A G . . PacBio=Poly;Sqnm=Poly 20 48126120 . A C . . PacBio=Poly;Sqnm=Poly 20 48157380 . G A . . PacBio=Poly;Sqnm=Poly 20 48233077 . C T . . PacBio=Poly;Sqnm=Poly 20 48488571 . G A . . PacBio=Poly;Sqnm=Poly 20 48534468 . G A . . PacBio=Poly;Sqnm=NoCall 20 48631385 . G C . . PacBio=Poly;Sqnm=Poly 20 48654970 . G A . . PacBio=Poly;Sqnm=NoCall 20 48708007 . C T . . PacBio=Poly;Sqnm=Poly 20 48979827 . C A . . PacBio=Poly;Sqnm=Poly 20 49100106 . G A . . PacBio=Poly;Sqnm=Poly 20 49509102 . G A . . PacBio=Poly;Sqnm=Poly 20 49631170 . G A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples 20 50210361 . C T . . PacBio=Poly;Sqnm=Poly 20 50309600 . C A . . PacBio=Poly;Sqnm=Poly 20 50681296 . T C . . PacBio=Poly;Sqnm=Poly 20 50750138 . A G . . PacBio=Poly;Sqnm=Poly 20 51639257 . G A . . PacBio=Mono;Sqnm=Poly 20 51814664 . T C . . PacBio=Poly;Sqnm=Poly 20 51891088 . C T . . PacBio=Poly;Sqnm=Poly 20 52299250 . A G . . PacBio=Poly;Sqnm=Poly 20 52363435 . G A . . PacBio=Poly;Sqnm=NoCall 20 52583941 . C T . . PacBio=Poly;Sqnm=Poly 20 52787584 . C T . . PacBio=Poly;Sqnm=Poly 20 53256945 . G A . . PacBio=Poly;Sqnm=Poly 20 54155398 . A G . . PacBio=Poly;Sqnm=Poly 20 54172374 . G T . . PacBio=Poly;Sqnm=Poly 20 54209446 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 54317862 . C T . . PacBio=Poly;Sqnm=Poly 20 54852735 . C T . . PacBio=Poly;Sqnm=NoCall 20 54889864 . G A . . PacBio=Poly;Sqnm=Poly 20 55208711 . G A . . PacBio=Poly;Sqnm=Poly 20 55220477 . G T . . PacBio=Poly;Sqnm=Poly 20 55224856 . G T . . PacBio=NoCall;Sqnm=NoCall 20 55441530 . C T . . PacBio=Poly;Sqnm=NoCall 20 55585710 . C T . . PacBio=Poly;Sqnm=Poly 20 55630163 . C T . . PacBio=Poly;Sqnm=Poly 20 56031994 . A G . . PacBio=Poly;Sqnm=Poly 20 56316071 . T G . . PacBio=Poly;Sqnm=Poly 20 56366198 . C T . . PacBio=Poly;Sqnm=Poly 20 56703987 . G A . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 56794829 . G C . . PacBio=Poly;Sqnm=Poly 20 56797026 . G A . . PacBio=Poly;Sqnm=Poly 20 56922427 . A G . . PacBio=Poly;Sqnm=Poly 20 57025102 . A T . . PacBio=Poly;Sqnm=Poly 20 57104529 . G A . . PacBio=Poly;Sqnm=Poly 20 57360225 . C T . . PacBio=Poly;Sqnm=Poly 20 57630386 . T A . . PacBio=NoCall;Sqnm=NoCall 20 57754033 . G A . . PacBio=Poly;Sqnm=Poly 20 57956631 . C T . . PacBio=Poly;Sqnm=Poly 20 57997801 . C T . . PacBio=Poly;Sqnm=NoCall 20 58046279 . C G . . PacBio=NoCall;Sqnm=NoCall 20 58186723 . A G . . PacBio=Poly;Sqnm=Poly 20 58214460 . C T . . PacBio=Poly;Sqnm=Poly 20 58317759 . A G . . PacBio=Poly;Sqnm=Poly 20 58491642 . A C . . PacBio=Poly;Sqnm=Poly 20 58560045 . C T . . PacBio=Poly;Sqnm=Poly 20 58629232 . C T . . PacBio=Poly;Sqnm=Poly 20 58805192 . G T . . PacBio=Poly;Sqnm=Poly 20 58869523 . A G . . PacBio=Poly;Sqnm=Poly 20 59337535 . T C . . PacBio=Poly;Sqnm=Poly 20 59441596 . G A . . PacBio=Poly;Sqnm=Poly 20 59445223 . G A . . PacBio=NoCall;Sqnm=NoCall 20 59605846 . C T . . PacBio=Poly;Sqnm=Poly 20 59864395 . G C . . PacBio=Poly;Sqnm=Poly 20 60099821 . G T . . PacBio=Poly;Sqnm=Poly 20 60290551 . A G . . PacBio=Mono;Sqnm=Mono;NotCalledInValidationSamples;Sanger=Poly 20 60362527 . G C . . PacBio=Poly;Sqnm=Poly 20 60516358 . C T . . PacBio=Poly;Sqnm=Poly 20 60559594 . C T . . PacBio=NoCall;Sqnm=Poly 20 60745115 . G A . . PacBio=Poly;Sqnm=Poly 20 60831300 . G A . . PacBio=Poly;Sqnm=Poly 20 60907675 . G A . . PacBio=Poly;Sqnm=Poly 20 61458191 . G A . . PacBio=Poly;Sqnm=Poly 20 61717607 . C T . . PacBio=Mono;Sqnm=Poly 20 61771154 . G A . . PacBio=Poly;Sqnm=Poly 20 61950497 . G A . . PacBio=Poly;Sqnm=Poly 20 62000091 . C T . . PacBio=Poly;Sqnm=Poly 20 62550780 . C T . . PacBio=NoCall;Sqnm=NoCall 20 62558259 . T C . . PacBio=Poly;Sqnm=Poly 20 62727205 . C T . . PacBio=Poly;Sqnm=Poly pysam-0.7.7/tests/vcf-examples/9.vcf0000664000076400007650000027233611754437212017134 0ustar andreasandreas##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.7.7/tests/vcf-examples/22.vcf0000664000076400007650000256374211754437212017215 0ustar andreasandreas##fileformat=VCFv4.0 ##FORMAT= ##FilterLiftedVariants="analysis_type=FilterLiftedVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/local/sequence/reference/BWA_ref/hg19/hg19.fasta rodBind=[/local/scratch/xyliu/0.915136538286792.sorted.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA15029 NA15036 NA15038 NA15056b NA15072 NA15144C NA15213_006 NA15215A NA15216_A2 NA15221b NA15223_6v2 NA15224_4 NA15226A NA15227b NA15236_6 NA15242_005 NA15245v2 NA15268 NA15324_A1 NA15385b NA15386A NA15510_A1 NA15590_4 NA15594_005 NA18500b NA18501 NA18502 NA18503 NA18504 NA18505 NA18506 NA18507 NA18508 NA18515 NA18516 NA18517 NA18521 NA18522 NA18523 NA18524_B1 NA18526_B2 NA18529_B1 NA18532_B1 NA18537_B1 NA18540_B1 NA18542_B1 NA18545_5 NA18547_B1 NA18550_B1 NA18555_A2 NA18561_A3 NA18562_B1 NA18563 NA18564_4 NA18566_3 NA18570_3 NA18571_3 NA18572_3 NA18573_B3 NA18576_4 NA18577_B1 NA18579_B1 NA18582_B1 NA18592_2 NA18593_B1 NA18594_B1 NA18603_B1 NA18605_B1 NA18608_B1 NA18609_B1 NA18611_B1 NA18612_B1 NA18620_3 NA18621_B1 NA18622_B1 NA18623_B1 NA18624 NA18632_3 NA18635_A1 NA18637_2 NA18852 NA18853 NA18854 NA18855 NA18856 NA18857 NA18858 NA18859 NA18860 NA18861 NA18862 NA18863 NA18870 NA18871 NA18872 NA18912 NA18913 NA18914 NA18940_3 NA19092 NA19093 NA19094 NA19098 NA19099 NA19100 NA19101 NA19102 NA19103 NA19116 NA19119b NA19120 NA19127 NA19128 NA19129 NA19130b NA19131 NA19132b NA19137 NA19138 NA19139 NA19140b NA19141 NA19142 NA19143 NA19144 NA19145 NA19152 NA19153 NA19154 NA19159 NA19160 NA19161 NA19171 NA19172 NA19173 NA19192 NA19193 NA19194 NA19200 NA19201 NA19202 NA19203 NA19204 NA19205 NA19206 NA19207 NA19208v2 NA19209 NA19210 NA19211 NA19221 NA19222 NA19223 NA19238 NA19239 NA19240 NA_pos103a NS12911_1 chr1 5911136 . T TGCCATTCCAAAGAGGCACTCA . PASS VC=INDEL;AC=28;AF=0.09;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 17054990 . G GA . PASS VC=INDEL;AC=25;AF=0.12;AN=200 GT ./. ./. 0/1 ./. 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. 0/0 ./. ./. 0/1 ./. ./. ./. ./. 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/1 ./. ./. ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. chr1 17390953 . CT C . PASS VC=INDEL;AC=118;AF=0.37;AN=316 GT 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 chr1 17754916 . CCT C . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_018715;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 18293100 . C CCTC . PASS VC=INDEL;AC=263;AF=0.84;AN=314 GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 18823397 . T TTAAT . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 19215209 . G GAG . PASS VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_003748;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 19943821 . CACAG C . PASS VC=INDEL;AC=12;AF=0.04;AN=308;refseq.name=NM_001032363;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 20092486 . GAAG G . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_181719;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 20977854 . A ATTC . PASS VC=INDEL;AC=152;AF=0.52;AN=292;refseq.name=NM_032409;refseq.positionType=exon GT 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 ./. 0/1 0/1 1/1 0/1 0/1 ./. 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 ./. ./. 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 ./. 0/0 ./. 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 0/0 0/1 0/1 1/1 ./. ./. 0/1 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/0 ./. 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 chr1 21275058 . CTTTG C . PASS VC=INDEL;AC=30;AF=0.1;AN=296;refseq.name=NM_003760;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 chr1 22642904 . A AAC . PASS VC=INDEL;AC=255;AF=0.85;AN=300 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 chr1 22844297 . ATCT A . PASS VC=INDEL;AC=162;AF=0.51;AN=316;refseq.name=NM_001083621;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 22844299 . CTTC C . PASS VC=INDEL;AC=160;AF=0.51;AN=314;refseq.name=NM_001083621;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 23162393 . AA A . PASS VC=INDEL;AC=44;AF=0.14;AN=316;refseq.name=NM_004442;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 23882634 . T TAGGTG . PASS VC=INDEL;AC=24;AF=0.08;AN=284 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 25799681 . CTCTG C . PASS VC=INDEL;AC=49;AF=0.21;AN=230;refseq.name=NM_018202;refseq.positionType=intron GT 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 1/1 ./. 1/1 0/0 0/1 1/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 1/1 0/1 ./. ./. 0/1 ./. 1/1 0/1 ./. 0/1 1/1 ./. ./. 0/1 ./. 0/1 ./. ./. 1/1 ./. 0/1 ./. 1/1 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 26081170 . CA C . PASS VC=INDEL;AC=17;AF=0.06;AN=308;refseq.name=NM_020379;refseq.positionType=intron GT 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 26240086 . GAT G . PASS VC=INDEL;AC=31;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 26725650 . A ATGAAG . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 26725655 . G GTGAAG . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 27425097 . CTGG C . PASS VC=INDEL;AC=40;AF=0.16;AN=248;refseq.name=NM_003047;refseq.positionType=terminator GT 1/1 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 chr1 27737240 . A AT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_006990;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 27744410 . GATCCATG G . PASS VC=INDEL;AC=166;AF=0.56;AN=296;refseq.name=NM_006990;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 ./. 0/1 0/0 ./. 0/0 ./. 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 ./. 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. ./. chr1 28156589 . G GGATG . PASS VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002713;refseq.positionType=promoter GT 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 28721777 . TA T . PASS VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 28721778 . AA A . PASS VC=INDEL;AC=287;AF=0.91;AN=316;refseq.name=NM_001048183;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 28907201 . GT G . PASS VC=INDEL;AC=3;AF=0.01;AN=224 GT 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. ./. chr1 29223339 . G GTGAG . PASS VC=INDEL;AC=203;AF=0.7;AN=292;refseq.name=NM_004437;refseq.positionType=intron GT 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 ./. 1/1 0/1 chr1 29223342 . A AGCAA . PASS VC=INDEL;AC=71;AF=0.29;AN=242;refseq.name=NM_004437;refseq.positionType=intron GT 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 ./. 1/1 0/1 ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. ./. ./. ./. 0/1 ./. 0/0 ./. ./. ./. 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 ./. ./. 0/0 chr1 29865521 . G GCTCCGT . PASS VC=INDEL;AC=115;AF=0.36;AN=316 GT 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 chr1 31128790 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31135886 . A AG . PASS VC=INDEL;AC=246;AF=0.92;AN=268 GT ./. 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 0/1 ./. 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. chr1 31503645 . AAAAGA A . PASS VC=INDEL;AC=5;AF=0.02;AN=314;refseq.name=NM_001020658;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31504005 . C CAT . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_001020658;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 chr1 31731414 . CCTCT C . PASS VC=INDEL;AC=40;AF=0.13;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31775152 . A ACTA . PASS VC=INDEL;AC=47;AF=0.15;AN=308;refseq.name=NM_016505;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 31882582 . G GGCCTCA . PASS VC=INDEL;AC=163;AF=0.59;AN=274 GT 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 ./. 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 0/1 ./. 0/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/1 0/1 ./. 0/0 0/1 ./. 0/1 ./. 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 chr1 32010706 . GG G . PASS VC=INDEL;AC=312;AF=1;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 32078865 . G GT . PASS VC=INDEL;AC=78;AF=0.25;AN=316 GT 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 33422344 . G GAA . PASS VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_153341;refseq.positionType=intron GT 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 chr1 33634618 . TC T . PASS VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_018207;refseq.positionType=intron GT 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 33965999 . CCCAGTTC C . PASS VC=INDEL;AC=203;AF=0.65;AN=314 GT 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 chr1 34176371 . GAAACATAAG G . PASS VC=INDEL;AC=252;AF=0.95;AN=266;refseq.name=NM_052896;refseq.positionType=intron GT 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 ./. ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 0/1 1/1 ./. ./. 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 chr1 34931817 . AT A . PASS VC=INDEL;AC=38;AF=0.12;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 35879227 . CAT C . PASS VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_005095;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 36429590 . A AG . PASS VC=INDEL;AC=181;AF=0.57;AN=316;refseq.name=NM_024852;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 chr1 36558240 . C CAC . PASS VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_017825;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 37034721 . ATACT A . PASS VC=INDEL;AC=44;AF=0.16;AN=282 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr1 37142202 . AATA A . PASS VC=INDEL;AC=24;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 37169424 . TA T . PASS VC=INDEL;AC=176;AF=0.56;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 chr1 37169427 . AA A . PASS VC=INDEL;AC=173;AF=0.56;AN=308 GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 chr1 37638341 . T TAT . PASS VC=INDEL;AC=11;AF=0.05;AN=222 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/1 ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. ./. 0/0 chr1 38077349 . CTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTA C . PASS VC=INDEL;AC=209;AF=0.77;AN=272;refseq.name=NM_001038633;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 ./. 1/1 ./. 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 ./. ./. ./. 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 0/0 0/1 0/0 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/1 chr1 38392549 . AT A . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005540;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 38664242 . TA T . PASS VC=INDEL;AC=93;AF=0.29;AN=316 GT 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 chr1 38739177 . GTG G . PASS VC=INDEL;AC=32;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 39288395 . CTTC C . PASS VC=INDEL;AC=36;AF=0.12;AN=306 GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 chr1 39615407 . C CGATAT . PASS VC=INDEL;AC=192;AF=0.63;AN=306;refseq.name=NM_012090;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 ./. 0/0 1/1 0/1 1/1 1/1 chr1 39615412 . T TGATAT . PASS VC=INDEL;AC=200;AF=0.63;AN=316;refseq.name=NM_012090;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 chr1 39736467 . T TATAT . PASS VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_012090;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 39936801 . GTG G . PASS VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_012090;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 40525320 . AACACAAGAAC A . PASS VC=INDEL;AC=21;AF=0.11;AN=196;refseq.name=NM_006367;refseq.positionType=intron GT ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/1 1/1 1/1 0/1 ./. 1/1 ./. 0/0 1/1 0/0 1/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/1 ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. chr1 40728529 . TA T . PASS VC=INDEL;AC=216;AF=0.68;AN=316;refseq.name=NM_005857;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 41281719 . CT C . PASS VC=INDEL;AC=142;AF=0.45;AN=316;refseq.name=NM_004700;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 chr1 41808814 . CT C . PASS VC=INDEL;AC=32;AF=0.1;AN=308 GT 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 41991662 . CCA C . PASS VC=INDEL;AC=17;AF=0.06;AN=304;refseq.name=NM_024503;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. chr1 42083551 . C CT . PASS VC=INDEL;AC=139;AF=0.44;AN=316;refseq.name=NM_024503;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 chr1 42531504 . G GATAG . PASS VC=INDEL;AC=199;AF=0.66;AN=302 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 ./. 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 ./. 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 chr1 42835720 . C CTTG . PASS VC=INDEL;AC=297;AF=0.94;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 42835723 . G GTTG . PASS VC=INDEL;AC=297;AF=0.94;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 42880843 . A ACA . PASS VC=INDEL;AC=179;AF=0.57;AN=316;refseq.name=NM_173642;refseq.positionType=exon GT 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 chr1 44114854 . C CGC . PASS VC=INDEL;AC=107;AF=0.45;AN=238;refseq.name=NM_014663;refseq.positionType=promoter GT 0/0 1/1 1/1 ./. 0/0 ./. ./. 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 ./. 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/0 1/1 ./. 0/0 0/0 0/1 0/1 ./. ./. ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/1 ./. 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 ./. 0/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/0 0/1 chr1 44231607 . CA C . PASS VC=INDEL;AC=216;AF=0.69;AN=314;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 ./. 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 44231608 . AA A . PASS VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 44327106 . GCTGTCAGGACTTGTATAGA G . PASS VC=INDEL;AC=193;AF=0.66;AN=294;refseq.name=NM_006279;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 ./. 1/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 1/1 chr1 44730823 . G GGAGA . PASS VC=INDEL;AC=295;AF=0.96;AN=306;refseq.name=NM_024066;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 44881687 . GCAT G . PASS VC=INDEL;AC=29;AF=0.09;AN=314;refseq.name=NM_018150;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 45223909 . GATTAGCTG G . PASS VC=INDEL;AC=167;AF=0.55;AN=306;refseq.name=NM_006845;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 ./. 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 46900444 . T TGTGGGAATGC . PASS VC=INDEL;AC=2;AF=0.01;AN=296 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 chr1 46900720 . C CTT . PASS VC=INDEL;AC=244;AF=0.79;AN=308 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 46900721 . T TTT . PASS VC=INDEL;AC=241;AF=0.79;AN=304 GT 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 47052336 . TGAAA T . PASS VC=INDEL;AC=76;AF=0.24;AN=316;refseq.name=NM_003684;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 47167062 . TT T . PASS VC=INDEL;AC=174;AF=0.64;AN=272;refseq.name=NM_014774;refseq.positionType=intron GT ./. 0/1 0/1 0/1 ./. 0/0 0/0 1/1 1/1 0/1 1/1 0/1 ./. ./. 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/0 0/1 ./. 1/1 1/1 1/1 ./. ./. 0/0 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 ./. 0/1 1/1 ./. 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/0 ./. 0/1 ./. 0/1 1/1 0/1 1/1 ./. 1/1 ./. 0/0 chr1 47324578 . CTACTACAAA C . PASS VC=INDEL;AC=150;AF=0.65;AN=232 GT 1/1 ./. ./. ./. ./. 0/1 0/0 0/1 0/0 ./. ./. 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/0 ./. 0/0 1/1 1/1 ./. 0/1 1/1 1/1 ./. 0/1 0/0 0/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 1/1 ./. 0/0 0/1 0/0 ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. 0/0 ./. 0/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. ./. ./. 0/1 ./. 0/1 0/1 0/1 ./. 0/1 chr1 47325281 . CA C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 47891688 . AT A . PASS VC=INDEL;AC=84;AF=0.29;AN=294 GT 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 ./. 0/0 ./. 0/0 ./. 0/0 1/1 1/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 47931769 . TTCTC T . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 48000154 . G GTTT . PASS VC=INDEL;AC=11;AF=0.05;AN=232 GT ./. 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr1 48146050 . CCTGA C . PASS VC=INDEL;AC=28;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 48520865 . CAGGGTGAGTAGGCCTGGGCAG C . PASS VC=INDEL;AC=4;AF=0.01;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 48520886 . GAG G . PASS VC=INDEL;AC=31;AF=0.14;AN=216 GT ./. 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 1/1 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/1 0/0 ./. ./. ./. chr1 48544917 . G GTGTT . PASS VC=INDEL;AC=43;AF=0.14;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 49109456 . AGAGC A . PASS VC=INDEL;AC=31;AF=0.14;AN=226;refseq.name=NM_032785;refseq.positionType=intron GT 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 0/1 ./. ./. ./. 0/1 0/1 0/1 chr1 49124365 . C CGAG . PASS VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 49124368 . G GGAG . PASS VC=INDEL;AC=93;AF=0.29;AN=316;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 49126514 . C CTG . PASS VC=INDEL;AC=89;AF=0.3;AN=296;refseq.name=NM_032785;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 50107735 . G GA . PASS VC=INDEL;AC=68;AF=0.22;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 50539498 . T TCT . PASS VC=INDEL;AC=312;AF=0.99;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 50652516 . A AGAA . PASS VC=INDEL;AC=247;AF=0.78;AN=316;refseq.name=NM_021952;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 51315116 . ACTG A . PASS VC=INDEL;AC=13;AF=0.04;AN=316;refseq.name=NM_007051;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 52336500 . TAATACA T . PASS VC=INDEL;AC=17;AF=0.07;AN=230;refseq.name=NM_002525;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/1 ./. ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 52798171 . A AT . PASS VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_004799;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 53554533 . A AT . PASS VC=INDEL;AC=33;AF=0.11;AN=294;refseq.name=NM_006671;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/1 chr1 53986946 . TG T . PASS VC=INDEL;AC=188;AF=0.59;AN=316;refseq.name=NM_147193;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 chr1 54168427 . C CTCTG . PASS VC=INDEL;AC=109;AF=0.35;AN=308;refseq.name=NM_147193;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 ./. 1/1 0/0 0/0 ./. 1/1 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 chr1 54558546 . T TAGAC . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 54558548 . G GACAG . PASS VC=INDEL;AC=66;AF=0.21;AN=316;refseq.name=NM_153035;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 54619996 . AC A . PASS VC=INDEL;AC=193;AF=0.64;AN=302;refseq.name=NM_201546;refseq.positionType=promoter GT 1/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 chr1 54757161 . C CCA . PASS VC=INDEL;AC=186;AF=0.59;AN=314;refseq.name=NM_001009955;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 chr1 54757166 . C CAC . PASS VC=INDEL;AC=185;AF=0.59;AN=312;refseq.name=NM_001009955;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 ./. 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 chr1 55566411 . TTAGTC T . PASS VC=INDEL;AC=207;AF=0.66;AN=316;refseq.name=NM_015306;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 55743440 . C CCT . PASS VC=INDEL;AC=261;AF=0.84;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 ./. 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 55888273 . T TC . PASS VC=INDEL;AC=265;AF=0.88;AN=302 GT 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 55888274 . C CC . PASS VC=INDEL;AC=271;AF=0.89;AN=306 GT 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 55892282 . T TAGAAAA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 55998244 . CGCACGCTC C . PASS VC=INDEL;AC=265;AF=0.84;AN=314 GT 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 chr1 56495367 . CTGAG C . PASS VC=INDEL;AC=76;AF=0.24;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 57353886 . C CTA . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_000562;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 57854490 . AAT A . PASS VC=INDEL;AC=24;AF=0.08;AN=312;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58391942 . G GAAA . PASS VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 58413348 . A AG . PASS VC=INDEL;AC=50;AF=0.22;AN=226;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 ./. ./. 0/1 0/0 ./. 0/1 0/1 0/1 1/1 0/0 ./. ./. 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 ./. ./. 0/1 ./. ./. 0/1 0/0 0/0 0/0 ./. ./. ./. 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. ./. 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 1/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/1 ./. 1/1 ./. 1/1 chr1 58550673 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58629900 . CAGA C . PASS VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_021080;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 58999156 . AT A . PASS VC=INDEL;AC=151;AF=0.53;AN=286;refseq.name=NM_145243;refseq.positionType=intron GT ./. 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/0 0/0 0/0 0/1 1/1 ./. 1/1 0/1 0/0 0/0 ./. 0/0 0/0 0/1 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 ./. 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 chr1 59009401 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_145243;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 59104181 . GA G . PASS VC=INDEL;AC=271;AF=0.89;AN=304 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 chr1 59319761 . AG A . PASS VC=INDEL;AC=195;AF=0.67;AN=290 GT 0/0 0/1 0/0 0/0 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 ./. ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 chr1 59319762 . GG G . PASS VC=INDEL;AC=200;AF=0.68;AN=296 GT 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 ./. 1/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 ./. 1/1 ./. 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 chr1 59630873 . CT C . PASS VC=INDEL;AC=155;AF=0.49;AN=316 GT 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 chr1 59635600 . TAT T . PASS VC=INDEL;AC=287;AF=0.91;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 60128716 . G GC . PASS VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 60128717 . C CC . PASS VC=INDEL;AC=309;AF=0.98;AN=316;refseq.name=NM_018291;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 60228311 . T TCT . PASS VC=INDEL;AC=250;AF=0.8;AN=314;refseq.name=NM_018291;refseq.positionType=exon GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 chr1 60460874 . A ACTA . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_152377;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 61786308 . ATCTTA A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_005595;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 chr1 62087979 . T TGACCTACTGTGCT . PASS VC=INDEL;AC=194;AF=0.63;AN=310 GT 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 62128942 . CTTGCACA C . PASS VC=INDEL;AC=123;AF=0.39;AN=316 GT 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 chr1 62940266 . T TG . PASS VC=INDEL;AC=133;AF=0.43;AN=312;refseq.name=NM_033407;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 chr1 63331690 . TA T . PASS VC=INDEL;AC=234;AF=0.74;AN=316 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 chr1 63331691 . AA A . PASS VC=INDEL;AC=232;AF=0.74;AN=314 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 chr1 63423181 . T TCAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 63907866 . A AATGTTT . PASS VC=INDEL;AC=229;AF=0.76;AN=300;refseq.name=NM_014288;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 chr1 63907868 . T TGTTTAT . PASS VC=INDEL;AC=229;AF=0.77;AN=298;refseq.name=NM_014288;refseq.positionType=intron GT ./. 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. ./. 0/1 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 63985884 . ATCAT A . PASS VC=INDEL;AC=91;AF=0.31;AN=298;refseq.name=NM_014288;refseq.positionType=intron GT ./. 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 1/1 ./. 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/1 chr1 63987096 . ATG A . PASS VC=INDEL;AC=37;AF=0.18;AN=202;refseq.name=NM_014288;refseq.positionType=intron GT ./. 0/0 0/1 ./. ./. ./. 0/0 0/1 ./. ./. ./. 0/0 ./. 0/1 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. ./. ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 chr1 64264921 . TTGTGTCAT T . PASS VC=INDEL;AC=136;AF=0.46;AN=298;refseq.name=NM_005012;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 chr1 64463351 . GT G . PASS VC=INDEL;AC=244;AF=0.77;AN=316;refseq.name=NM_005012;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 chr1 64627261 . A AAA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_005012;refseq.positionType=intron GT 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 65237568 . G GGTTA . PASS VC=INDEL;AC=237;AF=0.75;AN=316;refseq.name=NM_018211;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 chr1 65299673 . T TTAAG . PASS VC=INDEL;AC=10;AF=0.03;AN=314;refseq.name=NM_002227;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 65545194 . A AT . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 65545195 . T TT . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 66063617 . ATGT A . PASS VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_002303;refseq.positionType=intron GT 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 chr1 66198019 . A ACCATCCA . PASS VC=INDEL;AC=76;AF=0.26;AN=296 GT 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 ./. 0/0 ./. ./. 1/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 chr1 66460193 . T TC . PASS VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_001037341;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 66801086 . TGT T . PASS VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_001037341;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 66952677 . A ATC . PASS VC=INDEL;AC=158;AF=0.65;AN=244 GT 0/1 1/1 1/1 0/0 1/1 ./. ./. 0/1 0/0 0/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 ./. 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 0/0 1/1 0/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. ./. 1/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 1/1 ./. ./. 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/1 0/1 ./. ./. 0/1 ./. 0/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 0/1 ./. 0/1 1/1 chr1 67152254 . ATAATTTCACGA A . PASS VC=INDEL;AC=9;AF=0.03;AN=316;refseq.name=NM_032291;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 67206037 . AATTG A . PASS VC=INDEL;AC=50;AF=0.19;AN=268;refseq.name=NM_032291;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/1 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 ./. ./. 0/1 0/1 0/1 ./. 0/0 0/1 0/0 ./. 0/1 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 chr1 67459726 . T TT . PASS VC=INDEL;AC=54;AF=0.18;AN=300 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. chr1 68038796 . ACA A . PASS VC=INDEL;AC=21;AF=0.08;AN=264 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 chr1 68291788 . GC G . PASS VC=INDEL;AC=19;AF=0.06;AN=316;refseq.name=NM_018841;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 68570194 . CCCT C . PASS VC=INDEL;AC=110;AF=0.35;AN=310;refseq.name=NM_001002292;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 69008683 . C CA . PASS VC=INDEL;AC=68;AF=0.3;AN=230 GT 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/0 ./. ./. 0/0 1/1 ./. 1/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 1/1 ./. ./. 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/1 0/0 ./. ./. ./. 1/1 0/1 1/1 0/0 ./. 1/1 0/1 ./. 0/1 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/1 0/0 ./. ./. 1/1 ./. ./. 0/0 0/0 0/1 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 0/0 1/1 ./. ./. ./. 0/0 ./. 1/1 ./. ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. ./. 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 ./. chr1 69398928 . CAAC C . PASS VC=INDEL;AC=66;AF=0.21;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 69424885 . AG A . PASS VC=INDEL;AC=257;AF=0.81;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 69424886 . GG G . PASS VC=INDEL;AC=257;AF=0.81;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 69702172 . T TT . PASS VC=INDEL;AC=186;AF=0.59;AN=316 GT 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 69947085 . T TT . PASS VC=INDEL;AC=199;AF=0.87;AN=230 GT ./. 1/1 1/1 0/1 0/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/0 1/1 0/1 ./. ./. ./. 0/0 ./. 1/1 1/1 1/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/0 ./. ./. 1/1 ./. 1/1 ./. ./. 1/1 0/1 ./. 0/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/0 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. ./. ./. ./. ./. ./. 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 1/1 chr1 70116412 . T TAAT . PASS VC=INDEL;AC=236;AF=0.77;AN=308 GT 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 0/1 chr1 70794740 . AAAAC A . PASS VC=INDEL;AC=49;AF=0.17;AN=288;refseq.name=NM_030816;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/0 0/1 0/1 0/0 0/1 ./. ./. ./. 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 70796576 . TTACTT T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030816;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71101845 . TG T . PASS VC=INDEL;AC=38;AF=0.12;AN=310 GT 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71353307 . AT A . PASS VC=INDEL;AC=88;AF=0.28;AN=310;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 chr1 71366228 . AA A . PASS VC=INDEL;AC=123;AF=0.39;AN=314;refseq.name=NM_000957;refseq.positionType=intron GT 1/1 1/1 0/0 1/1 1/1 0/0 1/1 ./. 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 chr1 71366595 . A AAGTG . PASS VC=INDEL;AC=108;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 71366598 . T TGAGT . PASS VC=INDEL;AC=109;AF=0.34;AN=316;refseq.name=NM_000957;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 71693491 . TGAG T . PASS VC=INDEL;AC=32;AF=0.1;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 71693493 . AGGA A . PASS VC=INDEL;AC=34;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 72053145 . AG A . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_173808;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr1 72321086 . AA A . PASS VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_173808;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 chr1 73854019 . T TTTTA . PASS VC=INDEL;AC=181;AF=0.59;AN=308 GT 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 chr1 74227801 . AG A . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 74404505 . TTT T . PASS VC=INDEL;AC=23;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 74892891 . AG A . PASS VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_001112808;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 74896404 . ACTCAA A . PASS VC=INDEL;AC=26;AF=0.08;AN=316;refseq.name=NM_001112808;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 75049490 . C CT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001002912;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 75156563 . GCTT G . PASS VC=INDEL;AC=259;AF=0.82;AN=316 GT 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 75661521 . TTCTT T . PASS VC=INDEL;AC=7;AF=0.02;AN=312 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 76005746 . A AC . PASS VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_152697;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 chr1 76054645 . AT A . PASS VC=INDEL;AC=14;AF=0.05;AN=290;refseq.name=NM_152697;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 76110056 . ATCAT A . PASS VC=INDEL;AC=202;AF=0.7;AN=290 GT 0/0 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 ./. 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 1/1 ./. 1/1 1/1 0/0 0/1 0/0 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 ./. 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 1/1 chr1 76110059 . ATTCA A . PASS VC=INDEL;AC=198;AF=0.68;AN=290 GT ./. 1/1 1/1 0/1 1/1 0/1 0/0 1/1 ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/0 0/0 ./. 0/1 0/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 1/1 chr1 76603385 . A AA . PASS VC=INDEL;AC=45;AF=0.14;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 76647177 . T TA . PASS VC=INDEL;AC=44;AF=0.15;AN=292;refseq.name=NM_152996;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 76772246 . TAG T . PASS VC=INDEL;AC=71;AF=0.22;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 chr1 77019040 . G GA . PASS VC=INDEL;AC=123;AF=0.39;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 chr1 77019568 . TTCTG T . PASS VC=INDEL;AC=72;AF=0.23;AN=316;refseq.name=NM_152996;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr1 77147457 . T TG . PASS VC=INDEL;AC=307;AF=0.97;AN=316 GT 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 77154589 . T TA . PASS VC=INDEL;AC=300;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 77350958 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 77412672 . T TCAAA . PASS VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 77412677 . C CAAAC . PASS VC=INDEL;AC=183;AF=0.58;AN=316;refseq.name=NM_030965;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 77761353 . ATTCT A . PASS VC=INDEL;AC=87;AF=0.28;AN=310;refseq.name=NM_174858;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 chr1 78436001 . T TCT . PASS VC=INDEL;AC=139;AF=0.45;AN=308;refseq.name=NM_003902;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/0 0/0 0/0 chr1 78477804 . T TAAGAC . PASS VC=INDEL;AC=294;AF=0.93;AN=316;refseq.name=NM_007034;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 78533885 . CAG C . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 chr1 78533886 . AGA A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_017655;refseq.positionType=intron GT 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 chr1 78752617 . TC T . PASS VC=INDEL;AC=160;AF=0.51;AN=314 GT 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 79595269 . T TC . PASS VC=INDEL;AC=37;AF=0.12;AN=312 GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 79694557 . CTTGT C . PASS VC=INDEL;AC=173;AF=0.68;AN=254 GT 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 ./. ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 ./. ./. ./. ./. 0/0 0/1 0/1 ./. 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 1/1 0/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. 1/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 ./. ./. 1/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 chr1 80133716 . CA C . PASS VC=INDEL;AC=74;AF=0.27;AN=276 GT 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 1/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 ./. 0/1 0/0 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 ./. 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/0 0/0 chr1 80193527 . CA C . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 80279810 . T TT . PASS VC=INDEL;AC=69;AF=0.22;AN=314 GT 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 chr1 80415715 . C CATGTCTATTAT . PASS VC=INDEL;AC=197;AF=0.62;AN=316 GT 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 80415717 . T TGTCTATTATAT . PASS VC=INDEL;AC=197;AF=0.62;AN=316 GT 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 80606020 . GTAGGC G . PASS VC=INDEL;AC=282;AF=0.89;AN=316 GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 chr1 80684057 . A AA . PASS VC=INDEL;AC=217;AF=0.69;AN=316 GT 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 chr1 80857688 . AAATA A . PASS VC=INDEL;AC=97;AF=0.31;AN=316 GT 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 chr1 81007659 . A AC . PASS VC=INDEL;AC=185;AF=0.59;AN=312 GT 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/0 chr1 81007660 . C CC . PASS VC=INDEL;AC=185;AF=0.59;AN=314 GT 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/0 chr1 81912884 . C CT . PASS VC=INDEL;AC=15;AF=0.05;AN=298 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 chr1 82042397 . TCTT T . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 82264610 . TG T . PASS VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_012302;refseq.positionType=promoter GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 chr1 82264994 . G GGTAG . PASS VC=INDEL;AC=49;AF=0.16;AN=316;refseq.name=NM_012302;refseq.positionType=promoter GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 chr1 82280496 . ATGT A . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 82315714 . G GAGTG . PASS VC=INDEL;AC=38;AF=0.12;AN=306;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 82316526 . TT T . PASS VC=INDEL;AC=209;AF=0.67;AN=312;refseq.name=NM_012302;refseq.positionType=intron GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 chr1 82329993 . CATAT C . PASS VC=INDEL;AC=305;AF=0.97;AN=316;refseq.name=NM_012302;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 82710650 . AA A . PASS VC=INDEL;AC=297;AF=0.96;AN=310 GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 83144930 . TC T . PASS VC=INDEL;AC=153;AF=0.55;AN=278 GT 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/1 1/1 0/0 0/1 0/1 0/1 0/1 ./. 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 ./. 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/0 ./. 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 1/1 ./. 0/0 0/0 ./. 0/1 0/0 ./. 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 ./. 0/0 1/1 ./. ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 chr1 83208212 . C CAGAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 83208213 . A AGATA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 83581070 . C CCAGA . PASS VC=INDEL;AC=188;AF=0.74;AN=254 GT ./. ./. 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 ./. ./. ./. 1/1 1/1 ./. 0/0 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 0/0 1/1 0/1 0/1 ./. ./. 0/1 1/1 ./. 1/1 0/1 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. ./. ./. 0/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 ./. 1/1 0/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 chr1 84127066 . TCT T . PASS VC=INDEL;AC=71;AF=0.22;AN=316 GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr1 84822658 . TCAATTAAAACTCACAG T . PASS VC=INDEL;AC=45;AF=0.16;AN=286 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/1 1/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr1 85570521 . GTTC G . PASS VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_145172;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 chr1 86565855 . T TCT . PASS VC=INDEL;AC=20;AF=0.06;AN=316;refseq.name=NM_152890;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 86714492 . T TA . PASS VC=INDEL;AC=263;AF=0.88;AN=300 GT 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 chr1 86786541 . CAG C . PASS VC=INDEL;AC=7;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 86839425 . TACTT T . PASS VC=INDEL;AC=15;AF=0.05;AN=280;refseq.name=NM_001007022;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 chr1 87558067 . CACATAC C . PASS VC=INDEL;AC=285;AF=0.97;AN=294;refseq.name=NM_012262;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 chr1 88184554 . T TCA . PASS VC=INDEL;AC=40;AF=0.14;AN=276 GT 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/1 chr1 88351056 . A AGT . PASS VC=INDEL;AC=222;AF=0.7;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 chr1 88391828 . C CCTT . PASS VC=INDEL;AC=216;AF=0.7;AN=310 GT 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 88391834 . T TCTT . PASS VC=INDEL;AC=219;AF=0.69;AN=316 GT 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 chr1 88423056 . T TA . PASS VC=INDEL;AC=210;AF=0.8;AN=262 GT 1/1 0/0 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 ./. 1/1 ./. 0/0 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 88878932 . TGAAG T . PASS VC=INDEL;AC=222;AF=0.71;AN=314 GT 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 88934449 . T TA . PASS VC=INDEL;AC=215;AF=0.71;AN=304 GT 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 ./. 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 chr1 89147233 . C CTG . PASS VC=INDEL;AC=270;AF=0.94;AN=288;refseq.name=NM_006256;refseq.positionType=promoter GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. ./. 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 89147234 . T TGT . PASS VC=INDEL;AC=193;AF=0.91;AN=212;refseq.name=NM_006256;refseq.positionType=promoter GT ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 ./. 1/1 ./. ./. ./. ./. ./. 1/1 1/1 ./. 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. ./. ./. 1/1 1/1 ./. 0/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. ./. ./. ./. 1/1 ./. 1/1 ./. ./. ./. 0/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. ./. 1/1 chr1 90055475 . TT T . PASS VC=INDEL;AC=35;AF=0.11;AN=316;refseq.name=NM_015350;refseq.positionType=intron GT 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 90055577 . TATG T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_015350;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 90305331 . G GA . PASS VC=INDEL;AC=301;AF=0.95;AN=316;refseq.name=NM_018103;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 91238816 . G GT . PASS VC=INDEL;AC=86;AF=0.29;AN=296 GT 0/0 0/0 ./. 1/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 ./. 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 ./. 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 ./. 0/1 chr1 91308113 . GC G . PASS VC=INDEL;AC=8;AF=0.03;AN=282 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 chr1 91354296 . TT T . PASS VC=INDEL;AC=252;AF=0.83;AN=304 GT 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 chr1 91544957 . ACT A . PASS VC=INDEL;AC=99;AF=0.32;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 chr1 91566585 . GTTA G . PASS VC=INDEL;AC=139;AF=0.45;AN=312 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 chr1 92219769 . C CTCCTCAA . PASS VC=INDEL;AC=54;AF=0.17;AN=314;refseq.name=NM_003243;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 93167519 . C CTG . PASS VC=INDEL;AC=276;AF=1;AN=276;refseq.name=NM_005665;refseq.positionType=intron GT 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 93628710 . TACTC T . PASS VC=INDEL;AC=94;AF=0.31;AN=304;refseq.name=NM_016040;refseq.positionType=intron GT 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 chr1 93704043 . T TCTAGAAAAATC . PASS VC=INDEL;AC=7;AF=0.02;AN=306;refseq.name=NM_206886;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 94443843 . G GAGAG . PASS VC=INDEL;AC=88;AF=0.3;AN=292 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 ./. 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 ./. 0/0 chr1 94634727 . TGAGT T . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004815;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 95103314 . AGCATCCTAAA A . PASS VC=INDEL;AC=6;AF=0.03;AN=240 GT ./. ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 chr1 95167241 . TTAAC T . PASS VC=INDEL;AC=115;AF=0.36;AN=316 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 chr1 95167244 . ACTAA A . PASS VC=INDEL;AC=116;AF=0.37;AN=316 GT 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 chr1 95266356 . A AAAATAAGAATCCA . PASS VC=INDEL;AC=212;AF=0.83;AN=256 GT 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. ./. ./. 0/0 1/1 0/0 0/1 ./. 0/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/0 0/1 1/1 1/1 ./. 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 ./. 0/1 1/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. ./. ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 ./. ./. ./. chr1 95349846 . G GG . PASS VC=INDEL;AC=195;AF=0.65;AN=302;refseq.name=NM_001114106;refseq.positionType=intron GT 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 ./. 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 chr1 95638470 . GTAG G . PASS VC=INDEL;AC=9;AF=0.03;AN=306;refseq.name=NM_152487;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 96578762 . CAG C . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 1/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 chr1 97069290 . G GT . PASS VC=INDEL;AC=57;AF=0.18;AN=316 GT 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 97352585 . A AGA . PASS VC=INDEL;AC=167;AF=0.53;AN=316 GT 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 chr1 97471673 . T TTA . PASS VC=INDEL;AC=39;AF=0.16;AN=238 GT 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 1/1 ./. 0/1 ./. 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/0 0/1 ./. 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 chr1 97654513 . GTTAT G . PASS VC=INDEL;AC=17;AF=0.06;AN=302;refseq.name=NM_000110;refseq.positionType=intron GT ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 97728316 . AATA A . PASS VC=INDEL;AC=15;AF=0.05;AN=316;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 chr1 97862494 . TCCT T . PASS VC=INDEL;AC=47;AF=0.18;AN=256;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/1 ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 1/1 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/1 ./. ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. chr1 97940369 . TAACT T . PASS VC=INDEL;AC=37;AF=0.12;AN=306;refseq.name=NM_000110;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 ./. ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 98400957 . C CGATAT . PASS VC=INDEL;AC=290;AF=0.92;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 99032443 . T TTC . PASS VC=INDEL;AC=230;AF=0.79;AN=292 GT 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 ./. ./. ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 chr1 99032444 . T TCT . PASS VC=INDEL;AC=236;AF=0.8;AN=296 GT 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 ./. 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 1/1 0/0 1/1 chr1 99662955 . A AAGA . PASS VC=INDEL;AC=146;AF=0.46;AN=316 GT 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 99714941 . GTTACAG G . PASS VC=INDEL;AC=6;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 99848725 . AT A . PASS VC=INDEL;AC=50;AF=0.16;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100194878 . C CCT . PASS VC=INDEL;AC=248;AF=0.78;AN=316;refseq.name=NM_001013660;refseq.positionType=intron GT 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 100194903 . C CT . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_001013660;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100567908 . C CT . PASS VC=INDEL;AC=43;AF=0.14;AN=300;refseq.name=NM_194292;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 chr1 100793875 . CACTC C . PASS VC=INDEL;AC=105;AF=0.38;AN=274 GT 0/0 0/1 0/1 ./. 0/1 1/1 0/0 ./. 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 0/0 0/0 ./. 0/0 0/1 ./. 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 1/1 0/1 ./. ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 chr1 100808351 . TT T . PASS VC=INDEL;AC=27;AF=0.09;AN=294 GT ./. 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 100856872 . T TT . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_003672;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 chr1 101093845 . TTCTGTAGTCAC T . PASS VC=INDEL;AC=24;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 101295925 . CTA C . PASS VC=INDEL;AC=82;AF=0.26;AN=314 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 101442572 . T TT . PASS VC=INDEL;AC=99;AF=0.31;AN=316;refseq.name=NM_133496;refseq.positionType=exon GT 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr1 101482924 . CTGTG C . PASS VC=INDEL;AC=32;AF=0.1;AN=316;refseq.name=NM_001077394;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 101859015 . G GA . PASS VC=INDEL;AC=107;AF=0.34;AN=316 GT 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 chr1 102315705 . A ATCTC . PASS VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 chr1 102315708 . T TCTCT . PASS VC=INDEL;AC=185;AF=0.59;AN=316;refseq.name=NM_058170;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 chr1 103391817 . TTA T . PASS VC=INDEL;AC=0;AF=0;AN=244;refseq.name=NM_001854;refseq.positionType=intron GT 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 chr1 103722297 . TGT T . PASS VC=INDEL;AC=32;AF=0.1;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 104533187 . A AGTT . PASS VC=INDEL;AC=148;AF=0.47;AN=316 GT 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 chr1 104896267 . GAG G . PASS VC=INDEL;AC=48;AF=0.15;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 104896390 . ATATT A . PASS VC=INDEL;AC=38;AF=0.14;AN=268 GT 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 1/1 0/0 ./. 0/1 1/1 ./. 1/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/0 chr1 105259435 . CACTAAACGTGCC C . PASS VC=INDEL;AC=6;AF=0.02;AN=250 GT ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. 0/0 chr1 105451424 . A ATCTAGT . PASS VC=INDEL;AC=98;AF=0.31;AN=316 GT 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 chr1 105504523 . C CTTT . PASS VC=INDEL;AC=82;AF=0.29;AN=282 GT ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/1 ./. 1/1 0/0 0/1 0/0 ./. 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 1/1 chr1 105837170 . T TAA . PASS VC=INDEL;AC=67;AF=0.24;AN=280 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 ./. 0/0 0/1 1/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/0 chr1 105868766 . ATACTT A . PASS VC=INDEL;AC=92;AF=0.34;AN=274 GT ./. 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/0 ./. 1/1 ./. 1/1 0/1 1/1 0/0 ./. ./. ./. 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 1/1 0/1 0/1 0/0 ./. 1/1 0/1 ./. 0/1 ./. 1/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 chr1 106762526 . AACT A . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 106908645 . AC A . PASS VC=INDEL;AC=25;AF=0.08;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 107217236 . A AGGATCA . PASS VC=INDEL;AC=240;AF=0.79;AN=302 GT 1/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 ./. 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 ./. 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 107979567 . TT T . PASS VC=INDEL;AC=150;AF=0.55;AN=274;refseq.name=NM_001113226;refseq.positionType=intron GT 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 ./. ./. 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 0/0 1/1 ./. ./. 0/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 1/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 ./. 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 ./. 0/0 1/1 0/1 ./. 0/1 1/1 0/0 1/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 chr1 108737087 . GG G . PASS VC=INDEL;AC=99;AF=0.32;AN=308;refseq.name=NM_013386;refseq.positionType=intron GT 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 chr1 109186604 . A ATA . PASS VC=INDEL;AC=3;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 109295950 . TA T . PASS VC=INDEL;AC=54;AF=0.17;AN=312;refseq.name=NM_007269;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 109295955 . TTA T . PASS VC=INDEL;AC=57;AF=0.18;AN=310;refseq.name=NM_007269;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 109303951 . GTATAG G . PASS VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_007269;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 chr1 109429108 . G GGAGAAAT . PASS VC=INDEL;AC=33;AF=0.14;AN=234;refseq.name=NM_013296;refseq.positionType=intron GT 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 ./. 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/1 0/1 ./. ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 109565068 . C CTC . PASS VC=INDEL;AC=304;AF=0.96;AN=316;refseq.name=NM_014969;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr1 110418161 . CTTAG C . PASS VC=INDEL;AC=56;AF=0.18;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 110911466 . AT A . PASS VC=INDEL;AC=67;AF=0.22;AN=310;refseq.name=NM_004696;refseq.positionType=intron GT 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 chr1 111820993 . TTAAG T . PASS VC=INDEL;AC=46;AF=0.2;AN=232 GT 0/1 ./. 1/1 ./. 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/1 1/1 ./. 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/1 ./. ./. ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. ./. 0/1 ./. ./. 0/0 0/1 ./. 0/0 ./. 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 ./. ./. ./. chr1 111894729 . C CATG . PASS VC=INDEL;AC=32;AF=0.11;AN=302;refseq.name=NM_181643;refseq.positionType=exon GT 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 chr1 112384059 . G GG . PASS VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_004980;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 chr1 112440856 . A ACTTA . PASS VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_004980;refseq.positionType=intron GT 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 chr1 112896532 . CTAAC C . PASS VC=INDEL;AC=1;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 112896636 . CA C . PASS VC=INDEL;AC=199;AF=0.64;AN=312 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 chr1 112896637 . AA A . PASS VC=INDEL;AC=199;AF=0.63;AN=316 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 chr1 113322895 . TTCTA T . PASS VC=INDEL;AC=73;AF=0.3;AN=246 GT 0/0 ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/0 0/0 0/0 ./. ./. ./. 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. ./. ./. 0/0 0/1 1/1 0/0 0/1 ./. ./. 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. ./. ./. 0/0 0/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 1/1 0/0 0/1 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/0 chr1 113467083 . CC C . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003051;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 113635187 . C CTTTG . PASS VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 113635190 . T TGTTT . PASS VC=INDEL;AC=261;AF=0.83;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 113640553 . GA G . PASS VC=INDEL;AC=111;AF=0.35;AN=314;refseq.name=NM_014813;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 chr1 113640556 . AA A . PASS VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_014813;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 chr1 113689905 . GAG G . PASS VC=INDEL;AC=41;AF=0.13;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 114240320 . A AA . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_006608;refseq.positionType=exon GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 114339956 . C CTAAA . PASS VC=INDEL;AC=210;AF=0.78;AN=270;refseq.name=NM_018364;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 0/0 0/1 1/1 0/0 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 ./. 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 ./. ./. ./. 0/0 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 114565357 . CGGAGG C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 116298599 . A ACTT . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_001232;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr1 116435014 . ATAACCGA A . PASS VC=INDEL;AC=66;AF=0.26;AN=250 GT 1/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 ./. 1/1 ./. 0/0 0/1 0/1 0/0 0/0 0/1 ./. 1/1 1/1 0/1 0/1 ./. 0/0 1/1 ./. 0/0 1/1 0/1 1/1 ./. 1/1 0/0 ./. 1/1 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/1 chr1 116551982 . T TTAAAGC . PASS VC=INDEL;AC=31;AF=0.1;AN=304;refseq.name=NM_018420;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 116662025 . T TGA . PASS VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron GT 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 116662028 . G GAG . PASS VC=INDEL;AC=55;AF=0.17;AN=316;refseq.name=NM_152367;refseq.positionType=intron GT 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 117459931 . AAC A . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 117459932 . ACA A . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_020440;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 117592136 . TTG T . PASS VC=INDEL;AC=24;AF=0.08;AN=300 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 117722836 . C CA . PASS VC=INDEL;AC=36;AF=0.11;AN=316;refseq.name=NM_024626;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr1 120034138 . TCTAT T . PASS VC=INDEL;AC=99;AF=0.35;AN=284 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 ./. 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/0 ./. 0/1 0/0 0/0 0/1 ./. 1/1 1/1 0/0 0/0 chr1 120185496 . G GGATT . PASS VC=INDEL;AC=264;AF=0.84;AN=314;refseq.name=NM_001080470;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 120280730 . TAA T . PASS VC=INDEL;AC=73;AF=0.23;AN=314;refseq.name=NM_006623;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 chr1 144995277 . AG A . PASS VC=INDEL;AC=41;AF=0.16;AN=258;refseq.name=NM_014644;refseq.positionType=promoter GT 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/1 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/1 ./. 0/1 0/1 0/0 0/0 ./. ./. ./. 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 145060382 . A AG . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022359;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 146556039 . CCAAC C . PASS VC=INDEL;AC=64;AF=0.21;AN=310 GT 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr1 146768690 . TC T . PASS VC=INDEL;AC=289;AF=0.91;AN=316 GT 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 chr1 146979526 . CCT C . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 chr1 147047674 . AA A . PASS VC=INDEL;AC=101;AF=0.32;AN=314;refseq.name=NM_004326;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 chr1 147108091 . A AC . PASS VC=INDEL;AC=227;AF=0.72;AN=314 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 ./. 1/1 chr1 147392223 . CATGGCTC C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 147393527 . A AAGAA . PASS VC=INDEL;AC=10;AF=0.05;AN=218 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr1 147823728 . A AC . PASS VC=INDEL;AC=2;AF=0.01;AN=266 GT 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 chr1 151094921 . T TA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 151094936 . CCTTA C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 151743871 . AA A . PASS VC=INDEL;AC=98;AF=0.32;AN=308;refseq.name=NM_016178;refseq.positionType=terminator GT 1/1 0/1 ./. 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 ./. 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 chr1 152348228 . TTAT T . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 152442163 . AAACA A . PASS VC=INDEL;AC=212;AF=0.68;AN=310 GT 0/1 ./. 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 152572426 . G GT . PASS VC=INDEL;AC=70;AF=0.25;AN=280;refseq.name=NM_178434;refseq.positionType=promoter GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 1/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/1 ./. 0/1 ./. 0/0 ./. ./. 0/1 0/1 ./. 1/1 ./. 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 1/1 ./. 1/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/0 chr1 152797773 . C CC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_178348;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 153703019 . TGTGTCTCTGCTT T . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_023015;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 154741714 . TAT T . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_002249;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 155303581 . AT A . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 155559888 . C CTTAT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 156565049 . A AAC . PASS VC=INDEL;AC=314;AF=0.99;AN=316;refseq.name=NM_015590;refseq.positionType=exon GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 156572952 . T TGAA . PASS VC=INDEL;AC=39;AF=0.12;AN=312;refseq.name=NM_015590;refseq.positionType=promoter GT 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 156859572 . C CCT . PASS VC=INDEL;AC=219;AF=0.73;AN=300 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 chr1 156910892 . GCTCGTCTT G . PASS VC=INDEL;AC=39;AF=0.14;AN=270;refseq.name=NM_014784;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 chr1 157531425 . CA C . PASS VC=INDEL;AC=16;AF=0.06;AN=260 GT 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 ./. ./. 0/1 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 chr1 157807166 . TGTTA T . PASS VC=INDEL;AC=250;AF=0.81;AN=310;refseq.name=NM_005894;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 157818429 . AC A . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 157924621 . ATAAG A . PASS VC=INDEL;AC=24;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 157932325 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 158154060 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001766;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 158684734 . CA C . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 chr1 158886780 . A AAGAT . PASS VC=INDEL;AC=241;AF=0.76;AN=316 GT 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 158886783 . A ATAGA . PASS VC=INDEL;AC=240;AF=0.76;AN=314 GT 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 158984187 . G GAGGC . PASS VC=INDEL;AC=26;AF=0.13;AN=198;refseq.name=NM_005531;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 1/1 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 1/1 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 1/1 ./. ./. 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 ./. ./. ./. 1/1 1/1 1/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 1/1 1/1 ./. 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. 1/1 1/1 chr1 158984259 . AATT A . PASS VC=INDEL;AC=130;AF=0.49;AN=266;refseq.name=NM_005531;refseq.positionType=intron GT ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 ./. 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 ./. 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/1 ./. 1/1 0/0 0/1 0/1 1/1 0/1 ./. ./. 0/0 0/0 ./. 0/1 1/1 0/1 0/1 1/1 ./. ./. 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/1 ./. 0/1 0/1 ./. ./. ./. ./. ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr1 159500234 . CT C . PASS VC=INDEL;AC=19;AF=0.06;AN=316 GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 159741079 . TGT T . PASS VC=INDEL;AC=163;AF=0.52;AN=314 GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 chr1 160004099 . GATGTAGATAG G . PASS VC=INDEL;AC=3;AF=0.01;AN=314;refseq.name=NM_145167;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 160081222 . TGAAAAG T . PASS VC=INDEL;AC=5;AF=0.02;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 160430789 . C CAG . PASS VC=INDEL;AC=51;AF=0.16;AN=314 GT 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 160464965 . AGTGAATTTTAGA A . PASS VC=INDEL;AC=12;AF=0.06;AN=214;refseq.name=NM_052931;refseq.positionType=intron GT ./. 0/0 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/0 0/0 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/1 ./. 0/1 chr1 160578541 . C CA . PASS VC=INDEL;AC=277;AF=0.88;AN=316 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 161765879 . T TCTT . PASS VC=INDEL;AC=77;AF=0.25;AN=310;refseq.name=NM_007348;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 161826110 . TT T . PASS VC=INDEL;AC=0;AF=0;AN=308;refseq.name=NM_007348;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 162354200 . AACAC A . PASS VC=INDEL;AC=32;AF=0.12;AN=262;refseq.name=NM_001085375;refseq.positionType=exon GT 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/0 ./. 0/1 ./. 0/0 ./. ./. 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 1/1 chr1 162629796 . C CGTT . PASS VC=INDEL;AC=238;AF=0.75;AN=316;refseq.name=NM_001014796;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 163132415 . TCCTGAACA T . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_003617;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 163135904 . C CAGA . PASS VC=INDEL;AC=217;AF=0.84;AN=258;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 0/1 0/0 ./. 0/1 0/0 ./. 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 ./. 1/1 0/1 ./. 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 ./. 0/1 ./. 0/1 ./. 1/1 1/1 1/1 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 ./. 1/1 chr1 163136054 . T TTC . PASS VC=INDEL;AC=266;AF=0.84;AN=316;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 163136055 . T TCT . PASS VC=INDEL;AC=265;AF=0.84;AN=314;refseq.name=NM_003617;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 164351168 . ATTG A . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 164448310 . AAAC A . PASS VC=INDEL;AC=236;AF=0.75;AN=316 GT 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 164548574 . TT T . PASS VC=INDEL;AC=11;AF=0.04;AN=308;refseq.name=NM_002585;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr1 164790567 . C CT . PASS VC=INDEL;AC=164;AF=0.52;AN=314;refseq.name=NM_002585;refseq.positionType=intron GT 1/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 chr1 165207456 . TAGA T . PASS VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_177398;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 165218477 . AGAGATTACTCTG A . PASS VC=INDEL;AC=79;AF=0.28;AN=280;refseq.name=NM_177398;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 ./. 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/0 0/0 1/1 ./. 1/1 1/1 0/0 0/1 ./. ./. 1/1 0/0 1/1 0/1 0/1 ./. 0/1 1/1 1/1 ./. 0/1 0/1 1/1 ./. 0/0 0/1 ./. 0/1 1/1 0/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 chr1 165261980 . TA T . PASS VC=INDEL;AC=129;AF=0.42;AN=308;refseq.name=NM_177398;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 ./. 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 165286489 . AA A . PASS VC=INDEL;AC=23;AF=0.07;AN=314;refseq.name=NM_177398;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 165349359 . G GT . PASS VC=INDEL;AC=130;AF=0.42;AN=306 GT 0/1 ./. 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 chr1 165475542 . CT C . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 chr1 165627134 . AT A . PASS VC=INDEL;AC=144;AF=0.46;AN=314 GT 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 chr1 165652540 . GTTAA G . PASS VC=INDEL;AC=202;AF=0.66;AN=304;refseq.name=NM_000696;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 ./. 1/1 chr1 165685796 . GGCACAGAT G . PASS VC=INDEL;AC=155;AF=0.49;AN=314 GT 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 chr1 165686450 . TAGG T . PASS VC=INDEL;AC=144;AF=0.46;AN=316 GT 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 165686452 . GGAG G . PASS VC=INDEL;AC=145;AF=0.46;AN=316 GT 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 chr1 166083223 . CCAC C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_001017961;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 166602705 . TTGT T . PASS VC=INDEL;AC=73;AF=0.23;AN=316 GT 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 chr1 166639248 . A AAT . PASS VC=INDEL;AC=289;AF=0.91;AN=316 GT 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 166708316 . G GTAG . PASS VC=INDEL;AC=102;AF=0.32;AN=316 GT 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 chr1 167512714 . TTCCAAAACCGA T . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167513042 . CA C . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167516739 . T TAA . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003851;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 167675717 . T TTC . PASS VC=INDEL;AC=22;AF=0.07;AN=296;refseq.name=NM_052862;refseq.positionType=terminator GT 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 167682039 . CCAAA C . PASS VC=INDEL;AC=68;AF=0.22;AN=316 GT 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 167682041 . AAACA A . PASS VC=INDEL;AC=68;AF=0.22;AN=316 GT 0/0 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 chr1 167697899 . GTG G . PASS VC=INDEL;AC=50;AF=0.16;AN=316;refseq.name=NM_003953;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 167985326 . TG T . PASS VC=INDEL;AC=144;AF=0.49;AN=294;refseq.name=NM_001017977;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 ./. ./. 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 ./. 1/1 ./. 0/1 1/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 0/1 chr1 168053859 . ACTCA A . PASS VC=INDEL;AC=11;AF=0.03;AN=316;refseq.name=NM_153832;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 168133510 . CCTAAC C . PASS VC=INDEL;AC=96;AF=0.3;AN=316 GT 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 chr1 168200152 . GT G . PASS VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_199344;refseq.positionType=intron GT 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 chr1 168423776 . AGC A . PASS VC=INDEL;AC=4;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 169066627 . T TC . PASS VC=INDEL;AC=301;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 169066629 . C CC . PASS VC=INDEL;AC=301;AF=0.95;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 169095586 . T TAT . PASS VC=INDEL;AC=165;AF=0.52;AN=316;refseq.name=NM_001001787;refseq.positionType=intron GT 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 chr1 169214437 . CA C . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_013330;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 169875635 . AG A . PASS VC=INDEL;AC=2;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 170054566 . CAAAT C . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 170213713 . C CA . PASS VC=INDEL;AC=302;AF=0.96;AN=314 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 170231599 . C CA . PASS VC=INDEL;AC=178;AF=0.57;AN=314 GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 chr1 170412385 . A AA . PASS VC=INDEL;AC=247;AF=0.79;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/0 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 171564547 . T TT . PASS VC=INDEL;AC=141;AF=0.68;AN=206 GT 1/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 ./. 0/1 ./. ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. ./. ./. 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. 1/1 0/1 ./. 0/1 1/1 ./. 1/1 ./. ./. 0/1 ./. 0/1 ./. ./. ./. ./. 0/1 ./. 1/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 0/0 ./. ./. ./. ./. ./. 0/1 0/1 1/1 0/1 ./. 0/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 0/0 0/1 ./. 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. ./. ./. ./. 1/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 0/1 ./. ./. 0/1 ./. 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 0/1 chr1 171668398 . C CATC . PASS VC=INDEL;AC=42;AF=0.13;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 171779854 . AAAG A . PASS VC=INDEL;AC=128;AF=0.46;AN=278 GT 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 ./. 0/1 0/1 ./. ./. ./. 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 ./. 1/1 ./. 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/1 chr1 171799766 . A ACT . PASS VC=INDEL;AC=48;AF=0.18;AN=268 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/0 0/0 chr1 171806532 . C CAT . PASS VC=INDEL;AC=14;AF=0.05;AN=308 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 172312482 . AAG A . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_015569;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 172415351 . GA G . PASS VC=INDEL;AC=75;AF=0.24;AN=316;refseq.name=NM_139240;refseq.positionType=intron GT 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr1 172620138 . A ACT . PASS VC=INDEL;AC=134;AF=0.42;AN=316 GT 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 172620139 . C CTC . PASS VC=INDEL;AC=134;AF=0.43;AN=314 GT 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 173063473 . A ATGTC . PASS VC=INDEL;AC=124;AF=0.62;AN=200 GT 0/0 0/1 0/1 ./. 0/1 ./. ./. 1/1 0/1 0/0 0/1 ./. 0/1 1/1 ./. ./. 0/0 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 ./. 1/1 0/0 1/1 1/1 ./. ./. ./. ./. ./. ./. 1/1 ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 ./. 0/1 ./. 0/1 1/1 ./. 1/1 0/1 ./. 0/1 0/1 ./. ./. 0/1 0/1 ./. ./. 0/1 ./. 0/1 ./. ./. 0/1 ./. 1/1 0/1 ./. 1/1 ./. ./. 0/1 ./. 1/1 1/1 ./. 1/1 0/1 ./. ./. 0/0 ./. 0/1 1/1 1/1 ./. 1/1 1/1 0/0 ./. ./. 0/1 0/0 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. ./. 0/1 0/1 0/1 0/0 ./. ./. 0/0 1/1 1/1 1/1 0/0 0/0 ./. 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 ./. ./. 1/1 0/0 ./. 0/1 ./. ./. 1/1 0/0 ./. ./. ./. 1/1 0/1 ./. 0/1 1/1 ./. chr1 173541560 . CAA C . PASS VC=INDEL;AC=233;AF=0.74;AN=316;refseq.name=NM_178527;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 chr1 173749093 . T TC . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_014458;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 173755936 . T TGAAG . PASS VC=INDEL;AC=182;AF=0.58;AN=316;refseq.name=NM_014458;refseq.positionType=terminator GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 173870326 . ACTA A . PASS VC=INDEL;AC=235;AF=0.74;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 174411392 . T TTGTAT . PASS VC=INDEL;AC=251;AF=0.8;AN=314;refseq.name=NM_014857;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 174524160 . T TAT . PASS VC=INDEL;AC=212;AF=0.67;AN=316;refseq.name=NM_014857;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 175131961 . GA G . PASS VC=INDEL;AC=85;AF=0.28;AN=306 GT 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 1/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 1/1 ./. 0/1 0/0 0/1 chr1 175299777 . CAT C . PASS VC=INDEL;AC=18;AF=0.06;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 chr1 175355790 . GG G . PASS VC=INDEL;AC=199;AF=0.74;AN=270;refseq.name=NM_003285;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 ./. 1/1 ./. ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. ./. 0/0 0/1 ./. 0/1 chr1 175418807 . A AACA . PASS VC=INDEL;AC=118;AF=0.37;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 chr1 175420618 . A AG . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175443036 . AGGAGA A . PASS VC=INDEL;AC=1;AF=0;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175472120 . C CTAATCAGGATCTTGACATGTGACACAAGATCCTTGAG . PASS VC=INDEL;AC=14;AF=0.04;AN=316;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 175584762 . CT C . PASS VC=INDEL;AC=45;AF=0.14;AN=314;refseq.name=NM_003285;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 chr1 177236388 . C CG . PASS VC=INDEL;AC=167;AF=0.54;AN=312;refseq.name=NM_021165;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 ./. 0/1 ./. 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 chr1 177236389 . G GG . PASS VC=INDEL;AC=166;AF=0.53;AN=316;refseq.name=NM_021165;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 chr1 177558539 . G GAGA . PASS VC=INDEL;AC=7;AF=0.02;AN=290 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 177558541 . G GAAG . PASS VC=INDEL;AC=10;AF=0.03;AN=296 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 178521563 . TAAGAC T . PASS VC=INDEL;AC=21;AF=0.09;AN=246 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 1/1 1/1 ./. ./. 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 ./. ./. ./. 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/0 1/1 0/1 0/0 0/0 chr1 179038241 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_014864;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 179293907 . CAA C . PASS VC=INDEL;AC=34;AF=0.11;AN=314;refseq.name=NM_003101;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 chr1 179724329 . G GG . PASS VC=INDEL;AC=307;AF=0.97;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 179762445 . GT G . PASS VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 179762446 . TT T . PASS VC=INDEL;AC=85;AF=0.27;AN=316;refseq.name=NM_173509;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 179773170 . CTTGTC C . PASS VC=INDEL;AC=77;AF=0.28;AN=274;refseq.name=NM_173509;refseq.positionType=intron GT 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 ./. 0/0 0/0 0/0 ./. 0/0 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 1/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. 1/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 0/1 ./. 0/1 1/1 1/1 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 1/1 0/1 chr1 180108217 . T TTATC . PASS VC=INDEL;AC=229;AF=0.72;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr1 180722815 . TACTC T . PASS VC=INDEL;AC=4;AF=0.01;AN=316;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 180722816 . ACTCA A . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 180762626 . CAT C . PASS VC=INDEL;AC=12;AF=0.04;AN=296;refseq.name=NM_004736;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 180866670 . CCC C . PASS VC=INDEL;AC=73;AF=0.29;AN=256 GT 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 ./. 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 ./. 0/1 ./. 0/1 ./. ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/1 0/1 0/1 0/1 chr1 180974402 . A AA . PASS VC=INDEL;AC=0;AF=0;AN=298;refseq.name=NM_005819;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 chr1 181233905 . AA A . PASS VC=INDEL;AC=1;AF=0;AN=266 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 181456872 . CC C . PASS VC=INDEL;AC=2;AF=0.01;AN=300;refseq.name=NM_000721;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 181610646 . CT C . PASS VC=INDEL;AC=58;AF=0.18;AN=314;refseq.name=NM_000721;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 chr1 182087446 . G GTCT . PASS VC=INDEL;AC=198;AF=0.68;AN=292 GT 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 ./. ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 chr1 182739634 . TAAGA T . PASS VC=INDEL;AC=65;AF=0.21;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 chr1 182951675 . AGA A . PASS VC=INDEL;AC=78;AF=0.25;AN=316 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 chr1 183032447 . C CTAAG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183073109 . T TTG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183073111 . G GTG . PASS VC=INDEL;AC=125;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183077296 . A AG . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183097956 . G GTTA . PASS VC=INDEL;AC=127;AF=0.4;AN=314;refseq.name=NM_002293;refseq.positionType=intron GT 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 chr1 183145207 . G GTAG . PASS VC=INDEL;AC=35;AF=0.11;AN=312 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 183180446 . GG G . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_005562;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 183330737 . TAA T . PASS VC=INDEL;AC=197;AF=0.63;AN=312;refseq.name=NM_015039;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 chr1 183589923 . A ATCTT . PASS VC=INDEL;AC=117;AF=0.37;AN=314 GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 chr1 183712910 . AC A . PASS VC=INDEL;AC=131;AF=0.42;AN=312;refseq.name=NM_015149;refseq.positionType=intron GT 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 chr1 183806728 . T TG . PASS VC=INDEL;AC=229;AF=0.85;AN=270;refseq.name=NM_015149;refseq.positionType=intron GT 1/1 ./. 1/1 ./. ./. 0/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 1/1 1/1 0/0 1/1 ./. 1/1 0/0 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/0 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 183996005 . C CTATTA . PASS VC=INDEL;AC=27;AF=0.09;AN=316;refseq.name=NM_015101;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 184391018 . C CTA . PASS VC=INDEL;AC=68;AF=0.22;AN=312;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr1 184561827 . CAGA C . PASS VC=INDEL;AC=47;AF=0.15;AN=316;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 184577643 . T TC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_030806;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 185540897 . T TCCAG . PASS VC=INDEL;AC=136;AF=0.48;AN=286 GT 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 ./. 1/1 ./. 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 ./. 0/0 0/0 ./. 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 chr1 185865550 . C CAT . PASS VC=INDEL;AC=53;AF=0.17;AN=310;refseq.name=NM_031935;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr1 186378142 . CAGTT C . PASS VC=INDEL;AC=55;AF=0.21;AN=266;refseq.name=NM_017847;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 ./. 0/1 1/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 1/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 ./. ./. 0/0 0/0 0/1 0/1 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/1 ./. ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 ./. 0/1 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 chr1 186769215 . T TA . PASS VC=INDEL;AC=45;AF=0.14;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 186933480 . T TTAAT . PASS VC=INDEL;AC=135;AF=0.43;AN=316;refseq.name=NM_024420;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 187372829 . AGGCTT A . PASS VC=INDEL;AC=34;AF=0.11;AN=304 GT ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 187372830 . GGCTTG G . PASS VC=INDEL;AC=32;AF=0.1;AN=306 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 chr1 187685847 . CAATT C . PASS VC=INDEL;AC=112;AF=0.36;AN=314 GT 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr1 187781028 . C CT . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 chr1 187815820 . A ACAA . PASS VC=INDEL;AC=21;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 187899550 . AAA A . PASS VC=INDEL;AC=65;AF=0.21;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 chr1 188075358 . GTAAG G . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 chr1 188110355 . C CT . PASS VC=INDEL;AC=222;AF=0.71;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 ./. 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 ./. 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 chr1 188372559 . CAAG C . PASS VC=INDEL;AC=230;AF=0.73;AN=314 GT 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188397016 . C CA . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 188526820 . C CT . PASS VC=INDEL;AC=262;AF=0.91;AN=288 GT 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188533586 . G GTTCT . PASS VC=INDEL;AC=290;AF=0.92;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 188628449 . CAACT C . PASS VC=INDEL;AC=100;AF=0.32;AN=314 GT 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 chr1 189027168 . C CTG . PASS VC=INDEL;AC=146;AF=0.69;AN=212 GT 1/1 ./. ./. ./. ./. ./. 0/1 1/1 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 0/0 1/1 0/0 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/0 ./. 0/1 0/1 ./. ./. 0/1 ./. 1/1 ./. ./. ./. 0/1 0/1 0/1 ./. 1/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. ./. 1/1 ./. ./. 1/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. ./. ./. ./. ./. 1/1 0/1 ./. ./. ./. ./. 1/1 1/1 ./. ./. 1/1 1/1 1/1 ./. ./. 1/1 ./. ./. ./. chr1 189046798 . C CA . PASS VC=INDEL;AC=86;AF=0.27;AN=316 GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 chr1 189087000 . TTA T . PASS VC=INDEL;AC=159;AF=0.53;AN=302 GT 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 ./. 0/0 0/1 ./. 0/0 0/1 1/1 chr1 189190273 . AT A . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 189547870 . A AAT . PASS VC=INDEL;AC=194;AF=0.79;AN=246 GT 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 ./. 0/1 0/1 0/1 1/1 1/1 0/1 ./. ./. 0/1 ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 ./. ./. ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 ./. 0/1 ./. ./. 0/1 1/1 0/0 ./. 1/1 1/1 ./. ./. ./. 0/0 1/1 ./. ./. 1/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 ./. 0/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. ./. 0/1 ./. 1/1 0/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 189629285 . A ATAACT . PASS VC=INDEL;AC=158;AF=0.59;AN=266 GT 0/1 1/1 0/0 1/1 ./. 0/1 1/1 0/1 0/0 0/0 1/1 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/1 1/1 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 ./. 0/0 0/0 1/1 0/1 ./. 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/1 ./. 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. ./. 0/0 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 1/1 ./. ./. 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 1/1 1/1 0/1 0/1 chr1 189867802 . G GC . PASS VC=INDEL;AC=23;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 chr1 190095126 . CTAACA C . PASS VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 chr1 190095129 . ACATAA A . PASS VC=INDEL;AC=143;AF=0.45;AN=316;refseq.name=NM_199051;refseq.positionType=intron GT 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 chr1 190636901 . C CTAA . PASS VC=INDEL;AC=131;AF=0.42;AN=314 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 chr1 190886420 . AA A . PASS VC=INDEL;AC=76;AF=0.26;AN=292 GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 chr1 191196527 . A AAT . PASS VC=INDEL;AC=191;AF=0.6;AN=316 GT 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 chr1 191340485 . TTAGA T . PASS VC=INDEL;AC=175;AF=0.59;AN=296 GT 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 ./. 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 ./. 0/0 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 0/1 ./. ./. 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/1 1/1 0/1 chr1 191464816 . A ATTA . PASS VC=INDEL;AC=213;AF=0.7;AN=306 GT 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 chr1 191588586 . C CA . PASS VC=INDEL;AC=190;AF=0.61;AN=310 GT 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 ./. 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 chr1 191588587 . A AA . PASS VC=INDEL;AC=186;AF=0.61;AN=304 GT 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 chr1 191752595 . T TCTTT . PASS VC=INDEL;AC=132;AF=0.42;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/0 chr1 192047581 . TT T . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 192460381 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 192612585 . T TCA . PASS VC=INDEL;AC=80;AF=0.25;AN=316;refseq.name=NM_002927;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 chr1 192726770 . C CT . PASS VC=INDEL;AC=121;AF=0.39;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 193118950 . AGACT A . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_024529;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193158515 . CTG C . PASS VC=INDEL;AC=7;AF=0.02;AN=316;refseq.name=NM_003783;refseq.positionType=promoter GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193261423 . AAAGTA A . PASS VC=INDEL;AC=7;AF=0.02;AN=316 GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 193421510 . A ATCT . PASS VC=INDEL;AC=102;AF=0.33;AN=310 GT 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 chr1 193482947 . CAA C . PASS VC=INDEL;AC=71;AF=0.22;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 chr1 193569090 . C CG . PASS VC=INDEL;AC=85;AF=0.27;AN=312 GT 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 193877310 . GG G . PASS VC=INDEL;AC=106;AF=0.34;AN=316 GT 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 193881567 . T TT . PASS VC=INDEL;AC=4;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 194004698 . TCTT T . PASS VC=INDEL;AC=34;AF=0.11;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 chr1 194047765 . TAT T . PASS VC=INDEL;AC=48;AF=0.2;AN=238 GT ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/1 0/1 0/0 0/1 ./. ./. 0/0 ./. ./. 0/1 0/1 0/0 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 chr1 194160203 . TTAGT T . PASS VC=INDEL;AC=25;AF=0.12;AN=206 GT 0/1 0/0 0/1 0/0 ./. 0/1 0/0 ./. ./. ./. 0/1 ./. 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 ./. ./. 0/1 0/0 ./. ./. ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. ./. ./. ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 ./. ./. 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 chr1 194193740 . A AG . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 194339262 . ATGT A . PASS VC=INDEL;AC=67;AF=0.21;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 chr1 194487871 . C CCTAT . PASS VC=INDEL;AC=302;AF=0.97;AN=312 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 194520551 . GG G . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 194563981 . TAAT T . PASS VC=INDEL;AC=169;AF=0.53;AN=316 GT 1/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 chr1 194738670 . T TTT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 194763917 . CATG C . PASS VC=INDEL;AC=267;AF=0.84;AN=316 GT 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr1 195047681 . GG G . PASS VC=INDEL;AC=29;AF=0.1;AN=278 GT 0/0 0/0 ./. 0/0 0/0 0/0 1/1 1/1 0/0 ./. 0/0 1/1 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/0 0/1 0/0 1/1 1/1 chr1 195637390 . TA T . PASS VC=INDEL;AC=90;AF=0.29;AN=314 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 chr1 195637391 . AA A . PASS VC=INDEL;AC=89;AF=0.28;AN=316 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 chr1 195877296 . T TAA . PASS VC=INDEL;AC=232;AF=0.73;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 chr1 195877297 . A AAA . PASS VC=INDEL;AC=232;AF=0.73;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 chr1 195934123 . CCTAT C . PASS VC=INDEL;AC=185;AF=0.59;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 chr1 195934125 . TATCT T . PASS VC=INDEL;AC=184;AF=0.59;AN=312 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/1 ./. 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 chr1 196163677 . TT T . PASS VC=INDEL;AC=284;AF=0.9;AN=316 GT 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 196344374 . C CA . PASS VC=INDEL;AC=153;AF=0.53;AN=290;refseq.name=NM_198503;refseq.positionType=intron GT 0/0 0/0 0/0 ./. 0/0 ./. 0/0 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 ./. ./. 0/0 chr1 196448625 . ATG A . PASS VC=INDEL;AC=7;AF=0.03;AN=266;refseq.name=NM_198503;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 196448626 . TGTA T . PASS VC=INDEL;AC=8;AF=0.03;AN=302;refseq.name=NM_198503;refseq.positionType=intron GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 chr1 197406760 . GAA G . PASS VC=INDEL;AC=78;AF=0.25;AN=312;refseq.name=NM_201253;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 ./. 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 197613756 . ACCT A . PASS VC=INDEL;AC=25;AF=0.08;AN=316;refseq.name=NM_144977;refseq.positionType=intron GT 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 chr1 197690664 . T TG . PASS VC=INDEL;AC=291;AF=0.92;AN=316;refseq.name=NM_144977;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 chr1 198792990 . T TG . PASS VC=INDEL;AC=131;AF=0.41;AN=316 GT 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 198940301 . C CCTT . PASS VC=INDEL;AC=258;AF=0.82;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 chr1 198940306 . T TTCT . PASS VC=INDEL;AC=258;AF=0.82;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 1/1 chr1 199277515 . AC A . PASS VC=INDEL;AC=36;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr1 200575750 . AAATA A . PASS VC=INDEL;AC=97;AF=0.31;AN=314;refseq.name=NM_014875;refseq.positionType=intron GT 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 chr1 201173407 . AA A . PASS VC=INDEL;AC=56;AF=0.18;AN=314 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 chr1 201288249 . TATC T . PASS VC=INDEL;AC=209;AF=0.66;AN=316;refseq.name=NM_000299;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 chr1 201457641 . AA A . PASS VC=INDEL;AC=55;AF=0.18;AN=310;refseq.name=NM_004078;refseq.positionType=intron GT 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 1/1 1/1 chr1 201587178 . CA C . PASS VC=INDEL;AC=145;AF=0.47;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 chr1 201733889 . G GG . PASS VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_020443;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 chr1 203792216 . AA A . PASS VC=INDEL;AC=265;AF=0.93;AN=286;refseq.name=NM_014827;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 1/1 chr1 203829389 . CTCAAC C . PASS VC=INDEL;AC=195;AF=0.62;AN=316;refseq.name=NM_003094;refseq.positionType=promoter GT 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 chr1 203848383 . C CTT . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 203848384 . T TTT . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 204049028 . T TG . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_005686;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 204452618 . T TGT . PASS VC=INDEL;AC=141;AF=0.47;AN=300;refseq.name=NM_002646;refseq.positionType=intron GT 1/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 1/1 0/1 0/0 0/1 0/0 1/1 1/1 chr1 205036040 . T TG . PASS VC=INDEL;AC=69;AF=0.23;AN=302;refseq.name=NM_005076;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 205036041 . G GG . PASS VC=INDEL;AC=71;AF=0.23;AN=310;refseq.name=NM_005076;refseq.positionType=intron GT 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 206303222 . C CAGCCTAGCT . PASS VC=INDEL;AC=105;AF=0.33;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 chr1 206571046 . G GA . PASS VC=INDEL;AC=2;AF=0.01;AN=290;refseq.name=NM_015326;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. chr1 206862605 . G GA . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004759;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 206955760 . TGTAA T . PASS VC=INDEL;AC=95;AF=0.31;AN=310 GT 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 ./. 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 chr1 207260285 . T TCAATTCACAGGAGTATGTGA . PASS VC=INDEL;AC=197;AF=0.62;AN=316;refseq.name=NM_001017365;refseq.positionType=promoter GT 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr1 207277350 . CC C . PASS VC=INDEL;AC=201;AF=0.64;AN=316;refseq.name=NM_000715;refseq.positionType=promoter GT 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 chr1 207641329 . TTAAG T . PASS VC=INDEL;AC=13;AF=0.06;AN=216;refseq.name=NM_001006658;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/1 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. chr1 207824638 . A AATTC . PASS VC=INDEL;AC=153;AF=0.48;AN=316;refseq.name=NM_175710;refseq.positionType=intron GT 0/0 0/1 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 chr1 208201207 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_025179;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 208514674 . GTTAC G . PASS VC=INDEL;AC=165;AF=0.53;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 chr1 208514676 . TACTT T . PASS VC=INDEL;AC=166;AF=0.53;AN=314 GT 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 chr1 208609280 . GGAAG G . PASS VC=INDEL;AC=55;AF=0.21;AN=256 GT 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 1/1 0/1 ./. 0/1 ./. 1/1 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 ./. 1/1 0/0 1/1 0/1 ./. ./. 0/1 1/1 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr1 208643013 . CA C . PASS VC=INDEL;AC=36;AF=0.12;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 208643015 . AA A . PASS VC=INDEL;AC=39;AF=0.12;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 208763800 . C CA . PASS VC=INDEL;AC=175;AF=0.55;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 chr1 209124169 . T TA . PASS VC=INDEL;AC=226;AF=0.72;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 chr1 209124171 . A AA . PASS VC=INDEL;AC=226;AF=0.72;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 chr1 209639686 . A AG . PASS VC=INDEL;AC=203;AF=0.64;AN=316 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 chr1 209662878 . T TG . PASS VC=INDEL;AC=205;AF=0.65;AN=316 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 chr1 209936964 . T TCA . PASS VC=INDEL;AC=184;AF=0.58;AN=316;refseq.name=NM_025228;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 210007940 . TCT T . PASS VC=INDEL;AC=190;AF=0.6;AN=316;refseq.name=NM_014388;refseq.positionType=intron GT 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 chr1 210483472 . TG T . PASS VC=INDEL;AC=13;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 210485101 . A AGGAC . PASS VC=INDEL;AC=232;AF=0.8;AN=290 GT 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 ./. ./. 0/1 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 0/0 ./. 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 ./. 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. chr1 210713503 . TT T . PASS VC=INDEL;AC=303;AF=0.96;AN=316;refseq.name=NM_018194;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 211710916 . CC C . PASS VC=INDEL;AC=55;AF=0.17;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 211786200 . TA T . PASS VC=INDEL;AC=147;AF=0.56;AN=264 GT ./. 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 ./. 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 0/0 ./. ./. ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 ./. 1/1 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 ./. ./. 0/0 ./. 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/0 0/0 1/1 ./. 1/1 0/1 chr1 212767202 . TTT T . PASS VC=INDEL;AC=63;AF=0.2;AN=316;refseq.name=NM_001030287;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 213150090 . T TGT . PASS VC=INDEL;AC=64;AF=0.21;AN=300;refseq.name=NM_024749;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 ./. 1/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 ./. ./. 0/0 chr1 213160084 . A AG . PASS VC=INDEL;AC=129;AF=0.41;AN=312;refseq.name=NM_024749;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 chr1 213160085 . G GG . PASS VC=INDEL;AC=129;AF=0.41;AN=314;refseq.name=NM_024749;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 chr1 213393510 . AG A . PASS VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_012424;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 213790399 . C CGA . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 214136369 . CTTC C . PASS VC=INDEL;AC=93;AF=0.29;AN=316 GT 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 214365999 . C CTG . PASS VC=INDEL;AC=164;AF=0.59;AN=278 GT 1/1 0/1 1/1 0/0 0/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 ./. 0/0 0/1 1/1 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 ./. 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 ./. 0/1 0/1 ./. ./. ./. 1/1 ./. ./. 1/1 0/1 ./. 1/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 0/0 ./. 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 chr1 214573392 . G GTTC . PASS VC=INDEL;AC=271;AF=0.86;AN=316;refseq.name=NM_005401;refseq.positionType=intron GT 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 215120715 . AA A . PASS VC=INDEL;AC=36;AF=0.12;AN=312 GT 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 216179286 . T TCAAT . PASS VC=INDEL;AC=30;AF=0.09;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr1 216298294 . C CAG . PASS VC=INDEL;AC=113;AF=0.36;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 chr1 216298296 . G GAG . PASS VC=INDEL;AC=112;AF=0.35;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 chr1 216454053 . A AACA . PASS VC=INDEL;AC=224;AF=0.71;AN=316;refseq.name=NM_206933;refseq.positionType=intron GT 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 chr1 216780749 . C CC . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr1 216835074 . A AGTTT . PASS VC=INDEL;AC=89;AF=0.28;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 chr1 217026745 . AA A . PASS VC=INDEL;AC=13;AF=0.04;AN=304;refseq.name=NM_206594;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 217057204 . G GC . PASS VC=INDEL;AC=231;AF=0.73;AN=316;refseq.name=NM_206594;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 chr1 217363476 . CTATT C . PASS VC=INDEL;AC=40;AF=0.19;AN=212 GT 0/0 1/1 1/1 0/0 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 ./. 0/0 ./. 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/0 ./. 1/1 1/1 ./. ./. ./. 0/0 0/0 ./. 1/1 0/0 ./. 0/1 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. chr1 218217904 . C CG . PASS VC=INDEL;AC=130;AF=0.43;AN=302 GT 0/1 0/1 0/1 ./. 1/1 0/1 ./. 0/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 ./. 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. chr1 218473680 . CGAG C . PASS VC=INDEL;AC=16;AF=0.05;AN=316;refseq.name=NM_016052;refseq.positionType=intron GT 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 218574584 . A AT . PASS VC=INDEL;AC=21;AF=0.09;AN=236;refseq.name=NM_003238;refseq.positionType=intron GT 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. 0/1 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 218845277 . TTTGT T . PASS VC=INDEL;AC=97;AF=0.31;AN=314 GT 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 chr1 219001503 . T TC . PASS VC=INDEL;AC=176;AF=0.56;AN=316 GT 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 chr1 219293844 . A ACT . PASS VC=INDEL;AC=274;AF=0.89;AN=308 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/0 1/1 1/1 1/1 1/1 1/1 chr1 219293846 . T TCT . PASS VC=INDEL;AC=199;AF=0.9;AN=222 GT 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. 0/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. ./. ./. 1/1 1/1 ./. 1/1 ./. 1/1 ./. ./. 0/1 0/0 1/1 ./. 1/1 1/1 ./. ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 0/1 ./. 0/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 ./. ./. 0/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 1/1 1/1 1/1 ./. 0/1 1/1 ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. 1/1 ./. 1/1 ./. chr1 219467766 . AAC A . PASS VC=INDEL;AC=102;AF=0.32;AN=314 GT 0/0 1/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 chr1 219839015 . C CATGG . PASS VC=INDEL;AC=73;AF=0.24;AN=306 GT 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 chr1 221137225 . T TCTT . PASS VC=INDEL;AC=159;AF=0.61;AN=262 GT 0/0 ./. 0/1 0/1 0/1 ./. 1/1 1/1 ./. 0/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 1/1 ./. 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/1 0/0 0/1 0/1 ./. 1/1 0/1 1/1 ./. 0/1 1/1 0/0 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. 0/1 1/1 0/1 0/1 ./. 0/1 0/1 0/0 0/0 ./. 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/0 1/1 ./. 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 1/1 0/1 0/1 0/1 ./. 0/1 0/0 1/1 ./. ./. 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 chr1 221202698 . GA G . PASS VC=INDEL;AC=82;AF=0.26;AN=310 GT 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 chr1 221279126 . CC C . PASS VC=INDEL;AC=0;AF=0;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 221315912 . TTCT T . PASS VC=INDEL;AC=94;AF=0.3;AN=312 GT 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 chr1 222205539 . AATTGACC A . PASS VC=INDEL;AC=90;AF=0.29;AN=310 GT 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 222493300 . T TGA . PASS VC=INDEL;AC=310;AF=0.98;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 222493301 . G GAG . PASS VC=INDEL;AC=310;AF=0.98;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 222990213 . ATTTG A . PASS VC=INDEL;AC=9;AF=0.04;AN=254 GT 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/1 chr1 223387015 . CTG C . PASS VC=INDEL;AC=6;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 223657734 . A ATGAG . PASS VC=INDEL;AC=231;AF=0.99;AN=234 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 ./. ./. 0/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 0/1 ./. 1/1 1/1 1/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 chr1 223984835 . G GAA . PASS VC=INDEL;AC=194;AF=0.63;AN=306;refseq.name=NM_001031685;refseq.positionType=intron GT ./. 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 224264255 . A AG . PASS VC=INDEL;AC=150;AF=0.66;AN=228 GT 0/1 1/1 0/1 0/1 1/1 ./. 0/1 ./. 1/1 1/1 ./. ./. ./. 1/1 ./. 0/1 0/0 ./. ./. 0/1 1/1 0/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. 0/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. 1/1 ./. 0/1 1/1 0/0 ./. 1/1 1/1 ./. ./. 1/1 1/1 0/1 ./. 0/0 0/1 0/1 ./. 0/0 1/1 0/1 0/1 1/1 ./. 1/1 ./. ./. 1/1 0/0 0/1 ./. 1/1 0/0 ./. 0/1 0/0 0/1 ./. ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 ./. ./. ./. ./. 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 1/1 ./. ./. 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. ./. chr1 224264346 . TGAG T . PASS VC=INDEL;AC=154;AF=0.63;AN=244 GT 0/1 1/1 0/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 0/0 1/1 1/1 ./. 0/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/0 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. 0/0 ./. ./. 1/1 0/1 ./. 1/1 ./. 0/1 ./. 0/0 0/1 0/1 ./. 0/0 1/1 0/1 0/1 ./. 1/1 ./. 0/1 0/1 1/1 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/1 0/0 1/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/0 0/0 1/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 0/1 ./. 1/1 0/1 0/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 ./. 1/1 0/1 chr1 224833844 . A AAGACGTAAGACAGT . PASS VC=INDEL;AC=215;AF=0.68;AN=314;refseq.name=NM_152495;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 ./. 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 chr1 225662220 . CT C . PASS VC=INDEL;AC=203;AF=0.66;AN=306 GT 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 chr1 225974486 . T TG . PASS VC=INDEL;AC=187;AF=0.6;AN=310;refseq.name=NM_003133;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 225974487 . G GG . PASS VC=INDEL;AC=189;AF=0.6;AN=314;refseq.name=NM_003133;refseq.positionType=intron GT 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 226014266 . ATGG A . PASS VC=INDEL;AC=30;AF=0.1;AN=310;refseq.name=NM_000120;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr1 226014267 . TGGT T . PASS VC=INDEL;AC=31;AF=0.1;AN=316;refseq.name=NM_000120;refseq.positionType=intron GT 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 226878226 . ACTC A . PASS VC=INDEL;AC=45;AF=0.15;AN=306;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr1 226878233 . CTAC C . PASS VC=INDEL;AC=60;AF=0.21;AN=292;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 ./. ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 ./. 1/1 ./. ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/0 ./. 0/0 0/0 0/1 0/1 0/0 ./. 0/0 ./. 0/1 0/0 chr1 226913049 . GCCA G . PASS VC=INDEL;AC=14;AF=0.05;AN=302;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 226913051 . CACC C . PASS VC=INDEL;AC=6;AF=0.02;AN=280;refseq.name=NM_002221;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 227051261 . G GC . PASS VC=INDEL;AC=21;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 227252431 . TTTC T . PASS VC=INDEL;AC=21;AF=0.07;AN=316;refseq.name=NM_003607;refseq.positionType=intron GT 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr1 227401072 . GC G . PASS VC=INDEL;AC=122;AF=0.39;AN=316;refseq.name=NM_003607;refseq.positionType=intron GT 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 227560279 . G GTCATAG . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 228479392 . ATG A . PASS VC=INDEL;AC=12;AF=0.04;AN=316;refseq.name=NM_001098623;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 229074693 . TAGAGG T . PASS VC=INDEL;AC=102;AF=0.32;AN=316 GT 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 chr1 229075090 . ATAGCCTG A . PASS VC=INDEL;AC=30;AF=0.11;AN=264 GT 1/1 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. chr1 229336842 . CATTT C . PASS VC=INDEL;AC=19;AF=0.06;AN=300 GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 229631495 . A AC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_018230;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 229922597 . CCTT C . PASS VC=INDEL;AC=144;AF=0.46;AN=316 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 229922599 . TTCT T . PASS VC=INDEL;AC=142;AF=0.45;AN=314 GT 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 chr1 230272407 . GAG G . PASS VC=INDEL;AC=15;AF=0.05;AN=314;refseq.name=NM_004481;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 230625946 . T TGA . PASS VC=INDEL;AC=302;AF=0.96;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 230626726 . CTTTAAGTCCTGT C . PASS VC=INDEL;AC=59;AF=0.19;AN=314 GT 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 230626728 . TTAAGTCCTGTTT T . PASS VC=INDEL;AC=59;AF=0.19;AN=316 GT 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 chr1 230697057 . ACA A . PASS VC=INDEL;AC=152;AF=0.48;AN=316 GT 0/1 1/1 1/1 0/0 1/1 0/0 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 chr1 230952100 . GG G . PASS VC=INDEL;AC=34;AF=0.11;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 232200072 . CGACT C . PASS VC=INDEL;AC=86;AF=0.28;AN=312 GT 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 ./. 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 chr1 232606995 . GTCTG G . PASS VC=INDEL;AC=54;AF=0.17;AN=316;refseq.name=NM_020808;refseq.positionType=intron GT 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 1/1 chr1 232883964 . G GTT . PASS VC=INDEL;AC=279;AF=0.88;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 232883965 . T TTT . PASS VC=INDEL;AC=279;AF=0.88;AN=316 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 232944224 . AAGAA A . PASS VC=INDEL;AC=17;AF=0.05;AN=316;refseq.name=NM_019090;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 233013835 . C CT . PASS VC=INDEL;AC=38;AF=0.18;AN=214 GT 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. ./. 0/1 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 1/1 ./. ./. ./. 1/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/1 1/1 1/1 0/1 ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/1 0/0 ./. ./. ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/0 0/1 ./. 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. ./. 0/0 0/0 ./. 1/1 0/1 ./. 1/1 0/1 0/0 ./. 0/0 1/1 ./. ./. 0/0 1/1 ./. ./. 0/0 ./. 1/1 ./. 1/1 ./. ./. 0/0 ./. ./. chr1 233013837 . T TT . PASS VC=INDEL;AC=78;AF=0.25;AN=310 GT 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 chr1 233458691 . ACAC A . PASS VC=INDEL;AC=18;AF=0.06;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 chr1 233593090 . TT T . PASS VC=INDEL;AC=257;AF=0.82;AN=312 GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr1 233991847 . T TCA . PASS VC=INDEL;AC=220;AF=0.72;AN=306 GT 1/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 ./. 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 chr1 234635298 . G GT . PASS VC=INDEL;AC=205;AF=0.65;AN=316 GT 0/1 0/0 0/0 0/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 chr1 234704346 . TCT T . PASS VC=INDEL;AC=36;AF=0.12;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr1 235770627 . AATTA A . PASS VC=INDEL;AC=56;AF=0.18;AN=316;refseq.name=NM_004485;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236043714 . ATCCTGTGTTGATTTA A . PASS VC=INDEL;AC=6;AF=0.02;AN=294 GT ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236043717 . CTGTGTTGATTTATTA C . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 236118487 . TT T . PASS VC=INDEL;AC=12;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr1 236195380 . GTG G . PASS VC=INDEL;AC=163;AF=0.52;AN=316;refseq.name=NM_002508;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 chr1 236375505 . T TG . PASS VC=INDEL;AC=130;AF=0.42;AN=310 GT 0/0 ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 chr1 236555148 . T TA . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_145861;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr1 236723352 . CGACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACA C . PASS VC=INDEL;AC=72;AF=0.23;AN=314;refseq.name=NM_018072;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 236723354 . ACCTCGCTCAGACTCTGTGAGGTGCTGAATAAGCAACAGA A . PASS VC=INDEL;AC=72;AF=0.23;AN=312;refseq.name=NM_018072;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 chr1 236848307 . A AG . PASS VC=INDEL;AC=62;AF=0.21;AN=300;refseq.name=NM_001103;refseq.positionType=promoter GT 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. ./. 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr1 237009685 . TAGC T . PASS VC=INDEL;AC=6;AF=0.02;AN=292;refseq.name=NM_000254;refseq.positionType=intron GT 0/1 0/0 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237009687 . GCAG G . PASS VC=INDEL;AC=3;AF=0.01;AN=304;refseq.name=NM_000254;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237055125 . CA C . PASS VC=INDEL;AC=9;AF=0.03;AN=284;refseq.name=NM_000254;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 237277023 . C CA . PASS VC=INDEL;AC=18;AF=0.06;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 chr1 237535965 . AA A . PASS VC=INDEL;AC=0;AF=0;AN=280;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 chr1 237539975 . GCTTGA G . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_001035;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 chr1 237649833 . C CTCTT . PASS VC=INDEL;AC=140;AF=0.45;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 ./. 0/0 1/1 0/1 ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 237649835 . C CTTTC . PASS VC=INDEL;AC=138;AF=0.44;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 chr1 237995162 . T TTTGA . PASS VC=INDEL;AC=301;AF=0.96;AN=312;refseq.name=NM_001035;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 238017296 . T TCT . PASS VC=INDEL;AC=80;AF=0.25;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 chr1 238125441 . AGA A . PASS VC=INDEL;AC=26;AF=0.08;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 238152842 . C CGTAA . PASS VC=INDEL;AC=165;AF=0.52;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 chr1 238152845 . A AAGTA . PASS VC=INDEL;AC=166;AF=0.53;AN=316 GT 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 chr1 238257585 . TGAT T . PASS VC=INDEL;AC=159;AF=0.61;AN=262 GT 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 ./. 1/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/0 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 1/1 ./. 0/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 ./. 1/1 0/1 1/1 ./. ./. 0/0 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. ./. 0/1 1/1 1/1 chr1 238476744 . A ATCTA . PASS VC=INDEL;AC=283;AF=0.98;AN=290 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 chr1 238497833 . G GAGAA . PASS VC=INDEL;AC=232;AF=0.76;AN=304 GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 1/1 1/1 ./. 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/0 ./. ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 chr1 238623394 . C CTTGA . PASS VC=INDEL;AC=178;AF=0.58;AN=308 GT 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 ./. 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 ./. ./. 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 ./. 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 chr1 238699979 . T TATCT . PASS VC=INDEL;AC=97;AF=0.31;AN=314 GT 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 238921290 . CATTCAT C . PASS VC=INDEL;AC=188;AF=0.59;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 1/1 0/1 0/1 0/0 chr1 238933453 . C CA . PASS VC=INDEL;AC=26;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 238933454 . A AA . PASS VC=INDEL;AC=25;AF=0.08;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 239644576 . C CAA . PASS VC=INDEL;AC=46;AF=0.15;AN=300 GT 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 ./. 1/1 0/0 0/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 chr1 240115184 . GAAG G . PASS VC=INDEL;AC=62;AF=0.2;AN=316 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 chr1 240170484 . ATCA A . PASS VC=INDEL;AC=30;AF=0.1;AN=310 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 chr1 240469105 . A ACT . PASS VC=INDEL;AC=44;AF=0.14;AN=308;refseq.name=NM_020066;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr1 240556294 . A AG . PASS VC=INDEL;AC=180;AF=0.73;AN=248;refseq.name=NM_020066;refseq.positionType=intron GT ./. 0/1 1/1 ./. 1/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 ./. 0/0 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 ./. ./. ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 ./. 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 ./. 0/0 0/0 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 0/1 ./. 1/1 1/1 ./. 1/1 0/1 ./. ./. 0/1 ./. 1/1 1/1 0/0 0/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 ./. ./. ./. ./. 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/1 1/1 0/1 chr1 240750353 . A AT . PASS VC=INDEL;AC=1;AF=0;AN=208;refseq.name=NM_022469;refseq.positionType=intron GT 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. chr1 241292738 . CGAC C . PASS VC=INDEL;AC=16;AF=0.06;AN=254;refseq.name=NM_002924;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 0/0 0/0 chr1 241342365 . TTCAA T . PASS VC=INDEL;AC=54;AF=0.18;AN=308;refseq.name=NM_002924;refseq.positionType=intron GT 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 ./. 1/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 1/1 ./. 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 chr1 241864983 . A AGTCAAAC . PASS VC=INDEL;AC=235;AF=0.75;AN=314;refseq.name=NM_144625;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 chr1 241901460 . ACTG A . PASS VC=INDEL;AC=126;AF=0.4;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 241920499 . TGTAG T . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 241920501 . TAGGT T . PASS VC=INDEL;AC=5;AF=0.02;AN=316;refseq.name=NM_144625;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr1 242055743 . C CTG . PASS VC=INDEL;AC=47;AF=0.15;AN=314 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 chr1 242257290 . TC T . PASS VC=INDEL;AC=59;AF=0.22;AN=270;refseq.name=NM_152666;refseq.positionType=intron GT 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/1 ./. ./. ./. 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 ./. ./. 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/1 0/0 ./. 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 1/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 chr1 242281287 . T TCT . PASS VC=INDEL;AC=296;AF=0.95;AN=312;refseq.name=NM_152666;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr1 242328018 . CATTACACTACTTTT C . PASS VC=INDEL;AC=97;AF=0.4;AN=244;refseq.name=NM_152666;refseq.positionType=intron GT 1/1 0/1 0/1 ./. 1/1 0/0 0/1 0/0 1/1 0/1 ./. 0/0 ./. 0/1 0/0 0/1 0/1 ./. 0/1 0/0 1/1 0/0 0/1 ./. 0/0 0/1 1/1 1/1 0/1 ./. 0/0 0/1 1/1 0/1 1/1 0/0 ./. 0/0 ./. 1/1 0/0 0/1 0/1 0/0 0/1 0/1 ./. ./. ./. 0/1 0/1 ./. 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 1/1 ./. 0/0 0/0 1/1 0/1 0/1 ./. 1/1 0/1 1/1 0/1 ./. ./. 1/1 0/1 0/1 0/1 ./. ./. 0/0 1/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/1 ./. 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 ./. ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 ./. 0/0 0/0 chr1 242602261 . CC C . PASS VC=INDEL;AC=51;AF=0.16;AN=316;refseq.name=NM_152666;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 chr1 243409926 . AAGTT A . PASS VC=INDEL;AC=99;AF=0.32;AN=312;refseq.name=NM_014812;refseq.positionType=intron GT 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 chr1 243410210 . G GTAT . PASS VC=INDEL;AC=137;AF=0.43;AN=316;refseq.name=NM_014812;refseq.positionType=intron GT 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 chr1 243435760 . CATT C . PASS VC=INDEL;AC=26;AF=0.1;AN=272;refseq.name=NM_006642;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. chr1 244015225 . GTCTG G . PASS VC=INDEL;AC=70;AF=0.22;AN=316 GT 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 chr1 244033256 . GTTGA G . PASS VC=INDEL;AC=18;AF=0.06;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244186794 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244216819 . T TA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006352;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 chr1 244216822 . A AA . PASS VC=INDEL;AC=79;AF=0.25;AN=312;refseq.name=NM_006352;refseq.positionType=exon GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 chr1 244371962 . CAACTGGTCAAC C . PASS VC=INDEL;AC=2;AF=0.01;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244372739 . C CTA . PASS VC=INDEL;AC=70;AF=0.22;AN=312 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr1 244517491 . A AG . PASS VC=INDEL;AC=229;AF=0.72;AN=316;refseq.name=NM_001012970;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 chr1 244552134 . CATTT C . PASS VC=INDEL;AC=41;AF=0.13;AN=314;refseq.name=NM_001012970;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 244794244 . T TAAC . PASS VC=INDEL;AC=2;AF=0.01;AN=316;refseq.name=NM_173807;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 245242885 . A ATT . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 245242887 . T TTT . PASS VC=INDEL;AC=3;AF=0.01;AN=316;refseq.name=NM_032328;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr1 245310839 . T TTAAAG . PASS VC=INDEL;AC=156;AF=0.59;AN=266 GT 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 ./. 1/1 1/1 1/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 0/0 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/1 0/1 0/0 0/0 ./. 0/1 ./. 0/0 ./. ./. ./. 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 ./. 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/1 0/0 0/1 0/0 1/1 0/0 0/1 ./. ./. ./. 0/1 ./. 1/1 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 chr1 245453003 . G GCCAA . PASS VC=INDEL;AC=80;AF=0.26;AN=308;refseq.name=NM_018012;refseq.positionType=intron GT 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 chr1 245709104 . A AGTCAAC . PASS VC=INDEL;AC=221;AF=0.7;AN=316;refseq.name=NM_018012;refseq.positionType=intron GT 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 chr1 245868167 . G GTCTT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 245868172 . T TCTTT . PASS VC=INDEL;AC=137;AF=0.43;AN=316 GT 0/1 0/0 0/0 1/1 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 chr1 246124841 . A AAACAGAAG . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 246124843 . A ACAGAAGAA . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr1 246149511 . C CT . PASS VC=INDEL;AC=69;AF=0.32;AN=214;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/0 ./. ./. 1/1 ./. ./. ./. 0/1 ./. 0/0 ./. ./. 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. ./. ./. 1/1 0/1 ./. ./. 1/1 ./. 1/1 0/1 1/1 ./. 0/1 0/1 1/1 ./. 0/1 1/1 0/1 ./. 0/1 0/1 0/0 0/0 0/1 ./. 0/1 1/1 ./. ./. 1/1 ./. 1/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/0 ./. 0/1 ./. 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. ./. 0/0 ./. ./. 0/1 ./. chr1 246152615 . GC G . PASS VC=INDEL;AC=164;AF=0.52;AN=316;refseq.name=NM_022743;refseq.positionType=intron GT 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 chr1 247110970 . T TCA . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 chr1 247340579 . TTTCTT T . PASS VC=INDEL;AC=232;AF=0.74;AN=312 GT 1/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 ./. 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr1 247694106 . C CTCCGTGGCCTAAACGGGCAGCCGAGCCCG . PASS VC=INDEL;AC=124;AF=0.62;AN=200;refseq.name=NM_198074;refseq.positionType=exon GT ./. ./. 1/1 1/1 1/1 0/1 ./. 1/1 0/1 ./. 1/1 1/1 0/1 0/1 ./. 0/1 ./. 1/1 ./. 1/1 1/1 ./. 1/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 ./. ./. ./. 0/1 0/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/1 ./. 1/1 0/1 ./. ./. ./. 1/1 0/1 1/1 ./. ./. 1/1 0/1 1/1 ./. 1/1 1/1 1/1 ./. ./. ./. ./. ./. ./. ./. 0/1 0/1 ./. 0/1 ./. 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 ./. ./. 0/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 ./. chr1 248807991 . TATGA T . PASS VC=INDEL;AC=85;AF=0.34;AN=252 GT 0/0 ./. 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/1 ./. ./. 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/0 ./. 0/0 1/1 0/0 ./. 0/1 0/1 ./. ./. 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 1/1 ./. ./. 1/1 0/1 1/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 ./. ./. 0/1 ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/1 ./. 0/0 ./. 0/1 0/1 1/1 0/1 ./. ./. 0/0 1/1 0/1 0/0 0/1 ./. 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 chr1 248809274 . GAACA G . PASS VC=INDEL;AC=79;AF=0.26;AN=304 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 248809275 . AACAA A . PASS VC=INDEL;AC=79;AF=0.26;AN=306 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 chr1 248809277 . C CAATT . PASS VC=INDEL;AC=9;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr1 249122808 . C CAT . PASS VC=INDEL;AC=176;AF=0.58;AN=304;refseq.name=NM_030645;refseq.positionType=promoter GT 0/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 ./. 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 1/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 ./. 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/0 0/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 chr1 249129038 . GCCTCTAACTT G . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 311906 . TA T . PASS VC=INDEL;AC=148;AF=0.48;AN=308 GT 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 chr2 341060 . TC T . PASS VC=INDEL;AC=52;AF=0.17;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 1/1 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 chr2 623863 . GTTC G . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 623869 . CTTC C . PASS VC=INDEL;AC=283;AF=0.9;AN=314 GT 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 872231 . G GCC . PASS VC=INDEL;AC=46;AF=0.16;AN=284 GT 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 chr2 872234 . C CCC . PASS VC=INDEL;AC=53;AF=0.21;AN=248 GT 1/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 ./. 0/0 0/1 0/1 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 ./. ./. ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/1 ./. 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/1 ./. ./. ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/0 ./. chr2 1131016 . TTTAGG T . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 chr2 1146399 . T TA . PASS VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr2 1146400 . A AA . PASS VC=INDEL;AC=280;AF=0.89;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 chr2 1184342 . CAACTT C . PASS VC=INDEL;AC=94;AF=0.3;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 chr2 1369823 . AGC A . PASS VC=INDEL;AC=243;AF=0.77;AN=316;refseq.name=NM_018968;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 chr2 1371776 . T TTTAA . PASS VC=INDEL;AC=50;AF=0.16;AN=312;refseq.name=NM_018968;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 ./. 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 1371779 . A AATTA . PASS VC=INDEL;AC=38;AF=0.13;AN=282;refseq.name=NM_018968;refseq.positionType=terminator GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 1/1 0/1 0/1 0/0 ./. ./. 0/0 0/1 0/0 0/0 ./. ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 ./. 0/0 0/0 1/1 0/0 0/1 ./. ./. 1/1 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. chr2 1379755 . A AA . PASS VC=INDEL;AC=5;AF=0.02;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 1789405 . A AT . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr2 2440845 . A AA . PASS VC=INDEL;AC=87;AF=0.32;AN=272 GT ./. 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/1 1/1 ./. 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. ./. ./. 0/1 ./. 0/1 ./. 0/0 ./. 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/0 1/1 0/1 ./. 0/1 ./. 0/1 ./. 1/1 1/1 ./. 0/1 ./. 1/1 0/1 0/1 0/1 ./. 0/0 0/1 chr2 2656901 . TG T . PASS VC=INDEL;AC=278;AF=0.9;AN=310 GT 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 3126017 . G GG . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 3424142 . CGCTGAC C . PASS VC=INDEL;AC=112;AF=0.46;AN=244;refseq.name=NM_016030;refseq.positionType=intron GT 0/1 0/1 ./. 0/0 0/1 ./. 1/1 0/1 0/1 0/0 ./. 1/1 0/0 0/1 ./. ./. 0/1 0/0 0/0 0/1 ./. 0/1 1/1 ./. 0/0 0/1 ./. 1/1 0/1 0/1 0/1 ./. ./. 0/0 0/0 ./. 1/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 ./. 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 ./. ./. ./. 0/1 0/1 1/1 1/1 ./. 1/1 ./. 0/0 ./. 0/1 0/0 1/1 ./. ./. 1/1 ./. 0/1 0/0 0/1 ./. 0/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/1 ./. 0/0 0/1 ./. ./. 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 1/1 ./. chr2 3658789 . ACAAA A . PASS VC=INDEL;AC=95;AF=0.33;AN=284;refseq.name=NM_024027;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 ./. 0/0 ./. 0/0 ./. 0/1 chr2 3749151 . GGAA G . PASS VC=INDEL;AC=163;AF=0.53;AN=310;refseq.name=NM_018436;refseq.positionType=exon GT 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 ./. 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 chr2 3749158 . GAAG G . PASS VC=INDEL;AC=164;AF=0.53;AN=308;refseq.name=NM_018436;refseq.positionType=exon GT 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 1/1 0/1 0/1 ./. 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 chr2 4140967 . G GA . PASS VC=INDEL;AC=125;AF=0.4;AN=312 GT 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 chr2 4184693 . AGAG A . PASS VC=INDEL;AC=60;AF=0.22;AN=274 GT 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 ./. 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/1 1/1 0/0 0/1 0/1 ./. 0/0 0/0 0/1 0/1 0/1 ./. 0/0 chr2 4296243 . ACCTGGCCTTTT A . PASS VC=INDEL;AC=19;AF=0.06;AN=312 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr2 4604536 . ATCTG A . PASS VC=INDEL;AC=82;AF=0.27;AN=308 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 ./. 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 chr2 4607815 . TAT T . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 chr2 4874174 . CAT C . PASS VC=INDEL;AC=203;AF=0.64;AN=316 GT 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 chr2 4933418 . GATC G . PASS VC=INDEL;AC=86;AF=0.28;AN=304 GT 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 ./. 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 4987676 . A ACT . PASS VC=INDEL;AC=100;AF=0.32;AN=316 GT 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 chr2 4994909 . G GT . PASS VC=INDEL;AC=122;AF=0.41;AN=294 GT 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 ./. 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 chr2 5222830 . CTGTT C . PASS VC=INDEL;AC=127;AF=0.4;AN=314 GT 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 ./. 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 chr2 5418395 . T TAA . PASS VC=INDEL;AC=147;AF=0.47;AN=314 GT 1/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 chr2 5821332 . TTCAGTCCCCCTAATGCC T . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 chr2 5821334 . CAGTCCCCCTAATGCCTC C . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 chr2 7238500 . A ACTT . PASS VC=INDEL;AC=184;AF=0.58;AN=316 GT 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr2 7238505 . T TTCT . PASS VC=INDEL;AC=184;AF=0.58;AN=316 GT 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/0 chr2 7616680 . C CA . PASS VC=INDEL;AC=196;AF=0.62;AN=314 GT ./. 1/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 chr2 10714143 . CAA C . PASS VC=INDEL;AC=143;AF=0.47;AN=306;refseq.name=NM_024894;refseq.positionType=intron GT 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 ./. 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 1/1 ./. 0/1 chr2 11163207 . TCA T . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 11163209 . ACA A . PASS VC=INDEL;AC=63;AF=0.2;AN=316 GT 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 11454443 . TTGTC T . PASS VC=INDEL;AC=85;AF=0.27;AN=310;refseq.name=NM_004850;refseq.positionType=intron GT 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 ./. 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 11600452 . TT T . PASS VC=INDEL;AC=316;AF=1;AN=316;refseq.name=NM_198256;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 11843046 . C CAACT . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 chr2 11843047 . A AACTA . PASS VC=INDEL;AC=157;AF=0.5;AN=316 GT 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 chr2 12317135 . T TT . PASS VC=INDEL;AC=2;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 12787834 . GT G . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 12877501 . G GA . PASS VC=INDEL;AC=241;AF=0.76;AN=316;refseq.name=NM_021643;refseq.positionType=intron GT 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 chr2 13123234 . A ACTTA . PASS VC=INDEL;AC=273;AF=0.89;AN=308 GT ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 chr2 13297277 . GC G . PASS VC=INDEL;AC=23;AF=0.07;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 13446741 . T TCACT . PASS VC=INDEL;AC=105;AF=0.41;AN=256 GT 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 1/1 0/1 1/1 ./. ./. 0/1 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/1 1/1 0/1 0/0 0/0 0/0 1/1 ./. 0/1 ./. ./. 0/1 ./. 0/1 0/0 0/1 ./. 1/1 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 ./. ./. 0/1 0/1 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/1 0/1 ./. 0/0 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 ./. 1/1 0/1 1/1 0/1 ./. 0/1 1/1 1/1 ./. 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. ./. 0/0 0/1 1/1 ./. ./. 0/0 chr2 13637137 . TTGCTG T . PASS VC=INDEL;AC=19;AF=0.06;AN=308 GT 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 13829513 . T TT . PASS VC=INDEL;AC=91;AF=0.29;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 chr2 13967190 . TAGAT T . PASS VC=INDEL;AC=22;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 chr2 14096044 . AAA A . PASS VC=INDEL;AC=47;AF=0.16;AN=298 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/0 chr2 14214846 . C CT . PASS VC=INDEL;AC=40;AF=0.13;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 chr2 14381137 . A ATC . PASS VC=INDEL;AC=0;AF=0;AN=280 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 14428427 . G GC . PASS VC=INDEL;AC=242;AF=0.77;AN=316 GT 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 chr2 14428428 . C CC . PASS VC=INDEL;AC=241;AF=0.77;AN=314 GT 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 chr2 14685393 . C CTTC . PASS VC=INDEL;AC=29;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 chr2 15208721 . A AC . PASS VC=INDEL;AC=116;AF=0.38;AN=304 GT 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 ./. 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 0/0 ./. 1/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 ./. 1/1 0/1 chr2 15263072 . A AAGGA . PASS VC=INDEL;AC=86;AF=0.33;AN=262 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 1/1 ./. 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/1 0/1 0/0 0/0 ./. 1/1 0/0 0/0 0/0 ./. ./. 0/1 0/1 0/1 ./. 0/0 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 ./. 0/0 1/1 ./. 0/1 0/0 1/1 ./. 0/1 0/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 ./. ./. 0/1 0/0 0/0 chr2 15744484 . CT C . PASS VC=INDEL;AC=48;AF=0.15;AN=314;refseq.name=NM_004939;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 chr2 15907161 . G GACTG . PASS VC=INDEL;AC=60;AF=0.19;AN=314 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 chr2 16916657 . T TAGAA . PASS VC=INDEL;AC=153;AF=0.51;AN=298 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 chr2 16916659 . G GAAAG . PASS VC=INDEL;AC=145;AF=0.49;AN=294 GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 ./. 0/1 1/1 1/1 1/1 ./. 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/0 chr2 17460258 . C CC . PASS VC=INDEL;AC=54;AF=0.17;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 chr2 18018674 . TAT T . PASS VC=INDEL;AC=71;AF=0.23;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 chr2 18139969 . T TT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18291829 . TCT T . PASS VC=INDEL;AC=276;AF=0.87;AN=316 GT 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 chr2 18382578 . G GC . PASS VC=INDEL;AC=304;AF=0.97;AN=314 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 18386046 . ACAGA A . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18673070 . CT C . PASS VC=INDEL;AC=0;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 18704268 . C CCATGACAAGAACTGCT . PASS VC=INDEL;AC=210;AF=0.66;AN=316 GT 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 18954606 . T TGTA . PASS VC=INDEL;AC=272;AF=0.87;AN=314 GT 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 chr2 19229223 . A AG . PASS VC=INDEL;AC=230;AF=0.82;AN=280 GT 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 ./. ./. 1/1 chr2 19416083 . CAAT C . PASS VC=INDEL;AC=26;AF=0.08;AN=312 GT 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. 0/1 0/1 1/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 19486700 . C CGT . PASS VC=INDEL;AC=200;AF=0.9;AN=222 GT 0/1 ./. ./. ./. 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. ./. 0/1 ./. 1/1 ./. 0/1 ./. 0/1 0/1 0/1 ./. 1/1 ./. ./. ./. ./. 0/1 1/1 ./. ./. 0/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 ./. 0/1 0/1 0/1 0/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 0/1 ./. 1/1 1/1 1/1 1/1 1/1 ./. ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. chr2 19792293 . AAA A . PASS VC=INDEL;AC=92;AF=0.29;AN=316 GT 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 chr2 19850365 . ATA A . PASS VC=INDEL;AC=17;AF=0.06;AN=302 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 20061297 . A AATCA . PASS VC=INDEL;AC=10;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 20902911 . G GC . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_021925;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21209314 . GTG G . PASS VC=INDEL;AC=13;AF=0.04;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21319809 . GACAA G . PASS VC=INDEL;AC=64;AF=0.2;AN=316 GT 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 21692599 . AA A . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 chr2 22508039 . GCCT G . PASS VC=INDEL;AC=70;AF=0.23;AN=300 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 ./. 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/1 0/0 0/0 chr2 23055890 . CTT C . PASS VC=INDEL;AC=32;AF=0.1;AN=310 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 chr2 23059421 . CC C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23080285 . C CC . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23252488 . T TGTTT . PASS VC=INDEL;AC=261;AF=0.83;AN=314 GT 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 ./. 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 1/1 0/0 1/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 23656105 . CT C . PASS VC=INDEL;AC=78;AF=0.25;AN=314 GT 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 23929327 . T TAACT . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 25136190 . TC T . PASS VC=INDEL;AC=190;AF=0.68;AN=280;refseq.name=NM_004036;refseq.positionType=intron GT 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 ./. 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 ./. 1/1 0/1 1/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 ./. 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 ./. 1/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 0/1 0/1 ./. ./. ./. ./. 0/1 0/1 chr2 25696290 . CA C . PASS VC=INDEL;AC=7;AF=0.02;AN=314;refseq.name=NM_021907;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 25971939 . A AGTAAA . PASS VC=INDEL;AC=90;AF=0.28;AN=316;refseq.name=NM_018263;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 chr2 26471341 . T TTTC . PASS VC=INDEL;AC=10;AF=0.03;AN=316;refseq.name=NM_000183;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 chr2 26547936 . GAC G . PASS VC=INDEL;AC=69;AF=0.22;AN=308;refseq.name=NM_153835;refseq.positionType=intron GT 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 0/1 ./. ./. 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 chr2 26849198 . ACGGTT A . PASS VC=INDEL;AC=85;AF=0.28;AN=308;refseq.name=NM_001029881;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 ./. 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/1 chr2 26849199 . CGGTTC C . PASS VC=INDEL;AC=83;AF=0.27;AN=302;refseq.name=NM_001029881;refseq.positionType=intron GT 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 1/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 ./. 0/0 0/1 chr2 27134249 . ATA A . PASS VC=INDEL;AC=100;AF=0.32;AN=316;refseq.name=NM_020134;refseq.positionType=intron GT 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 chr2 27787778 . AAATTAAAATTCTAC A . PASS VC=INDEL;AC=10;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 28368075 . CACAG C . PASS VC=INDEL;AC=0;AF=0;AN=306;refseq.name=NM_199193;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 28792105 . A AATA . PASS VC=INDEL;AC=100;AF=0.32;AN=308;refseq.name=NM_153021;refseq.positionType=intron GT 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 ./. 1/1 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 ./. 1/1 0/1 chr2 29191749 . GA G . PASS VC=INDEL;AC=87;AF=0.28;AN=316 GT 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr2 29191750 . AA A . PASS VC=INDEL;AC=86;AF=0.27;AN=316 GT 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 chr2 29738576 . TA T . PASS VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 29738577 . AA A . PASS VC=INDEL;AC=284;AF=0.9;AN=316;refseq.name=NM_004304;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 30158127 . C CA . PASS VC=INDEL;AC=192;AF=0.61;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/0 chr2 30158129 . A AA . PASS VC=INDEL;AC=192;AF=0.61;AN=316 GT 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 1/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/0 chr2 30645653 . A AAGCTTTTCTAATGAACATCTACAAGACTGTTGTG . PASS VC=INDEL;AC=303;AF=0.96;AN=316 GT 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 chr2 30727159 . C CAGTCTATATGCC . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_182551;refseq.positionType=intron GT 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 chr2 30727390 . GTTG G . PASS VC=INDEL;AC=31;AF=0.1;AN=314;refseq.name=NM_182551;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr2 30855218 . CCATGGGA C . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_182551;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 30937800 . GATTTT G . PASS VC=INDEL;AC=14;AF=0.06;AN=244 GT 0/0 ./. ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 ./. ./. ./. 0/0 0/1 0/0 ./. 0/1 0/1 0/1 ./. ./. 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 0/0 0/0 ./. 0/1 ./. ./. 0/1 ./. ./. chr2 31084461 . AATAAAATACAG A . PASS VC=INDEL;AC=36;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 chr2 31249797 . ATATC A . PASS VC=INDEL;AC=34;AF=0.11;AN=316;refseq.name=NM_024572;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 31249799 . ATCTA A . PASS VC=INDEL;AC=47;AF=0.16;AN=302;refseq.name=NM_024572;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 1/1 0/0 0/0 ./. 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 1/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 chr2 31374768 . AGTA A . PASS VC=INDEL;AC=13;AF=0.05;AN=278 GT 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 chr2 31499486 . C CC . PASS VC=INDEL;AC=11;AF=0.03;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 32845664 . A AT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 32845666 . T TT . PASS VC=INDEL;AC=138;AF=0.44;AN=316 GT 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 33393523 . AGCAA A . PASS VC=INDEL;AC=10;AF=0.03;AN=308;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 33403610 . ATTG A . PASS VC=INDEL;AC=46;AF=0.15;AN=316;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 chr2 33478311 . TGAGT T . PASS VC=INDEL;AC=2;AF=0.01;AN=314;refseq.name=NM_206943;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 33542959 . TT T . PASS VC=INDEL;AC=258;AF=0.82;AN=316;refseq.name=NM_206943;refseq.positionType=intron GT 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 33760624 . C CC . PASS VC=INDEL;AC=5;AF=0.02;AN=216;refseq.name=NM_170672;refseq.positionType=intron GT 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. ./. ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 chr2 33899643 . G GGAG . PASS VC=INDEL;AC=261;AF=0.83;AN=316 GT 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 chr2 34119549 . A AA . PASS VC=INDEL;AC=45;AF=0.14;AN=316 GT 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 chr2 34427438 . A AT . PASS VC=INDEL;AC=175;AF=0.76;AN=230 GT 0/1 0/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 ./. ./. 0/1 1/1 ./. ./. ./. ./. 0/0 0/1 0/1 ./. ./. ./. 0/1 1/1 0/1 0/1 0/1 1/1 ./. 0/1 1/1 ./. 1/1 ./. 1/1 0/1 ./. ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 0/1 0/1 0/1 1/1 ./. 1/1 1/1 ./. 0/1 1/1 ./. 0/1 ./. ./. ./. ./. 1/1 1/1 ./. 1/1 1/1 ./. 1/1 1/1 0/1 ./. 1/1 0/1 0/1 1/1 ./. 0/1 1/1 0/1 ./. 0/1 1/1 1/1 0/1 0/0 0/0 0/1 ./. 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/0 ./. ./. 1/1 1/1 ./. 1/1 0/1 0/1 ./. 1/1 ./. 0/1 0/1 0/1 1/1 ./. ./. 0/1 0/1 ./. 1/1 0/0 1/1 1/1 0/1 chr2 34841691 . TGAAT T . PASS VC=INDEL;AC=165;AF=0.79;AN=210 GT ./. ./. ./. 1/1 ./. ./. ./. 0/1 ./. 1/1 0/1 ./. 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 ./. ./. ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 ./. 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 ./. 1/1 1/1 ./. ./. 1/1 1/1 ./. ./. 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/0 ./. ./. ./. ./. 1/1 ./. 0/1 1/1 ./. 0/1 0/1 0/0 1/1 1/1 1/1 ./. 1/1 1/1 1/1 0/1 0/0 ./. ./. ./. 0/1 ./. ./. 1/1 0/1 ./. ./. 0/1 ./. ./. 0/1 0/1 1/1 ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 0/0 1/1 ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/0 0/1 1/1 1/1 ./. 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 ./. ./. 0/1 1/1 0/1 ./. ./. chr2 35025338 . G GG . PASS VC=INDEL;AC=227;AF=0.72;AN=314 GT 0/1 0/0 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 0/1 1/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 chr2 35255151 . TCT T . PASS VC=INDEL;AC=29;AF=0.09;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 35667838 . A AGG . PASS VC=INDEL;AC=54;AF=0.21;AN=252 GT 0/0 ./. ./. ./. 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/0 ./. 0/0 0/0 ./. ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. ./. ./. 0/1 0/0 0/1 ./. 0/1 0/1 0/1 0/0 ./. 0/1 0/1 0/1 ./. 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 35668564 . A AG . PASS VC=INDEL;AC=275;AF=0.87;AN=316 GT 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 chr2 36779604 . C CTT . PASS VC=INDEL;AC=130;AF=0.44;AN=298;refseq.name=NM_001042548;refseq.positionType=exon GT 1/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 ./. 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 ./. 0/0 1/1 1/1 1/1 0/0 0/0 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 ./. 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 chr2 37233064 . ACT A . PASS VC=INDEL;AC=48;AF=0.16;AN=302;refseq.name=NM_019024;refseq.positionType=intron GT 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 ./. 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 ./. 0/0 chr2 37865906 . GA G . PASS VC=INDEL;AC=161;AF=0.51;AN=314 GT 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 ./. 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 chr2 37960289 . A AG . PASS VC=INDEL;AC=1;AF=0;AN=302 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. chr2 38003881 . T TAGA . PASS VC=INDEL;AC=312;AF=0.99;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 38079466 . CAT C . PASS VC=INDEL;AC=93;AF=0.3;AN=308 GT 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 ./. 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 ./. 0/1 0/0 chr2 38476518 . T TCA . PASS VC=INDEL;AC=179;AF=0.57;AN=316 GT 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 chr2 38682923 . T TTTCTCTCT . PASS VC=INDEL;AC=35;AF=0.11;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 chr2 38990657 . C CACTT . PASS VC=INDEL;AC=241;AF=0.76;AN=316 GT 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 chr2 39202671 . TCAC T . PASS VC=INDEL;AC=68;AF=0.22;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 ./. 1/1 1/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/0 chr2 39848964 . GACTA G . PASS VC=INDEL;AC=92;AF=0.3;AN=304 GT 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 ./. 0/1 0/0 0/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 1/1 chr2 40095196 . TCTT T . PASS VC=INDEL;AC=22;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 40207026 . AA A . PASS VC=INDEL;AC=1;AF=0;AN=314 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 chr2 40328669 . A ATC . PASS VC=INDEL;AC=182;AF=0.58;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 1/1 chr2 40396501 . G GTCAG . PASS VC=INDEL;AC=13;AF=0.04;AN=310;refseq.name=NM_001112802;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 chr2 40446174 . T TCTACCTGCAACCCTTGATTGGCCTC . PASS VC=INDEL;AC=196;AF=0.62;AN=314;refseq.name=NM_001112802;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 ./. 0/0 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 40527545 . T TGC . PASS VC=INDEL;AC=69;AF=0.22;AN=316;refseq.name=NM_001112802;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 chr2 40764424 . TATG T . PASS VC=INDEL;AC=6;AF=0.02;AN=314 GT ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 40840587 . A ATTG . PASS VC=INDEL;AC=15;AF=0.06;AN=242 GT ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 ./. 0/1 0/0 ./. ./. ./. ./. 0/0 ./. ./. 0/0 0/1 0/0 0/1 ./. 0/0 ./. 1/1 0/0 ./. 0/1 0/0 0/1 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 ./. 1/1 0/0 1/1 0/0 0/0 0/1 ./. 0/0 0/1 ./. ./. ./. 0/0 0/0 chr2 41367520 . A AT . PASS VC=INDEL;AC=187;AF=0.6;AN=314 GT 1/1 1/1 0/0 0/0 0/0 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 chr2 41554849 . TCAGA T . PASS VC=INDEL;AC=231;AF=0.74;AN=314 GT ./. 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 41554851 . AGACA A . PASS VC=INDEL;AC=233;AF=0.74;AN=316 GT 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 chr2 41628974 . G GA . PASS VC=INDEL;AC=282;AF=0.9;AN=314 GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 41628975 . A AA . PASS VC=INDEL;AC=281;AF=0.9;AN=312 GT 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 41838136 . GGC G . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 42604189 . CTTATGGGTTAC C . PASS VC=INDEL;AC=3;AF=0.01;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 42773644 . C CC . PASS VC=INDEL;AC=111;AF=0.35;AN=316 GT 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 chr2 43140881 . TA T . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 43205232 . A AAG . PASS VC=INDEL;AC=287;AF=0.91;AN=316 GT 0/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 chr2 43324908 . C CA . PASS VC=INDEL;AC=316;AF=1;AN=316 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 43570900 . TCT T . PASS VC=INDEL;AC=84;AF=0.27;AN=316;refseq.name=NM_022065;refseq.positionType=intron GT 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/1 0/0 chr2 44397082 . AAGAGTA A . PASS VC=INDEL;AC=39;AF=0.12;AN=316;refseq.name=NM_177968;refseq.positionType=intron GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 chr2 44735716 . TAAAC T . PASS VC=INDEL;AC=189;AF=0.6;AN=316;refseq.name=NM_024766;refseq.positionType=intron GT 1/1 0/0 0/0 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 chr2 45472533 . T TATA . PASS VC=INDEL;AC=284;AF=0.92;AN=308 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 45472535 . T TAAT . PASS VC=INDEL;AC=291;AF=0.92;AN=316 GT 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 chr2 47399270 . TCA T . PASS VC=INDEL;AC=140;AF=0.44;AN=316;refseq.name=NM_001743;refseq.positionType=intron GT 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 chr2 48032874 . ACTAT A . PASS VC=INDEL;AC=254;AF=0.8;AN=316;refseq.name=NM_000179;refseq.positionType=intron GT 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 chr2 49026643 . A AA . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 49468159 . C CTCTT . PASS VC=INDEL;AC=57;AF=0.18;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 chr2 49514324 . GAAGAA G . PASS VC=INDEL;AC=179;AF=0.58;AN=310 GT 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 0/1 ./. 0/0 0/0 0/0 1/1 0/1 ./. 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 1/1 chr2 49982314 . T TT . PASS VC=INDEL;AC=196;AF=0.64;AN=304 GT 1/1 0/1 1/1 1/1 0/0 ./. 0/0 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. ./. 0/1 0/1 0/0 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 chr2 50152899 . TTTTC T . PASS VC=INDEL;AC=26;AF=0.1;AN=268;refseq.name=NM_004801;refseq.positionType=intron GT ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 0/0 ./. 0/1 ./. 0/0 0/1 0/1 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/1 ./. ./. ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 ./. 0/1 ./. 0/1 0/0 0/0 0/1 0/0 0/0 0/0 chr2 50693504 . AAC A . PASS VC=INDEL;AC=193;AF=0.63;AN=306;refseq.name=NM_004801;refseq.positionType=intron GT 0/0 1/1 1/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 1/1 1/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 ./. 0/0 1/1 0/1 0/1 1/1 1/1 1/1 0/0 ./. 1/1 0/1 ./. ./. 0/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/1 1/1 0/1 chr2 50703696 . C CTG . PASS VC=INDEL;AC=287;AF=0.91;AN=314;refseq.name=NM_004801;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 50703699 . T TGT . PASS VC=INDEL;AC=285;AF=0.9;AN=316;refseq.name=NM_004801;refseq.positionType=intron GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 chr2 51260591 . T TAT . PASS VC=INDEL;AC=0;AF=0;AN=316;refseq.name=NM_004801;refseq.positionType=promoter GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 51281539 . TT T . PASS VC=INDEL;AC=252;AF=0.8;AN=316 GT 0/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 chr2 51315220 . A ATT . PASS VC=INDEL;AC=55;AF=0.19;AN=292 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 ./. 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 ./. 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 ./. 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 ./. 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 chr2 51315221 . T TTT . PASS VC=INDEL;AC=56;AF=0.19;AN=300 GT 0/0 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 ./. 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 ./. 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 chr2 51355364 . TTT T . PASS VC=INDEL;AC=30;AF=0.1;AN=304 GT 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 chr2 52397945 . A ATGCTATTCCAATATCTCAG . PASS VC=INDEL;AC=33;AF=0.15;AN=214 GT 0/1 ./. 0/0 0/0 0/1 0/0 0/0 0/0 ./. ./. ./. 0/1 ./. ./. ./. 0/1 ./. 0/1 0/1 ./. 0/1 0/1 ./. 0/1 ./. 0/0 0/1 0/0 ./. 0/0 ./. ./. 0/0 0/0 ./. 0/0 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 ./. 0/0 0/0 ./. ./. 0/1 0/0 ./. 0/1 ./. ./. 0/1 0/0 0/1 0/1 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 ./. ./. 0/1 ./. 0/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 ./. ./. ./. 0/0 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/1 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/1 0/0 0/1 chr2 52643648 . G GAG . PASS VC=INDEL;AC=140;AF=0.53;AN=266 GT 0/1 ./. 0/0 0/1 0/1 1/1 0/0 0/0 1/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 ./. 0/0 0/1 0/0 0/0 0/1 0/1 0/0 ./. ./. 0/1 0/0 0/1 0/0 0/1 1/1 ./. 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/0 ./. 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 1/1 0/0 ./. ./. ./. 0/0 ./. 1/1 0/1 0/1 0/0 0/1 ./. 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 ./. 1/1 1/1 0/1 ./. 1/1 1/1 1/1 0/1 0/0 ./. 0/1 0/1 1/1 ./. ./. ./. 0/1 1/1 ./. 1/1 0/1 ./. ./. 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 ./. 0/1 1/1 ./. 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 ./. 0/0 1/1 0/0 1/1 0/1 0/0 1/1 chr2 53056176 . G GAG . PASS VC=INDEL;AC=131;AF=0.49;AN=270 GT 1/1 0/0 0/1 ./. ./. 0/0 ./. 1/1 0/1 0/1 0/1 ./. ./. ./. ./. 0/1 1/1 0/1 ./. 0/1 ./. 0/1 ./. 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 ./. 0/0 ./. 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 ./. 1/1 ./. 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/1 0/1 0/1 0/0 ./. 0/1 0/0 ./. 0/0 0/1 0/1 ./. 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 ./. 1/1 chr2 53674036 . AA A . PASS VC=INDEL;AC=106;AF=0.34;AN=310 GT 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/1 0/0 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 ./. 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 chr2 53737951 . AGGAT A . PASS VC=INDEL;AC=107;AF=0.35;AN=302 GT 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 ./. 0/0 ./. 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 ./. 1/1 1/1 0/1 0/0 ./. 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 ./. 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 chr2 54573230 . AACA A . PASS VC=INDEL;AC=62;AF=0.2;AN=316;refseq.name=NM_001100396;refseq.positionType=intron GT 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/0 0/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 chr2 54726113 . G GA . PASS VC=INDEL;AC=269;AF=0.87;AN=308;refseq.name=NM_003128;refseq.positionType=intron GT 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 ./. 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 ./. 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 54726287 . T TGTTA . PASS VC=INDEL;AC=269;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron GT 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 54783793 . C CTT . PASS VC=INDEL;AC=270;AF=0.85;AN=316;refseq.name=NM_003128;refseq.positionType=intron GT 0/1 0/0 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 chr2 55080611 . GCTTT G . PASS VC=INDEL;AC=3;AF=0.01;AN=310 GT 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 55174675 . AC A . PASS VC=INDEL;AC=6;AF=0.02;AN=306 GT 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. chr2 55208953 . A ATATGAATCACATACAAGCTAAGAAAC . PASS VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 chr2 55208955 . A ATGAATCACATACAAGCTAAGAAACTA . PASS VC=INDEL;AC=211;AF=0.67;AN=316;refseq.name=NM_020532;refseq.positionType=intron GT 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 chr2 55284481 . AA A . PASS VC=INDEL;AC=90;AF=0.28;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 chr2 55355370 . CTG C . PASS VC=INDEL;AC=0;AF=0;AN=316 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 55473492 . AA A . PASS VC=INDEL;AC=27;AF=0.11;AN=236;refseq.name=NM_002453;refseq.positionType=exon GT 0/1 ./. 0/0 ./. 0/0 0/1 0/1 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/1 ./. 0/1 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. ./. 0/0 0/0 ./. 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/1 0/1 ./. 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/1 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/0 ./. 0/0 0/1 0/0 ./. ./. 0/0 ./. 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. ./. 0/1 0/0 0/1 ./. 0/0 0/1 0/0 0/0 ./. 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/0 ./. 0/0 0/0 0/0 ./. chr2 56088199 . TA T . PASS VC=INDEL;AC=21;AF=0.07;AN=316 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 chr2 56603301 . G GT . PASS VC=INDEL;AC=118;AF=0.39;AN=306;refseq.name=NM_001080433;refseq.positionType=intron GT 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 ./. 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 1/1 1/1 ./. 1/1 0/0 0/1 0/1 1/1 ./. 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/0 chr2 57161556 . CCTT C . PASS VC=INDEL;AC=24;AF=0.1;AN=230 GT 0/1 ./. ./. 0/0 0/0 ./. 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 ./. ./. 0/1 ./. 0/0 0/0 ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 ./. 0/1 ./. 0/0 0/0 0/1 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 0/0 0/1 ./. 0/0 ./. ./. ./. 0/0 ./. 0/1 0/1 ./. 0/1 ./. 0/1 0/1 ./. ./. ./. 0/1 0/0 0/0 0/1 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 ./. 0/0 0/0 0/1 ./. 0/0 0/0 ./. 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. ./. ./. 0/1 ./. ./. ./. ./. 0/0 chr2 58167700 . AA A . PASS VC=INDEL;AC=220;AF=0.73;AN=300 GT 0/1 1/1 0/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 ./. 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/1 ./. 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 ./. 0/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 ./. 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 ./. 1/1 1/1 ./. 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 ./. 0/1 1/1 chr2 58193832 . A ACAA . PASS VC=INDEL;AC=35;AF=0.16;AN=222 GT 0/1 0/1 ./. 0/0 ./. ./. 0/0 0/0 0/0 ./. 0/1 0/0 ./. ./. 0/1 1/1 ./. ./. ./. 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/1 ./. 0/1 0/0 0/0 0/0 0/0 1/1 ./. 0/0 0/0 ./. ./. 0/0 ./. 0/0 0/1 1/1 0/0 ./. 0/0 ./. 0/0 ./. 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 ./. 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 0/1 ./. 0/0 ./. 0/0 0/0 0/1 0/0 ./. 0/1 ./. ./. 0/0 ./. 0/1 ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 0/1 0/0 0/1 ./. 0/0 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. ./. 1/1 0/0 0/1 0/0 ./. 0/1 ./. 0/1 0/0 0/0 ./. 0/0 0/0 0/0 0/1 ./. 0/0 ./. 0/0 0/0 chr2 58274884 . C CAGG . PASS VC=INDEL;AC=125;AF=0.4;AN=314;refseq.name=NM_006296;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/0 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 chr2 58274891 . A AGGA . PASS VC=INDEL;AC=123;AF=0.4;AN=308;refseq.name=NM_006296;refseq.positionType=intron GT 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 1/1 0/0 ./. 0/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 ./. 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 ./. 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 chr2 58283746 . A ACT . PASS VC=INDEL;AC=268;AF=0.88;AN=304;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 ./. 1/1 ./. 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 ./. 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 58283749 . C CTC . PASS VC=INDEL;AC=266;AF=0.86;AN=308;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 ./. 0/1 0/1 ./. 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 ./. 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 ./. 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 chr2 58385305 . T TCTTA . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 chr2 58385307 . T TTACT . PASS VC=INDEL;AC=79;AF=0.25;AN=316;refseq.name=NM_006296;refseq.positionType=intron GT 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/0 pysam-0.7.7/tests/vcf-examples/5.vcf0000664000076400007650000040703711754437212017126 0ustar andreasandreas##fileformat=VCFv4.0 ##fileDate=2011-07-18 ##source=Platypus_Version_0.1 ##platypusOptions={'bamFiles': ['/data/lindah/illumina_projects/rimmer_indels/AllData.bam'], 'labels': None, 'refFile': '/ib/groups/bsg/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 256, 'maxSize': 250, 'parseNCBI': 0, 'ploidy': 2, 'bufferSize': 1000000, 'nCPU': 1, 'minFlank': 3, 'minPosterior': 5, 'logFileName': 'log.txt', 'regions': ['20'], 'processRegionSize': 30000000, 'maxVariants': 8, 'maxReads': 5000000, 'genIndels': 1, 'minReads': 2, 'dataType': 'population', 'minMapQual': 20, 'rlen': 150, 'nInd': 1, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'strandFilter': 0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 0, 'output': 'test.vcf', 'minBaseQual': 20} ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AllData.bam 20 67500 . T TTGGTATCTAG . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CCTGATTTCCTTGGTATTAAA;TC=20;TR=8 GT:GL:GQ 0/1:-198.02,-21.47,-166.02:100 20 69506 . G GAC,GACACAC . PASS FR=0.5,0.5;HP=1;NF=1,3;NR=1,0;PP=44.0,72.0;SC=TGGACACGTGGACACACACAC;TC=20;TR=2,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 70484 . CTCTT C . PASS FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTCTATGTCTCTCTTTCTCTT;TC=31;TR=16 GT:GL:GQ 0/1:-189.04,-24.53,-147.47:100 20 72104 . TA T . PASS FR=0.5;HP=4;NF=9;NR=10;PP=100.0;SC=TTTAAGTCTGTAAAACCATAC;TC=39;TR=19 GT:GL:GQ 0/1:-173.69,-34.04,-169.85:100 20 74729 . G GT . PASS FR=0.5;HP=9;NF=4;NR=4;PP=100.0;SC=AAGTTTTTTGGTTTTTTTTTA;TC=29;TR=8 GT:GL:GQ 0/1:-83.86,-25.71,-59.16:100 20 117309 . G GCAGGATTTCAT . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CAGGATTTCTGCAGGATTTCA;TC=25;TR=8 GT:GL:GQ 0/1:-259.57,-46.67,-146.18:100 20 119645 . G GT . PASS FR=1.0;HP=5;NF=6;NR=5;PP=100.0;SC=TTGTTTGTTTGTTGTTGTTGT;TC=16;TR=11 GT:GL:GQ 1/1:-157.48,-18.84,-7.1:77 20 120122 . A AAG . PASS FR=1.0;HP=6;NF=10;NR=8;PP=100.0;SC=ATAAAGAAAAAAATTTTAAAA;TC=27;TR=18 GT:GL:GQ 1/1:-266.98,-24.1,-5.49:100 20 120750 . C CAATT . PASS FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TTTTATAAAACAATTGAGACT;TC=21;TR=20 GT:GL:GQ 1/1:-319.22,-18.71,-2.07:100 20 122806 . T TTA . PASS FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=CAGAAAAGAATTATATATATA;TC=29;TR=15 GT:GL:GQ 0/1:-181.3,-19.86,-96.14:100 20 126155 . GCAAA G . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=GCAATGTGCGGCAAACAAAGG;TC=32;TR=10 GT:GL:GQ 0/1:-122.73,-27.0,-209.16:100 20 126310 . ACC A . PASS FR=0.5;HP=5;NF=3;NR=8;PP=100.0;SC=GATGGCTCCTACCCCCGTTTC;TC=26;TR=11 GT:GL:GQ 0/1:-153.97,-42.91,-110.82:100 20 131505 . CTCT C . PASS FR=1.0;HP=2;NF=11;NR=11;PP=100.0;SC=TACTTGTGATCTCTTGTCTTT;TC=24;TR=22 GT:GL:GQ 1/1:-487.46,-251.24,-235.3:100 20 131948 . C CCA . PASS FR=1.0;HP=1;NF=2;NR=11;PP=100.0;SC=TTATCTTACACCACACACACA;TC=27;TR=13 GT:GL:GQ 1/1:-201.6,-36.32,-23.94:100 20 135116 . T TTTGCATTCACAGGAAGACTATAAATA . PASS FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TCTAGAGAAGTGCTCTCCAAT;TC=15;TR=3 GT:GL:GQ 1/1:-603.73,-461.77,-448.12:100 20 135119 . TC T . PASS FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=AGAGAAGTGCTCTCCAATAGA;TC=21;TR=4 GT:GL:GQ 1/1:-603.73,-576.89,-572.06:100 20 137518 . GTA G . PASS FR=0.5005;HP=2;NF=5;NR=5;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=21;TR=10 GT:GL:GQ 1/0:-210.61,-46.97,-32.7:29 20 138178 . GC G . PASS FR=1.0;HP=3;NF=21;NR=5;PP=100.0;SC=CTTCTGGAAAGCCTGGCCATG;TC=29;TR=26 GT:GL:GQ 1/1:-267.55,-29.21,-9.21:100 20 138570 . ATATGTGTGTG ATG,A . PASS FR=0.5,0.5;HP=2;NF=6,2;NR=9,2;PP=100.0,10.0;SC=TCAAATATATATATGTGTGTG;TC=28;TR=15,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:65 20 140396 . TTTG T . PASS FR=1.0;HP=2;NF=15;NR=4;PP=100.0;SC=AGGTTTTTGCTTTGTTGTTGT;TC=34;TR=19 GT:GL:GQ 1/1:-246.82,-30.67,-15.42:100 20 144832 . C CT . PASS FR=1.0;HP=3;NF=12;NR=22;PP=100.0;SC=TCCTAAAACTCTTGTAATATC;TC=35;TR=34 GT:GL:GQ 1/1:-541.89,-322.78,-299.72:100 20 144884 . CCTT C . PASS FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=TGTAATGACACCTTCTTTTTC;TC=29;TR=25 GT:GL:GQ 1/1:-590.4,-430.25,-411.02:100 20 145257 . G GC . PASS FR=1.0;HP=2;NF=11;NR=8;PP=100.0;SC=ATGGTGGCAGGGCCTGTAATC;TC=21;TR=19 GT:GL:GQ 1/1:-258.74,-106.61,-91.83:100 20 153298 . T TTC . PASS FR=1.0;HP=2;NF=13;NR=17;PP=100.0;SC=CAGGATTTCTTTGTTTTAAGA;TC=34;TR=30 GT:GL:GQ 1/1:-447.58,-228.67,-205.19:100 20 160111 . A AT . PASS FR=1.0;HP=10;NF=8;NR=9;PP=100.0;SC=GAGCTCTTGAATTTTTTTTTT;TC=25;TR=17 GT:GL:GQ 1/1:-115.49,-38.32,-28.08:85 20 163607 . A AAT . PASS FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=ACATTAAATGATTCAAATGAT;TC=31;TR=26 GT:GL:GQ 1/1:-308.34,-35.98,-14.5:100 20 163741 . T TACACAC . PASS FR=0.5243;HP=1;NF=13;NR=6;PP=100.0;SC=GAACCCTCTGTACACACACAC;TC=28;TR=19 GT:GL:GQ 0/1:-416.01,-75.48,-55.48:13 20 164279 . G GAAAAC . PASS FR=0.5;HP=8;NF=1;NR=1;PP=100.0;SC=GAAAAGAAAAGAAAAGAAAAC;TC=34;TR=2 GT:GL:GQ 0/1:-492.01,-428.61,-448.28:100 20 164284 . G GAAAAC,C . PASS FR=0.5,0.5;HP=8;NF=5,10;NR=11,9;PP=100.0,100.0;SC=GAAAAGAAAAGAAAACTCATC;TC=33;TR=16,19 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 176386 . CGTGTGT C . PASS FR=1.0;HP=2;NF=3;NR=2;PP=100.0;SC=TAATCCCATTCGTGTGTGTGT;TC=25;TR=5 GT:GL:GQ 1/1:-176.18,-68.1,-61.92:77 20 179735 . TTAAAA T . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=ACCTTTGATCTTAAAATAAAA;TC=27;TR=8 GT:GL:GQ 0/1:-142.0,-61.37,-164.64:100 20 218255 . A AG . PASS FR=0.5;HP=1;NF=5;NR=3;PP=100.0;SC=TGCTCACTGCAATAAAAAGAA;TC=17;TR=8 GT:GL:GQ 0/1:-99.61,-20.66,-85.67:100 20 222539 . C CA . PASS FR=0.5;HP=2;NF=1;NR=9;PP=100.0;SC=TACCCAGCTACTTCTCTTAAG;TC=31;TR=10 GT:GL:GQ 0/1:-113.51,-40.72,-197.06:100 20 230058 . CAT C . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=GACTCCATCTCATAAAAAAAA;TC=33;TR=8 GT:GL:GQ 0/1:-215.64,-148.07,-177.0:100 20 236459 . G GAT . PASS FR=0.5001;HP=2;NF=1;NR=1;PP=100.0;SC=TTGGAATACAGATATATATAT;TC=14;TR=2 GT:GL:GQ 0/1:-82.0,-46.74,-54.25:35 20 237649 . CAGAT C . PASS FR=0.5;HP=2;NF=1;NR=1;PP=79.0;SC=AGATAGATGACAGATAGATAG;TC=23;TR=2 GT:GL:GQ 0/1:-209.52,-180.44,-254.54:100 20 237816 . A AT . PASS FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CATTTTCATCATTTTAATAAC;TC=32;TR=11 GT:GL:GQ 0/1:-124.3,-28.61,-145.84:100 20 243223 . C CT . PASS FR=0.5;HP=1;NF=12;NR=4;PP=100.0;SC=ATCTGTGTGACTGTGATCAAA;TC=33;TR=16 GT:GL:GQ 0/1:-191.55,-34.68,-144.05:100 20 246483 . T TTAAA . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AGACTCCATCTTAAATAAATA;TC=25;TR=7 GT:GL:GQ 0/1:-110.34,-17.05,-40.1:100 20 251373 . ACTT A . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=TTGCTCCAGCACTTCTTCTGG;TC=19;TR=5 GT:GL:GQ 0/1:-99.2,-52.91,-150.48:100 20 271135 . G GC . PASS FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AAGACCGAGGGCGACCTCGAG;TC=16;TR=7 GT:GL:GQ 1/1:-163.65,-94.48,-85.08:78 20 286648 . TAAATA T . PASS FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=TCTAAATAAATAAATAAAAGG;TC=22;TR=10 GT:GL:GQ 0/1:-240.51,-100.72,-176.05:100 20 299585 . AC A . PASS FR=1.0;HP=2;NF=4;NR=7;PP=21.0;SC=ACAGGGAGAGACCTTGTCGAA;TC=14;TR=11 GT:GL:GQ 1/1:-152.36,-140.91,-138.05:46 20 334317 . TC T . PASS FR=1.0;HP=6;NF=9;NR=8;PP=100.0;SC=CCTGGATCCTTCCCCCCTTCT;TC=24;TR=17 GT:GL:GQ 1/1:-177.37,-48.79,-33.34:100 20 337392 . ACC A . PASS FR=0.5;HP=6;NF=5;NR=1;PP=100.0;SC=CCTTGTTACCACCCCTCCCTG;TC=19;TR=6 GT:GL:GQ 0/1:-91.61,-45.67,-115.7:100 20 340044 . GCAC G . PASS FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=ATGAAGGCTGGCACCACCAGT;TC=22;TR=7 GT:GL:GQ 0/1:-122.54,-28.81,-115.11:100 20 343323 . A ATG . PASS FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GATAAACAGGATGTCCACCAG;TC=23;TR=12 GT:GL:GQ 0/1:-150.99,-48.03,-125.5:100 20 346702 . AGCCTCCCAAAGGAG A . PASS FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=CACCCACCTCAGCCTCCCAAA;TC=17;TR=7 GT:GL:GQ 0/1:-191.1,-120.01,-173.49:100 20 347858 . A AAAACAAAC . PASS FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=TCCGTCTCCAAAAACAAACAA;TC=22;TR=3 GT:GL:GQ 0/1:-270.04,-201.07,-226.88:100 20 347878 . A AAAAC . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=AAAAAACAAAACAAACAAACA;TC=22;TR=3 GT:GL:GQ 0/1:-258.23,-262.98,-327.72:100 20 348365 . G GT . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=ACGGCCCATGGGATCGAATAG;TC=19;TR=9 GT:GL:GQ 0/1:-127.12,-35.07,-72.46:100 20 349321 . ACT A . PASS FR=0.5;HP=3;NF=10;NR=3;PP=100.0;SC=CCAGGCCTCCACTCTCTGCTG;TC=20;TR=13 GT:GL:GQ 0/1:-183.61,-95.19,-129.48:100 20 355549 . A AC . PASS FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=AACAACAACAAAAAAAAAAAC;TC=24;TR=21 GT:GL:GQ 1/1:-171.74,-97.15,-84.12:100 20 356670 . T TCAAA . PASS FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=AGACACTGCCTCAAAAAAACA;TC=16;TR=6 GT:GL:GQ 0/1:-204.44,-131.78,-155.8:100 20 356675 . A AAAAC . PASS FR=1.0;HP=6;NF=2;NR=3;PP=100.0;SC=CTGCCTCAAAAAAACAAACAA;TC=17;TR=5 GT:GL:GQ 1/1:-201.68,-85.68,-76.1:85 20 358147 . CA C . PASS FR=1.0;HP=4;NF=10;NR=5;PP=100.0;SC=TGGGATTTGACAAACCCAGCT;TC=18;TR=15 GT:GL:GQ 1/1:-150.87,-32.16,-20.25:100 20 360927 . TAA T . PASS FR=1.0;HP=7;NF=4;NR=7;PP=100.0;SC=ATGTGCTTTATAAAAAAGGGG;TC=18;TR=11 GT:GL:GQ 1/1:-185.94,-114.38,-104.3:84 20 380790 . C CT . PASS FR=1.0;HP=3;NF=16;NR=12;PP=100.0;SC=CACCACACCCCGACCCTAATT;TC=32;TR=28 GT:GL:GQ 1/1:-323.67,-24.71,-1.84:100 20 385989 . T TA . PASS FR=0.5;HP=7;NF=7;NR=4;PP=100.0;SC=AGATTTTTTTTAAAAAACTCT;TC=29;TR=11 GT:GL:GQ 0/1:-131.67,-23.75,-80.28:100 20 386575 . GTTCT G . PASS FR=0.5;HP=3;NF=2;NR=3;PP=100.0;SC=TGATAAGAATGTTCTTTCTTT;TC=24;TR=5 GT:GL:GQ 0/1:-109.28,-29.71,-86.14:100 20 387657 . G GA . PASS FR=1.0;HP=8;NF=13;NR=19;PP=100.0;SC=ATGCTGAGAAGAAAAAATGAA;TC=38;TR=32 GT:GL:GQ 1/1:-284.64,-52.81,-28.53:100 20 396023 . A AAAAC . PASS FR=1.0;HP=4;NF=9;NR=9;PP=100.0;SC=AAAAAAAACAAAAACAAACAA;TC=25;TR=18 GT:GL:GQ 1/1:-279.26,-33.44,-17.73:100 20 403158 . GA G . PASS FR=0.5;HP=2;NF=4;NR=7;PP=89.0;SC=ATCTATGAAGGAAGGACAGCA;TC=20;TR=11 GT:GL:GQ 0/1:-137.87,-107.23,-160.58:100 20 405057 . A AC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=AAACACATACACAGACCTCCT;TC=25;TR=9 GT:GL:GQ 0/1:-136.78,-33.82,-124.47:100 20 421805 . T TCCA . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=AGAACACATTTCCAACTAAAC;TC=29;TR=6 GT:GL:GQ 0/1:-108.14,-30.52,-185.93:100 20 425206 . GTTTT G . PASS FR=0.5;HP=7;NF=2;NR=7;PP=100.0;SC=TTGTTTGTTTGTTTTGTTTTT;TC=25;TR=9 GT:GL:GQ 0/1:-158.57,-21.01,-100.22:100 20 430158 . GA G . PASS FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=AGAGTCGCTTGAAACCCAGGA;TC=16;TR=6 GT:GL:GQ 0/1:-74.97,-35.93,-74.51:100 20 434939 . G GA . PASS FR=0.5;HP=10;NF=6;NR=2;PP=100.0;SC=AAGAAAAAAGGAAAAAAAAAA;TC=22;TR=8 GT:GL:GQ 0/1:-99.4,-65.02,-85.64:92 20 436981 . TTTCATCCA T . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=AGGTGTGTCCTTTCATCCATT;TC=27;TR=3 GT:GL:GQ 0/1:-88.19,-26.08,-154.96:100 20 525046 . G GT . PASS FR=0.5;HP=10;NF=5;NR=8;PP=100.0;SC=AAAATACAGTGTTTTTTTTTC;TC=33;TR=13 GT:GL:GQ 0/1:-160.44,-103.25,-141.37:100 20 538639 . C CA . PASS FR=1.0;HP=9;NF=14;NR=9;PP=100.0;SC=ACCACCACAACAAAAAAACCC;TC=36;TR=23 GT:GL:GQ 1/1:-261.69,-66.02,-42.16:100 20 539756 . G GT . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=AATGTGAGCAGTCTAGGTAAA;TC=24;TR=8 GT:GL:GQ 0/1:-130.62,-70.51,-165.77:100 20 540198 . T TG . PASS FR=1.0;HP=1;NF=9;NR=16;PP=100.0;SC=AGAGTCGCTGTTATTAAAACC;TC=26;TR=25 GT:GL:GQ 1/1:-262.05,-37.69,-19.11:100 20 545849 . A AT . PASS FR=1.0;HP=9;NF=6;NR=13;PP=100.0;SC=CTCTGGACTGATTTTTTTTTA;TC=24;TR=19 GT:GL:GQ 1/1:-225.47,-140.74,-126.39:100 20 555243 . C CT . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=TTGGGGCCTCCTGGGTCCCAG;TC=23;TR=7 GT:GL:GQ 0/1:-124.01,-59.66,-144.99:100 20 559298 . TACAC T . PASS FR=0.5081;HP=1;NF=1;NR=1;PP=100.0;SC=GGCACACATGTACACACACAC;TC=20;TR=2 GT:GL:GQ 0/1:-95.31,-59.31,-62.75:17 20 570945 . A AACAC . PASS FR=1.0;HP=1;NF=7;NR=2;PP=100.0;SC=AGAAGGCAATAACACACACAC;TC=28;TR=9 GT:GL:GQ 1/1:-281.44,-73.27,-58.53:100 20 576287 . T TTTA . PASS FR=1.0;HP=3;NF=2;NR=9;PP=100.0;SC=CTGGAAAAGTTTTATTATTAT;TC=26;TR=11 GT:GL:GQ 1/1:-188.46,-27.21,-14.74:100 20 593205 . AG A . PASS FR=0.5;HP=6;NF=2;NR=2;PP=100.0;SC=GGGAGTGCGGAGGGGACTCCT;TC=14;TR=4 GT:GL:GQ 0/1:-90.79,-21.16,-46.9:100 20 635817 . C CAGAAAAAAA . PASS FR=1.0;HP=1;NF=6;NR=7;PP=100.0;SC=GAGACTCTCTCAGAAAAAAAA;TC=23;TR=13 GT:GL:GQ 1/1:-318.1,-28.61,-13.35:100 20 666340 . AAATAATAATAAT AAATAAT,A . PASS FR=0.5,0.5;HP=2;NF=1,2;NR=3,3;PP=100.0,100.0;SC=ATACAAATACAAATAATAATA;TC=16;TR=4,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 671463 . AGTGT A . PASS FR=1.0;HP=1;NF=6;NR=2;PP=100.0;SC=CATGCATGCAAGTGTGTGTGT;TC=25;TR=8 GT:GL:GQ 1/1:-248.41,-147.67,-140.04:63 20 675799 . G GTA . PASS FR=0.5;HP=2;NF=7;NR=3;PP=100.0;SC=TAATGAACATGTATATATACA;TC=20;TR=10 GT:GL:GQ 0/1:-154.12,-35.67,-66.33:100 20 704073 . CTCT C . PASS FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=CTTCATTCTTCTCTTTTCTTT;TC=20;TR=6 GT:GL:GQ 0/1:-159.89,-91.96,-171.96:100 20 704111 . C CTTTCT . PASS FR=0.5;HP=4;NF=2;NR=3;PP=100.0;SC=TTCCTCCTCTCTTTGTCTAGT;TC=20;TR=5 GT:GL:GQ 0/1:-189.74,-115.92,-237.08:100 20 714136 . TA T . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTGTGGTTGTTAACTGTAGTC;TC=30;TR=25 GT:GL:GQ 1/1:-253.68,-26.24,-6.67:100 20 715254 . G GGT,GGTGTGT . PASS FR=0.5,0.5;HP=1;NF=3,4;NR=0,1;PP=57.0,100.0;SC=ATAGTTTATAGGTGTGTGTGT;TC=23;TR=3,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 715847 . C CA . PASS FR=1.0;HP=7;NF=10;NR=6;PP=100.0;SC=GGCTCCGTCTCAAAAAAATAA;TC=26;TR=16 GT:GL:GQ 1/1:-157.25,-40.0,-26.17:100 20 718268 . A AAATAAT . PASS FR=0.5;HP=3;NF=1;NR=1;PP=81.0;SC=AAAAAATACAAAATAATAATA;TC=15;TR=2 GT:GL:GQ 0/1:-64.86,-29.69,-87.73:100 20 724447 . A AG . PASS FR=0.5;HP=2;NF=12;NR=9;PP=100.0;SC=GGGTGTTGTGAGACTGATTGA;TC=42;TR=21 GT:GL:GQ 0/1:-229.53,-40.83,-188.06:100 20 726275 . CAGA C . PASS FR=0.5;HP=3;NF=10;NR=10;PP=100.0;SC=ACATATATAACAGAAGGAGAG;TC=41;TR=20 GT:GL:GQ 0/1:-286.26,-52.94,-197.08:100 20 728851 . CT C . PASS FR=0.5;HP=1;NF=5;NR=1;PP=21.0;SC=GATCACACCACTGCAGTCCAG;TC=22;TR=6 GT:GL:GQ 0/1:-200.76,-185.85,-212.48:67 20 732117 . CTTTATTTTAT C . PASS FR=0.9998;HP=4;NF=1;NR=1;PP=80.0;SC=TCAGGTATGTCTTTATTTTAT;TC=14;TR=2 GT:GL:GQ 1/1:-96.6,-68.07,-66.69:34 20 739616 . CGTGTGTGT C . PASS FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=TAAAAGTGCTCGTGTGTGTGT;TC=20;TR=8 GT:GL:GQ 1/1:-222.59,-24.43,-16.81:63 20 744662 . A ACAGGTCAAT . PASS FR=0.5;HP=1;NF=3;NR=4;PP=100.0;SC=AAAGGACAAGACAGATCCCTG;TC=16;TR=7 GT:GL:GQ 0/1:-105.45,-32.23,-150.03:100 20 746855 . A AG . PASS FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CTGGGATTACAGTGTGAGCCA;TC=22;TR=14 GT:GL:GQ 1/1:-242.45,-177.27,-167.62:80 20 747680 . A ATAG . PASS FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=CTTGTTGGTAATAGCAAGTTA;TC=17;TR=6 GT:GL:GQ 0/1:-177.8,-96.72,-120.09:100 20 755106 . C CA . PASS FR=1.0;HP=3;NF=7;NR=15;PP=100.0;SC=GCTGAGAGGTCAAACCACAAA;TC=27;TR=22 GT:GL:GQ 1/1:-255.81,-41.84,-23.33:100 20 757564 . T TG . PASS FR=0.5;HP=3;NF=3;NR=1;PP=78.0;SC=GGTGGAGCCATGGGTGTCAAA;TC=10;TR=4 GT:GL:GQ 0/1:-67.44,-38.36,-58.29:89 20 757919 . A AC . PASS FR=0.5;HP=9;NF=3;NR=9;PP=100.0;SC=AAAAAACAAAAAAAAAACACC;TC=27;TR=12 GT:GL:GQ 0/1:-172.2,-112.42,-144.61:100 20 762893 . G GA . PASS FR=1.0;HP=6;NF=8;NR=9;PP=100.0;SC=TCTTGGGGGGGAAAAAATGGG;TC=24;TR=17 GT:GL:GQ 1/1:-215.19,-64.36,-48.0:100 20 782496 . CAAATAAAT C . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=GACTCTGCCTCAAATAAATAA;TC=17;TR=3 GT:GL:GQ 0/1:-87.5,-27.65,-92.5:100 20 786252 . AAG A . PASS FR=1.0;HP=5;NF=4;NR=13;PP=100.0;SC=TTAATTAAAAAAGATATTGCA;TC=19;TR=17 GT:GL:GQ 1/1:-216.25,-31.31,-17.45:100 20 786764 . T TA . PASS FR=1.0;HP=3;NF=17;NR=12;PP=100.0;SC=ACTATATATATAATATATTTT;TC=33;TR=29 GT:GL:GQ 1/1:-388.27,-147.23,-125.36:100 20 787870 . T TTTTATTTATTTATTTATTTA . PASS FR=1.0;HP=3;NF=2;NR=1;PP=100.0;SC=ATATCAAGCATTTTATTTATT;TC=19;TR=3 GT:GL:GQ 1/1:-317.88,-65.36,-53.59:99 20 787893 . T TATTTATTTA . PASS FR=0.5;HP=4;NF=1;NR=1;PP=100.0;SC=TTTATTTATTTTTGAGATGGA;TC=20;TR=2 GT:GL:GQ 0/1:-356.98,-227.18,-263.76:5 20 789767 . T TA . PASS FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CAAAGCCAATTAAAAAAAAAA;TC=29;TR=13 GT:GL:GQ 1/1:-124.57,-44.47,-30.25:100 20 795148 . T TTTTA . PASS FR=1.0;HP=4;NF=9;NR=1;PP=100.0;SC=ATAAGTTTATTTTTATTTATT;TC=16;TR=10 GT:GL:GQ 1/1:-136.44,-12.46,-4.83:63 20 797336 . GA G . PASS FR=1.0;HP=10;NF=18;NR=11;PP=100.0;SC=CCATTTATGTGAAAAAAAAAA;TC=35;TR=29 GT:GL:GQ 1/1:-156.82,-42.02,-20.72:100 20 801157 . T TTTC . PASS FR=1.0;HP=6;NF=1;NR=6;PP=100.0;SC=CTTCTCTTTCTTTTTTTCTTT;TC=13;TR=7 GT:GL:GQ 1/1:-142.57,-41.24,-32.92:92 20 825082 . TGCCCAGGTC T . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CTGCTCAGGTTGCCCAGGTCG;TC=8;TR=6 GT:GL:GQ 1/0:-180.72,-60.67,-71.61:61 20 833239 . ACT A . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=GGAGAAATAGACTCTCTCTCT;TC=21;TR=8 GT:GL:GQ 0/1:-96.13,-31.34,-89.12:100 20 835500 . TTGTG T . PASS FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GTGTTTGTGTTTGTGTGTGTG;TC=29;TR=10 GT:GL:GQ 1/1:-258.26,-62.01,-52.79:77 20 855678 . TC T . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=TCTTTTTCTTTCTTTTTTTTC;TC=28;TR=8 GT:GL:GQ 0/1:-124.38,-62.93,-124.85:100 20 860945 . A AG . PASS FR=0.5;HP=6;NF=2;NR=6;PP=100.0;SC=GTATATTAAGAGGGGGTGAAA;TC=23;TR=8 GT:GL:GQ 0/1:-96.52,-33.16,-85.46:100 20 863148 . C CTAT . PASS FR=0.5;HP=2;NF=3;NR=12;PP=100.0;SC=CCAGAGAAGGCTATTGCTCTC;TC=37;TR=15 GT:GL:GQ 0/1:-223.19,-48.7,-208.9:100 20 899789 . CTCTT C . PASS FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=TTTCCTTCTTCTCTTTCTTTC;TC=21;TR=4 GT:GL:GQ 0/1:-62.34,-23.94,-85.48:100 20 900698 . T TC . PASS FR=1.0;HP=4;NF=11;NR=5;PP=100.0;SC=AGGAAGGCAGTCCCCTTTCCT;TC=29;TR=16 GT:GL:GQ 1/1:-292.54,-113.13,-95.49:100 20 902060 . T TG,G . PASS FR=0.5,0.5;HP=5;NF=2,7;NR=2,4;PP=100.0,100.0;SC=TTGACTGCCCTCCTCCACTTT;TC=19;TR=4,11 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 909945 . TTATGG TTGG,T . PASS FR=0.5,0.5;HP=2;NF=10,8;NR=5,5;PP=100.0,100.0;SC=TTAGTTTAGTTTATGGTATCC;TC=32;TR=15,13 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 913303 . A AT . PASS FR=1.0;HP=10;NF=9;NR=4;PP=100.0;SC=AGATTTAAAGATTTTTTTTTT;TC=21;TR=13 GT:GL:GQ 1/1:-227.97,-180.37,-171.35:75 20 922916 . A AT . PASS FR=1.0;HP=6;NF=2;NR=1;PP=27.0;SC=TTATTTATTTATTTATTTTTT;TC=7;TR=3 GT:GL:GQ 1/1:-68.71,-54.63,-52.11:41 20 933970 . GTTAT G . PASS FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=CAGGCTAATTGTTATTTATTT;TC=24;TR=10 GT:GL:GQ 1/1:-169.08,-10.86,-0.46:87 20 934153 . A AT . PASS FR=1.0;HP=7;NF=4;NR=5;PP=100.0;SC=ATTTTTTTGTATTTTTTAATA;TC=11;TR=9 GT:GL:GQ 1/1:-123.08,-66.05,-59.03:57 20 945474 . CAT C . PASS FR=1.0;HP=2;NF=2;NR=6;PP=100.0;SC=CACACACACACATATATATAT;TC=31;TR=8 GT:GL:GQ 1/1:-229.9,-58.37,-41.73:100 20 954102 . A ATTGT . PASS FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TGTTTGTTTTATTGTTTGTTT;TC=30;TR=5 GT:GL:GQ 0/1:-77.28,-28.19,-134.91:100 20 972071 . A AT . PASS FR=0.5;HP=8;NF=7;NR=5;PP=100.0;SC=ATTAAAAAAGATTTTTTTTGT;TC=27;TR=12 GT:GL:GQ 0/1:-76.99,-19.47,-57.49:100 20 995685 . CAAAT C . PASS FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AACTCTATCTCAAATAAATAA;TC=15;TR=5 GT:GL:GQ 1/1:-96.06,-12.82,-6.68:77 20 1000562 . TTTCA T . PASS FR=0.5;HP=2;NF=10;NR=1;PP=100.0;SC=TCACCCTTTCTTTCATTCACT;TC=23;TR=11 GT:GL:GQ 0/1:-127.76,-31.92,-110.25:100 20 1005659 . CTCAG C . PASS FR=1.0;HP=3;NF=15;NR=6;PP=100.0;SC=AACAAACAAACTCAGTCTGTC;TC=34;TR=21 GT:GL:GQ 1/1:-379.32,-49.71,-26.34:100 20 1018266 . CAAT C . PASS FR=1.0;HP=4;NF=10;NR=7;PP=100.0;SC=GAAGTAACAACAATAATAATA;TC=26;TR=17 GT:GL:GQ 1/1:-307.78,-61.51,-42.82:100 20 1023817 . C CCCT . PASS FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=CAGTGCCCACCCCTCCTCTCC;TC=22;TR=10 GT:GL:GQ 1/1:-230.45,-50.55,-37.14:100 20 1024121 . A AT . PASS FR=1.0;HP=6;NF=5;NR=3;PP=100.0;SC=CGGGTCAGGCATTTTTTATCA;TC=16;TR=8 GT:GL:GQ 1/1:-95.55,-28.09,-20.26:65 20 1042261 . CCCTG C . PASS FR=1.0;HP=2;NF=10;NR=10;PP=100.0;SC=CCAAACCCAACCCTGCCTGGC;TC=25;TR=20 GT:GL:GQ 1/1:-365.29,-133.94,-117.57:100 20 1050585 . AT A . PASS FR=1.0;HP=10;NF=9;NR=15;PP=100.0;SC=TTCTAATTCCATTTTTTTTTT;TC=33;TR=24 GT:GL:GQ 1/1:-288.37,-205.98,-189.27:100 20 1059991 . G GAATT . PASS FR=1.0;HP=2;NF=10;NR=6;PP=100.0;SC=AACATTTGTTGAATTAATTAA;TC=25;TR=16 GT:GL:GQ 1/1:-290.89,-32.75,-16.81:100 20 1072882 . CAG C . PASS FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=ATCAGAAAAACAGAGACCACA;TC=23;TR=11 GT:GL:GQ 0/1:-124.42,-26.5,-135.46:100 20 1084744 . TG T . PASS FR=1.0;HP=5;NF=9;NR=12;PP=100.0;SC=ACCATAAATGTGGGGCTACTG;TC=23;TR=21 GT:GL:GQ 1/1:-326.86,-192.89,-179.07:100 20 1100621 . TAG T . PASS FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=GCTTCTCAAATAGAGTCTTAA;TC=23;TR=9 GT:GL:GQ 0/1:-166.5,-71.13,-124.84:100 20 1105206 . C CAT . PASS FR=1.0;HP=1;NF=15;NR=11;PP=100.0;SC=AATTTATCCACGTGTACCAGA;TC=32;TR=26 GT:GL:GQ 1/1:-427.57,-192.92,-171.28:100 20 1114638 . C CTCTT . PASS FR=1.0;HP=4;NF=9;NR=17;PP=100.0;SC=TGTGTCCTCTCTTTGTATTTG;TC=34;TR=26 GT:GL:GQ 1/1:-420.88,-72.2,-49.92:100 20 1118278 . GAA G . PASS FR=1.0;HP=5;NF=13;NR=8;PP=100.0;SC=AGAAAAGGGAGAAAAGGAGGC;TC=24;TR=21 GT:GL:GQ 1/1:-206.9,-16.17,-0.92:100 20 1127807 . TCATCATCATCATCAC T . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=ATCATCATCATCATCATCATC;TC=18;TR=5 GT:GL:GQ 1/0:-246.11,-143.41,-171.3:100 20 1133620 . GC G . PASS FR=1.0;HP=3;NF=17;NR=8;PP=100.0;SC=TAAGGACCAAGCCCTGTTTAT;TC=28;TR=25 GT:GL:GQ 1/1:-266.52,-52.99,-34.3:100 20 1162839 . AG A . PASS FR=0.5;HP=10;NF=1;NR=6;PP=100.0;SC=GGGGTGGGGGAGGGGGTAGAA;TC=27;TR=7 GT:GL:GQ 0/1:-154.34,-117.72,-158.43:100 20 1165265 . TACAC T . PASS FR=1.0;HP=1;NF=2;NR=1;PP=100.0;SC=CACACGCGCGTACACACACAC;TC=13;TR=3 GT:GL:GQ 1/1:-65.7,-24.93,-20.64:52 20 1168799 . T TAC . PASS FR=0.5;HP=3;NF=1;NR=3;PP=100.0;SC=ATATATATAATACACACACAC;TC=33;TR=4 GT:GL:GQ 0/1:-146.28,-74.63,-149.77:100 20 1194678 . A AT . PASS FR=1.0;HP=8;NF=13;NR=12;PP=100.0;SC=TACAAGATTAATTTTTTTTGT;TC=37;TR=25 GT:GL:GQ 1/1:-428.37,-300.25,-279.55:89 20 1195705 . AAAG A . PASS FR=1.0;HP=2;NF=10;NR=12;PP=100.0;SC=AGAGATGGCCAAAGAAGACAT;TC=27;TR=22 GT:GL:GQ 1/1:-481.8,-237.54,-219.64:100 20 1200593 . GA G . PASS FR=0.5;HP=5;NF=7;NR=5;PP=100.0;SC=TTTTTTAAAAGATCAACAAAA;TC=31;TR=12 GT:GL:GQ 0/1:-291.7,-258.36,-302.47:100 20 1202056 . C CT . PASS FR=0.5;HP=6;NF=2;NR=1;PP=73.0;SC=TTCTTTCTTTCTTTCTTTCTT;TC=17;TR=3 GT:GL:GQ 0/1:-78.02,-50.24,-96.3:100 20 1217230 . C CT . PASS FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=TGAATCTGAACTTTCTCTATT;TC=29;TR=13 GT:GL:GQ 0/1:-136.34,-37.11,-139.78:100 20 1238533 . TATC T . PASS FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=ATTCCCTTATTATCCTTTTAA;TC=32;TR=14 GT:GL:GQ 0/1:-203.0,-27.66,-145.09:100 20 1258183 . GTGTC G . PASS FR=0.5;HP=2;NF=9;NR=7;PP=100.0;SC=CTGTGCATGTGTGTCTGTGTG;TC=40;TR=16 GT:GL:GQ 0/1:-393.66,-270.04,-334.02:100 20 1258199 . C CTG . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=GTGTGTGTATCTGTGTGTGTG;TC=39;TR=18 GT:GL:GQ 1/1:-443.43,-273.82,-255.93:100 20 1258268 . C CTG . PASS FR=1.0;HP=1;NF=14;NR=7;PP=100.0;SC=GTATGTGTGCCTGTGTGTGTG;TC=36;TR=21 GT:GL:GQ 1/1:-385.28,-210.98,-205.13:73 20 1258437 . GTGTGCCTGTGTGTGTC G . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=GCCTGTGTATGTGTGCCTGTG;TC=40;TR=7 GT:GL:GQ 0/1:-300.85,-170.75,-363.46:100 20 1258704 . C CTGTT . PASS FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=GTGTGTGTGTCTGTGTGTGTA;TC=34;TR=9 GT:GL:GQ 0/1:-182.12,-58.28,-233.67:100 20 1270442 . CA C . PASS FR=1.0;HP=2;NF=5;NR=12;PP=100.0;SC=CACTGCACTCCAAGCCTAGGT;TC=17;TR=17 GT:GL:GQ 1/1:-162.61,-26.2,-14.46:98 20 1272295 . CTCTGT C . PASS FR=1.0;HP=1;NF=13;NR=7;PP=100.0;SC=CCAAGTTCTGCTCTGTTGATT;TC=25;TR=20 GT:GL:GQ 1/1:-389.78,-103.27,-85.17:100 20 1272815 . C CATAG . PASS FR=1.0;HP=2;NF=11;NR=10;PP=100.0;SC=TAGTCTAAGGCATAGCATCCT;TC=27;TR=21 GT:GL:GQ 1/1:-368.78,-50.48,-32.46:100 20 1291149 . GCAA G . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGGATACAGCAACAACAGT;TC=25;TR=5 GT:GL:GQ 0/1:-151.35,-93.7,-185.23:100 20 1292033 . C CTTGT . PASS FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=CTTACATTTGCTTGTTTGATA;TC=29;TR=12 GT:GL:GQ 0/1:-444.32,-314.49,-337.3:100 20 1292718 . GT G . PASS FR=1.0;HP=8;NF=9;NR=3;PP=100.0;SC=TAATTTTTTAGTTTTTTTTGT;TC=17;TR=12 GT:GL:GQ 1/1:-140.26,-85.11,-76.3:73 20 1292776 . T TA . PASS FR=1.0;HP=1;NF=14;NR=10;PP=100.0;SC=CTCCTGGACTTAGTGATCCTC;TC=25;TR=24 GT:GL:GQ 1/1:-310.19,-119.02,-102.21:100 20 1303648 . A AG . PASS FR=0.5;HP=4;NF=6;NR=2;PP=100.0;SC=GGCAACACTCACCCGGCTGAG;TC=19;TR=8 GT:GL:GQ 0/1:-115.57,-32.83,-76.0:100 20 1312294 . A AT . PASS FR=1.0;HP=7;NF=5;NR=6;PP=100.0;SC=CACCTGGCTAATTTTTTTATT;TC=17;TR=11 GT:GL:GQ 1/1:-196.82,-109.27,-98.21:93 20 1318554 . TCCCACAGAGAAGTCC T . PASS FR=1.0;HP=3;NF=5;NR=4;PP=100.0;SC=ACCTAAGCATTCCCACAGAGA;TC=12;TR=9 GT:GL:GQ 1/1:-228.16,-15.45,-7.14:62 20 1322791 . G GCACACA,GCACACACA . PASS FR=0.5,0.5;HP=1;NF=3,3;NR=0,4;PP=43.0,100.0;SC=GAGAACAAATGCACACACACA;TC=18;TR=3,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 1333430 . C CT . PASS FR=1.0;HP=2;NF=18;NR=9;PP=100.0;SC=ATGAAGGTGACTTCTCAGGTG;TC=32;TR=27 GT:GL:GQ 1/1:-276.34,-27.55,-7.09:100 20 1342649 . AT A . PASS FR=1.0;HP=6;NF=17;NR=10;PP=100.0;SC=AGTGTATGAGATTTTTTGTTA;TC=29;TR=27 GT:GL:GQ 1/1:-209.72,-24.22,-4.14:100 20 1349439 . C CCCT . PASS FR=0.5;HP=4;NF=2;NR=6;PP=100.0;SC=CCCACATTCCCCCTCCTCTGA;TC=22;TR=8 GT:GL:GQ 0/1:-157.47,-56.31,-133.86:100 20 1358694 . C CAGTTTGGGCACTAACACCTACTT . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CTATACGGGTCAGTTTGGGCA;TC=19;TR=5 GT:GL:GQ 0/1:-272.45,-105.91,-212.24:100 20 1364390 . G GA . PASS FR=1.0;HP=2;NF=9;NR=6;PP=100.0;SC=GATCAAGTGGGAGATCACTTG;TC=25;TR=15 GT:GL:GQ 1/1:-334.68,-154.31,-139.66:100 20 1369478 . CG C . PASS FR=0.5;HP=2;NF=7;NR=4;PP=100.0;SC=TAAAAACCAACGAGGCTCCAC;TC=23;TR=11 GT:GL:GQ 0/1:-184.87,-113.86,-180.77:100 20 1372404 . GA G . PASS FR=1.0;HP=7;NF=8;NR=5;PP=100.0;SC=GAGGGAGTGGGAAAAAAAGAG;TC=17;TR=13 GT:GL:GQ 1/1:-147.21,-77.38,-68.31:75 20 1379453 . C CTG . PASS FR=1.0;HP=2;NF=4;NR=11;PP=100.0;SC=TGCCAGGACTCTCCTCGCTGT;TC=19;TR=15 GT:GL:GQ 1/1:-192.19,-47.83,-35.2:100 20 1381135 . AG A . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=CTTGAGGACAAGGCATTATAG;TC=26;TR=8 GT:GL:GQ 0/1:-99.07,-46.56,-212.4:100 20 1386382 . AGAG A . PASS FR=0.5;HP=3;NF=7;NR=1;PP=100.0;SC=ACTAATTAAAAGAGAACCCTG;TC=26;TR=8 GT:GL:GQ 0/1:-184.22,-117.09,-276.56:100 20 1389225 . CGTGTGT C . PASS FR=1.0;HP=1;NF=1;NR=1;PP=100.0;SC=TATGAAGACTCGTGTGTGTGT;TC=12;TR=2 GT:GL:GQ 1/1:-80.8,-37.12,-33.18:48 20 1392633 . AT A . PASS FR=0.5;HP=9;NF=8;NR=5;PP=100.0;SC=AAGCCAACACATTTTTTTTTC;TC=29;TR=13 GT:GL:GQ 0/1:-142.17,-103.31,-156.4:100 20 1399660 . A AAAAAC . PASS FR=0.5;HP=2;NF=1;NR=7;PP=100.0;SC=TGTTTATGTTAGAAACAAAAC;TC=28;TR=8 GT:GL:GQ 0/1:-237.24,-123.87,-245.2:100 20 1401887 . T TC . PASS FR=0.5;HP=6;NF=3;NR=5;PP=100.0;SC=TGACTTTTTTTCTCCCTGAGA;TC=26;TR=8 GT:GL:GQ 0/1:-140.81,-26.64,-103.7:100 20 1403888 . G GT . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=CAGAGAGGGCGTAAGATTGGA;TC=18;TR=8 GT:GL:GQ 0/1:-134.33,-94.6,-144.84:100 20 1411174 . G GT . PASS FR=1.0;HP=1;NF=14;NR=18;PP=100.0;SC=TTCCAACAGTGACAAGGGTTT;TC=34;TR=32 GT:GL:GQ 1/1:-370.91,-42.86,-18.85:100 20 1411544 . TG T . PASS FR=0.5;HP=4;NF=7;NR=2;PP=36.0;SC=ATTTATAAAATGTTTTTGTTG;TC=28;TR=9 GT:GL:GQ 0/1:-275.92,-257.59,-310.84:82 20 1420200 . CT C . PASS FR=1.0;HP=2;NF=13;NR=7;PP=100.0;SC=AAGATGGAACCTTAAGTTCAA;TC=24;TR=20 GT:GL:GQ 1/1:-229.24,-45.08,-29.19:100 20 1421627 . GC G . PASS FR=1.0;HP=4;NF=12;NR=6;PP=100.0;SC=GGAGCCCAACGCCCATTTAAA;TC=24;TR=18 GT:GL:GQ 1/1:-219.35,-32.03,-15.65:100 20 1428402 . A ATCTAT . PASS FR=0.5;HP=2;NF=6;NR=3;PP=100.0;SC=AATAGCTGATATCAGTTAAGG;TC=30;TR=9 GT:GL:GQ 0/1:-414.87,-348.43,-419.1:100 20 1428454 . TC T . PASS FR=0.5;HP=2;NF=11;NR=7;PP=100.0;SC=TTACACCGACTCTGTGCAGGT;TC=37;TR=18 GT:GL:GQ 0/1:-456.05,-415.06,-465.1:100 20 1448428 . AC A . PASS FR=1.0;HP=2;NF=12;NR=6;PP=100.0;SC=ACGGTAAACAACCTTCCCGCG;TC=21;TR=18 GT:GL:GQ 1/1:-289.43,-190.83,-179.1:98 20 1450561 . A AAATAAT . PASS FR=1.0;HP=8;NF=6;NR=4;PP=100.0;SC=CTGTCTCAAAAAAAAATAATA;TC=23;TR=10 GT:GL:GQ 1/1:-324.02,-170.06,-160.02:94 20 1454025 . GCACACACGCA G . PASS FR=1.0;HP=1;NF=5;NR=3;PP=100.0;SC=ACGCACACATGCACACACGCA;TC=23;TR=8 GT:GL:GQ 1/1:-298.98,-49.31,-43.52:72 20 1455718 . AC A . PASS FR=0.5;HP=8;NF=5;NR=3;PP=100.0;SC=TGGTGGTAGCACCCCCCCAGG;TC=26;TR=8 GT:GL:GQ 0/1:-122.23,-68.33,-113.23:100 20 1466298 . C CCA . PASS FR=0.5;HP=1;NF=3;NR=2;PP=100.0;SC=CACACACACACCACACACACA;TC=25;TR=5 GT:GL:GQ 0/1:-174.97,-31.68,-40.82:42 20 1470727 . TG T . PASS FR=1.0;HP=4;NF=9;NR=10;PP=100.0;SC=CAACAATCATTGGGGAATATT;TC=24;TR=19 GT:GL:GQ 1/1:-243.08,-66.7,-50.7:100 20 1473489 . ATAATT A . PASS FR=0.5;HP=2;NF=13;NR=9;PP=100.0;SC=TTACTTACAAATAATTTTATT;TC=35;TR=22 GT:GL:GQ 0/1:-297.03,-26.79,-121.41:100 20 1475430 . C CTCT . PASS FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CTCATTTCTTCTCTTTTCATT;TC=31;TR=12 GT:GL:GQ 0/1:-179.5,-26.21,-143.42:100 20 1477952 . AGTCTACACGT A . PASS FR=0.5;HP=1;NF=1;NR=2;PP=100.0;SC=TTGTCTTTTCAGTCTACACGT;TC=26;TR=3 GT:GL:GQ 0/1:-132.31,-83.49,-272.8:100 20 1485444 . TGAGAGAGA T . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGAGAGAGA;TC=17;TR=3 GT:GL:GQ 1/0:-294.27,-239.82,-244.87:100 20 1498426 . G GA . PASS FR=1.0;HP=6;NF=18;NR=13;PP=100.0;SC=TACAACGGAAGAAAAGCCTAA;TC=33;TR=31 GT:GL:GQ 1/1:-335.62,-79.86,-57.15:100 20 1499276 . TGAGA T . PASS FR=0.5;HP=2;NF=4;NR=2;PP=100.0;SC=TCAAAGTGAATGAGAGAGAGG;TC=23;TR=6 GT:GL:GQ 0/1:-190.39,-128.87,-245.46:100 20 1500650 . A AG . PASS FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=AAGGAGCAGCAGTTCTGAGAG;TC=19;TR=17 GT:GL:GQ 1/1:-187.24,-32.97,-19.25:100 20 1510246 . CA C . PASS FR=1.0;HP=10;NF=15;NR=6;PP=100.0;SC=AACTCTGTCTCAAAAAAAAAA;TC=29;TR=21 GT:GL:GQ 1/1:-113.89,-25.37,-8.27:100 20 1510966 . C CTA . PASS FR=1.0;HP=2;NF=10;NR=3;PP=100.0;SC=TTTTATCTCTCTGTGTCATTT;TC=21;TR=13 GT:GL:GQ 1/1:-215.34,-14.55,0.0:100 20 1512623 . TTGTC T . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=ACTCCATAGATTGTCTGGGTA;TC=27;TR=9 GT:GL:GQ 0/1:-204.17,-64.36,-220.46:100 20 1516154 . A AAG . PASS FR=0.5;HP=1;NF=9;NR=1;PP=100.0;SC=GTTTTATAAGAAGAGAGAGAG;TC=28;TR=10 GT:GL:GQ 0/1:-197.81,-103.51,-159.44:100 20 1524117 . G GTGA . PASS FR=1.0;HP=2;NF=12;NR=14;PP=100.0;SC=TGGGATCAGGGTATTCCCTTC;TC=27;TR=26 GT:GL:GQ 1/1:-368.49,-35.51,-15.43:100 20 1525024 . CT C . PASS FR=0.5;HP=7;NF=3;NR=3;PP=96.0;SC=CCTTCTTTGTCTTTTTTGATC;TC=18;TR=6 GT:GL:GQ 0/1:-53.12,-20.94,-98.55:100 20 1525853 . G GT . PASS FR=0.5;HP=5;NF=7;NR=4;PP=100.0;SC=CCTGAAGTGTGTTTTCCAACT;TC=29;TR=11 GT:GL:GQ 0/1:-133.05,-52.13,-148.67:100 20 1597255 . TG T . PASS FR=0.5;HP=2;NF=13;NR=3;PP=100.0;SC=GTAAAAGTACTGGAAGAAAAG;TC=39;TR=16 GT:GL:GQ 0/1:-269.31,-182.14,-334.79:100 20 1627288 . ATTTGT A . PASS FR=0.5;HP=3;NF=4;NR=2;PP=100.0;SC=ACTTTTTTTCATTTGTTTTGT;TC=20;TR=6 GT:GL:GQ 0/1:-133.15,-70.66,-175.26:100 20 1629280 . T TAATAAAATAA . PASS FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=ACTTAAAGTATAATAAAATAA;TC=18;TR=5 GT:GL:GQ 0/1:-155.63,-27.66,-95.67:100 20 1648829 . CTTTCTTTTTCTTTTCT C . PASS FR=0.5;HP=6;NF=1;NR=1;PP=74.0;SC=TTCTTTCTTTCTTTCTTTTTC;TC=20;TR=2 GT:GL:GQ 0/1:-191.4,-160.88,-232.59:100 20 1653387 . T TTTG . PASS FR=0.5;HP=2;NF=2;NR=7;PP=100.0;SC=CGGCCAATCATTTGTTGTTGT;TC=25;TR=9 GT:GL:GQ 0/1:-189.9,-54.75,-106.65:100 20 1656519 . GT G . PASS FR=0.5;HP=9;NF=4;NR=5;PP=100.0;SC=GAGCTGCACTGTTTTTTTTCT;TC=20;TR=9 GT:GL:GQ 0/1:-62.34,-19.97,-47.7:100 20 1658890 . ACT A . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=CATGTGATACACTGTGGGCCC;TC=27;TR=8 GT:GL:GQ 0/1:-198.65,-163.08,-324.51:100 20 1660493 . AT A . PASS FR=0.5;HP=1;NF=6;NR=5;PP=100.0;SC=CATTTGGGAGATGCTATTACC;TC=31;TR=11 GT:GL:GQ 0/1:-160.86,-59.8,-177.36:100 20 1661355 . TG T . PASS FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=GAAAAACACATGATTATCCAT;TC=34;TR=13 GT:GL:GQ 0/1:-171.31,-99.84,-269.81:100 20 1661478 . G GT . PASS FR=0.5;HP=9;NF=7;NR=5;PP=100.0;SC=ATACTTTCTTGTTTTTTTGGC;TC=35;TR=12 GT:GL:GQ 0/1:-150.06,-61.16,-108.32:100 20 1661816 . C CA . PASS FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=AATTTGCAATCATACAGAAAG;TC=24;TR=7 GT:GL:GQ 0/1:-96.53,-29.07,-136.56:100 20 1662592 . GATATAACTA G . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=TATGGATATGGATATAACTAA;TC=23;TR=9 GT:GL:GQ 0/1:-238.09,-62.84,-220.35:100 20 1665050 . A ATG . PASS FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=ATACACACATATATATATGTA;TC=34;TR=12 GT:GL:GQ 0/1:-151.91,-67.61,-244.28:100 20 1667770 . TG T . PASS FR=0.5;HP=6;NF=5;NR=5;PP=100.0;SC=AGGGTTATGATGGGGGGAGAA;TC=29;TR=10 GT:GL:GQ 0/1:-75.51,-17.52,-115.09:100 20 1674714 . A AT . PASS FR=1.0;HP=6;NF=12;NR=9;PP=100.0;SC=AAGGAGAATCATTTTTTCTTA;TC=26;TR=21 GT:GL:GQ 1/1:-198.16,-29.36,-11.98:100 20 1679689 . TACACAC TACACACACAC,T . PASS FR=0.5,0.5;HP=3;NF=2,1;NR=0,1;PP=100.0,100.0;SC=TTAGATGCCCTACACACACAC;TC=23;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 1680048 . G GA . PASS FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=GAAAACAACAGAAAAAAAACT;TC=30;TR=13 GT:GL:GQ 0/1:-157.3,-90.19,-130.66:100 20 1680109 . GA G . PASS FR=0.5;HP=4;NF=9;NR=8;PP=100.0;SC=AACAGCAAGAGAAATTATAAA;TC=32;TR=17 GT:GL:GQ 0/1:-210.03,-97.05,-217.17:100 20 1682621 . A AT . PASS FR=1.0;HP=3;NF=18;NR=11;PP=100.0;SC=AATATATCATATTACACAGTG;TC=31;TR=29 GT:GL:GQ 1/1:-304.45,-32.07,-10.59:100 20 1683112 . T TC . PASS FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=CAAACCCTCTTCCTATACCAC;TC=23;TR=17 GT:GL:GQ 1/1:-265.19,-181.47,-172.55:74 20 1683153 . CA C . PASS FR=0.5;HP=2;NF=5;NR=7;PP=100.0;SC=GCAGCAGCTGCAAGAAGTCTC;TC=22;TR=12 GT:GL:GQ 0/1:-291.99,-237.27,-279.09:100 20 1683250 . ATAGCTCTACCAGT A . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AGTTCGAATCATAGCTCTACC;TC=22;TR=9 GT:GL:GQ 0/1:-267.9,-88.45,-154.18:100 20 1683813 . C CT . PASS FR=0.5;HP=6;NF=12;NR=13;PP=100.0;SC=AAGAGAATGTCTTTTTAAAAT;TC=53;TR=25 GT:GL:GQ 0/1:-327.36,-122.23,-224.07:100 20 1683959 . C CA . PASS FR=0.5;HP=8;NF=4;NR=9;PP=100.0;SC=TCAACAATGACAAAAAAAGCA;TC=24;TR=13 GT:GL:GQ 0/1:-130.55,-27.62,-42.34:66 20 1684576 . A AATGTATAATAC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=96.0;SC=ATACTGTTTAAATATTTCCTG;TC=24;TR=9 GT:GL:GQ 0/1:-370.23,-353.25,-494.05:100 20 1688002 . AAAAC A . PASS FR=1.0;HP=3;NF=4;NR=6;PP=100.0;SC=ACTCCCTCTCAAAACAAACAA;TC=22;TR=10 GT:GL:GQ 1/1:-132.2,-18.69,-9.78:74 20 1690549 . CCT C . PASS FR=0.5;HP=3;NF=6;NR=6;PP=100.0;SC=GAAATCTTCCCCTGTCTGTGA;TC=32;TR=12 GT:GL:GQ 0/1:-184.81,-148.16,-332.53:100 20 1694183 . CT C . PASS FR=0.5;HP=3;NF=8;NR=5;PP=100.0;SC=TATACAAAGACTTTATAACCA;TC=29;TR=13 GT:GL:GQ 0/1:-144.04,-44.56,-141.78:100 20 1699510 . T TCCCA . PASS FR=0.5;HP=3;NF=10;NR=2;PP=100.0;SC=AATGTCTCATTCCCACATCCT;TC=19;TR=12 GT:GL:GQ 0/1:-164.23,-17.54,-74.37:100 20 1701571 . TTAAAATAAAA T . PASS FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=CATCTCAAAATTAAAATAAAA;TC=21;TR=7 GT:GL:GQ 0/1:-177.13,-95.66,-194.53:100 20 1716144 . A AGTGT . PASS FR=0.5;HP=8;NF=3;NR=4;PP=100.0;SC=GGTTTTTTTTAGTGTGTGTGT;TC=23;TR=7 GT:GL:GQ 0/1:-151.21,-52.44,-109.8:100 20 1719870 . TG T . PASS FR=0.5;HP=1;NF=3;NR=11;PP=100.0;SC=ATCAAACCTCTGTGGGAGAGA;TC=27;TR=14 GT:GL:GQ 0/1:-146.54,-22.92,-111.48:100 20 1721789 . GT G . PASS FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=GCACTTGGGAGTTTTTTTTTC;TC=23;TR=10 GT:GL:GQ 0/1:-60.27,-22.43,-60.17:100 20 1722316 . CCTTT C . PASS FR=1.0;HP=2;NF=2;NR=1;PP=100.0;SC=TTTCTCTCTTCCTTTCTTTCT;TC=7;TR=3 GT:GL:GQ 1/1:-85.7,-30.24,-25.46:57 20 1727042 . T TA . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=AATTAAATTATATAGAGGAAG;TC=20;TR=18 GT:GL:GQ 1/1:-223.19,-104.73,-92.26:100 20 1728298 . G GT . PASS FR=1.0;HP=4;NF=11;NR=14;PP=100.0;SC=AAGAACAGAGGTTTTAAGCAT;TC=28;TR=25 GT:GL:GQ 1/1:-297.24,-94.99,-75.97:100 20 1730788 . T TGATA . PASS FR=1.0;HP=3;NF=3;NR=6;PP=100.0;SC=AGATGATAAATGATAGATAGA;TC=36;TR=9 GT:GL:GQ 1/1:-190.89,-23.51,-13.12:87 20 1731625 . CA C . PASS FR=1.0;HP=9;NF=5;NR=8;PP=100.0;SC=GACTCCATCTCAAAAAAAAAG;TC=23;TR=13 GT:GL:GQ 1/1:-93.68,-29.69,-18.4:95 20 1734082 . AAAAAT A . PASS FR=0.5;HP=4;NF=6;NR=3;PP=100.0;SC=CAATAGCTATAAAAATAAAAT;TC=38;TR=9 GT:GL:GQ 0/1:-124.98,-23.78,-220.83:100 20 1738324 . T TC . PASS FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=ACACTCCTTTTCCTTCATGAT;TC=22;TR=17 GT:GL:GQ 1/1:-213.69,-47.59,-33.85:100 20 1738519 . A AG . PASS FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=CTGTCAAACTAGCCTCTGGCT;TC=29;TR=24 GT:GL:GQ 1/1:-269.52,-42.45,-23.17:100 20 1741051 . T TAA . PASS FR=1.0;HP=1;NF=12;NR=12;PP=100.0;SC=TAAATATATATGACTATTTTT;TC=35;TR=24 GT:GL:GQ 1/1:-395.96,-52.09,-26.1:100 20 1745352 . A ACAATAATCACATCAAAGAT . PASS FR=1.0;HP=2;NF=4;NR=8;PP=100.0;SC=CAAGACCATTACACTAATCAC;TC=17;TR=12 GT:GL:GQ 1/1:-425.27,-43.37,-23.58:100 20 1746606 . GTA G . PASS FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=ATATATATGTGTATATATATA;TC=9;TR=5 GT:GL:GQ 1/1:-98.72,-49.48,-45.34:50 20 1768362 . G GAA . PASS FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=TAGAGTGATGGAAGAGACTGG;TC=27;TR=21 GT:GL:GQ 1/1:-269.69,-41.32,-23.11:100 20 1778684 . A AGTGCTT . PASS FR=0.5;HP=2;NF=1;NR=1;PP=83.0;SC=ATTGCCCTCCATTGGAGGCTG;TC=14;TR=2 GT:GL:GQ 1/0:-256.33,-220.54,-244.27:69 20 1833292 . TA T . PASS FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=ATATTATGTATAATCTCAATT;TC=25;TR=10 GT:GL:GQ 0/1:-147.42,-89.75,-210.06:100 20 1848829 . CTTTTCT C . PASS FR=1.0;HP=8;NF=6;NR=15;PP=100.0;SC=CTTTTCTTTTCTTTTCTTTTC;TC=25;TR=21 GT:GL:GQ 1/1:-409.42,-172.01,-156.56:100 20 1848853 . CTT C . PASS FR=0.5;HP=4;NF=3;NR=4;PP=100.0;SC=CTTTCTTTCTCTTTCTTTCTT;TC=26;TR=7 GT:GL:GQ 0/1:-469.4,-397.68,-416.1:83 20 1848877 . C CTT . PASS FR=0.9999;HP=4;NF=2;NR=1;PP=100.0;SC=TTCTTTCTTTCTCTTTCTTTC;TC=26;TR=3 GT:GL:GQ 1/1:-373.17,-284.63,-280.27:37 20 1852149 . CCA C . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=CACCCCCTCTCCACACACACA;TC=23;TR=5 GT:GL:GQ 0/1:-139.51,-90.17,-161.53:100 20 1855569 . AACACAC A . PASS FR=1.0;HP=1;NF=7;NR=3;PP=100.0;SC=GTCACTCTACAACACACACAC;TC=14;TR=10 GT:GL:GQ 1/1:-159.46,-18.21,-11.49:84 20 1857852 . TC T . PASS FR=1.0;HP=6;NF=4;NR=19;PP=100.0;SC=CCCGTGTCCATCCCCCCTGTA;TC=58;TR=23 GT:GL:GQ 1/1:-667.45,-637.23,-632.11:63 20 1857976 . G GT . PASS FR=1.0;HP=5;NF=12;NR=1;PP=100.0;SC=GCTTTGTTTTGTCAGTTGTTT;TC=22;TR=13 GT:GL:GQ 1/1:-196.6,-28.45,-14.03:100 20 1872437 . AT A . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TCCCTGGCTAATTCCCCCCAC;TC=23;TR=6 GT:GL:GQ 0/1:-111.11,-55.77,-134.66:100 20 1890990 . CTT C . PASS FR=1.0;HP=5;NF=11;NR=12;PP=100.0;SC=TGTTTCATTACTTTTTAACTT;TC=24;TR=23 GT:GL:GQ 1/1:-245.45,-38.39,-20.54:100 20 1895466 . T TATAG . PASS FR=1.0;HP=1;NF=11;NR=5;PP=100.0;SC=AGATTAGAATTAGCCCAGCTC;TC=24;TR=16 GT:GL:GQ 1/1:-500.31,-454.72,-448.18:79 20 1895484 . ACT A . PASS FR=1.0;HP=1;NF=14;NR=4;PP=52.0;SC=CTCAGATGTGACTCTTCCAGA;TC=23;TR=18 GT:GL:GQ 1/1:-454.69,-436.37,-433.13:53 20 1912065 . AC A . PASS FR=0.5;HP=2;NF=7;NR=8;PP=100.0;SC=TGCCTTCATCACTGTTCCCAT;TC=25;TR=15 GT:GL:GQ 0/1:-166.95,-40.53,-113.76:100 20 1930288 . TAAG T . PASS FR=0.5;HP=2;NF=9;NR=4;PP=100.0;SC=TATAAGTTGTTAAGAAGAAAA;TC=31;TR=13 GT:GL:GQ 0/1:-196.67,-58.02,-140.92:100 20 1940722 . GTT G . PASS FR=0.5;HP=2;NF=6;NR=7;PP=100.0;SC=AAAAACCCAGGTTATATATAC;TC=25;TR=13 GT:GL:GQ 0/1:-178.3,-32.72,-93.72:100 20 1940980 . G GA . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=AACTACTCAGGGGCTGAGATG;TC=20;TR=8 GT:GL:GQ 0/1:-91.81,-43.36,-126.02:100 20 1941170 . A AC . PASS FR=0.5;HP=1;NF=10;NR=2;PP=100.0;SC=ATACCTGTATAGAAAAAAAGT;TC=31;TR=12 GT:GL:GQ 0/1:-250.35,-208.27,-291.77:100 20 1943171 . T TG . PASS FR=0.5;HP=7;NF=1;NR=1;PP=56.0;SC=AGGGGAAGCCTGGGGGGGTTG;TC=19;TR=2 GT:GL:GQ 0/1:-65.38,-41.58,-85.08:100 20 1949783 . C CT . PASS FR=0.5;HP=10;NF=3;NR=4;PP=100.0;SC=GTGCTGAGCCCTTTTTTTTTT;TC=26;TR=7 GT:GL:GQ 0/1:-82.34,-46.95,-63.27:73 20 1959266 . A ATG . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=CAACCTGAATATGTGTGTGTG;TC=24;TR=7 GT:GL:GQ 0/1:-140.42,-42.47,-66.02:100 20 1967894 . GATGA G . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=TTGAGTGATTGATGAATGAAT;TC=24;TR=6 GT:GL:GQ 0/1:-113.7,-41.87,-83.28:100 20 1977448 . A ACACACACACG . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=ACACACACACATAGAAGGCCA;TC=32;TR=2 GT:GL:GQ 0/1:-253.96,-71.96,-163.76:100 20 1996777 . CT C . PASS FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=GTGTTTTAGGCTGTTATTTCA;TC=21;TR=11 GT:GL:GQ 0/1:-127.06,-33.79,-125.68:100 20 1997708 . CAT C . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CACACACACACATACAAAATA;TC=31;TR=9 GT:GL:GQ 0/1:-145.15,-85.85,-245.36:100 20 2004765 . T TG . PASS FR=0.5;HP=1;NF=2;NR=2;PP=76.0;SC=AGGATTTTTCTATCAGTCCAC;TC=12;TR=4 GT:GL:GQ 0/1:-54.31,-25.7,-84.4:100 20 2034931 . G GTTC . PASS FR=0.5;HP=2;NF=6;NR=4;PP=100.0;SC=AGATAGGTAAGTTCTTCCCCA;TC=24;TR=10 GT:GL:GQ 0/1:-162.21,-52.77,-146.87:100 20 2035677 . AACACAC AAC,A . PASS FR=0.5,0.5;HP=2;NF=2,3;NR=0,2;PP=39.0,100.0;SC=TTTTATAATAAACACACACAC;TC=29;TR=2,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:88 20 2050099 . AATTG A . PASS FR=0.5;HP=2;NF=10;NR=5;PP=100.0;SC=TCTTATTCTTAATTGATCTAA;TC=35;TR=15 GT:GL:GQ 0/1:-259.54,-91.86,-224.89:100 20 2052246 . AC A . PASS FR=0.5;HP=1;NF=3;NR=6;PP=100.0;SC=GGTCCCAGCTACTCAGGAGGC;TC=19;TR=9 GT:GL:GQ 0/1:-113.96,-44.77,-115.57:100 20 2053863 . C CA . PASS FR=0.5;HP=9;NF=3;NR=4;PP=96.0;SC=ACTAAAAATACAAAAAAAATA;TC=16;TR=7 GT:GL:GQ 0/1:-46.07,-13.04,-34.97:98 20 2054845 . AAAGAGGAAAAAG A . PASS FR=0.5;HP=4;NF=7;NR=1;PP=100.0;SC=AAAAGAGGAAAAAGAGGAAAA;TC=27;TR=8 GT:GL:GQ 0/1:-251.05,-86.54,-294.87:100 20 2055452 . AAAGG A . PASS FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=AAGAAAAGAAAAAGGAAGGAA;TC=27;TR=8 GT:GL:GQ 0/1:-227.92,-152.39,-281.38:100 20 2077127 . AAC A . PASS FR=0.5;HP=3;NF=1;NR=3;PP=97.0;SC=TCTCTACTAAAACACACACAC;TC=17;TR=4 GT:GL:GQ 0/1:-57.31,-24.65,-94.33:100 20 2078747 . CCT C . PASS FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=AGAAAATTCCCCTGTGGCCCT;TC=15;TR=5 GT:GL:GQ 0/1:-78.54,-32.73,-103.05:100 20 2120509 . AAAGGT A . PASS FR=0.5;HP=2;NF=8;NR=1;PP=100.0;SC=CTGAAATGAGAAAGGTAAGGA;TC=19;TR=9 GT:GL:GQ 0/1:-189.27,-90.48,-174.84:100 20 2122413 . CT C . PASS FR=0.5;HP=4;NF=3;NR=8;PP=100.0;SC=GTAACCTACCCTTTTCCACCT;TC=23;TR=11 GT:GL:GQ 0/1:-132.75,-34.8,-69.03:100 20 2126052 . T TCTATGTGA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=CATTTCCGTTTCTATGTGACC;TC=22;TR=4 GT:GL:GQ 0/1:-179.74,-76.1,-178.95:100 20 2131707 . T TGG . PASS FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=CCCTGTTGCCTGACCTGAGCC;TC=20;TR=8 GT:GL:GQ 0/1:-145.56,-92.76,-163.87:100 20 2153043 . C CTTTATTTA . PASS FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=GGTGACATCACTTTATTTATT;TC=21;TR=3 GT:GL:GQ 0/1:-97.11,-28.78,-48.32:87 20 2155932 . C CAT . PASS FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=AATTAAAAAACATATATATAT;TC=32;TR=7 GT:GL:GQ 0/1:-176.17,-66.01,-150.43:100 20 2160585 . AT A . PASS FR=0.5;HP=7;NF=9;NR=11;PP=100.0;SC=GTTTTTAAATATTTTTTAATT;TC=41;TR=20 GT:GL:GQ 0/1:-237.9,-137.73,-264.06:100 20 2162113 . A ATT . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TATCAGGAATAATTTTTTTTT;TC=25;TR=6 GT:GL:GQ 0/1:-145.37,-128.61,-213.61:100 20 2165761 . GTTAT G . PASS FR=0.5;HP=3;NF=4;NR=1;PP=100.0;SC=CTAATAACCTGTTATTTATTT;TC=28;TR=5 GT:GL:GQ 0/1:-79.63,-28.99,-73.78:100 20 2171122 . CAAACA C . PASS FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=AACAAACAGACAAACAAAACA;TC=18;TR=5 GT:GL:GQ 0/1:-113.12,-57.95,-91.54:100 20 2171346 . TA T . PASS FR=0.5;HP=8;NF=4;NR=5;PP=100.0;SC=AATTTTTTTTTAAAATCCTTA;TC=20;TR=9 GT:GL:GQ 0/1:-174.43,-122.88,-194.49:100 20 2171402 . T TA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=92.0;SC=TGATTGATCCTAACTTAATGA;TC=23;TR=4 GT:GL:GQ 0/1:-112.12,-79.99,-224.63:100 20 2198337 . AAG A . PASS FR=0.5;HP=2;NF=17;NR=3;PP=100.0;SC=CAACCAAAGAAAGAATGGGAG;TC=38;TR=20 GT:GL:GQ 0/1:-234.35,-51.22,-161.95:100 20 2199055 . G GCCACACACTTCTAAA . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=AGGGGGAAGTGCCATCAGATG;TC=20;TR=7 GT:GL:GQ 0/1:-318.25,-129.11,-238.35:100 20 2199168 . T TG . PASS FR=0.5;HP=9;NF=3;NR=6;PP=100.0;SC=TGAGATTTGGTGGGGGGGACA;TC=37;TR=9 GT:GL:GQ 0/1:-144.44,-70.03,-129.92:100 20 2209336 . A AGTG . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=GCTGGAGTGCAGTGGTACAAT;TC=18;TR=5 GT:GL:GQ 0/1:-105.48,-46.83,-99.81:100 20 2215492 . T TA . PASS FR=1.0;HP=1;NF=17;NR=16;PP=100.0;SC=TGGATGAACGTATTTATTTAA;TC=37;TR=33 GT:GL:GQ 1/1:-589.49,-315.53,-293.02:100 20 2215506 . G GT . PASS FR=1.0;HP=3;NF=18;NR=13;PP=100.0;SC=TATTTAACCAGTTTCTCTTGA;TC=36;TR=31 GT:GL:GQ 1/1:-602.79,-346.63,-325.98:100 20 2216792 . CAG C . PASS FR=0.5;HP=1;NF=6;NR=7;PP=100.0;SC=TGCGTTCATGCAGTTTATGGG;TC=25;TR=13 GT:GL:GQ 0/1:-181.42,-37.01,-108.03:100 20 2217535 . CCT C . PASS FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=CATTGCATCACCTGCCTCTGA;TC=32;TR=12 GT:GL:GQ 0/1:-224.94,-75.19,-157.78:100 20 2218702 . CA C . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=AATCACGACTCATTGTAGCCT;TC=18;TR=8 GT:GL:GQ 0/1:-111.7,-55.95,-90.25:100 20 2221607 . TTTTCTTTCTTTCTTTTTCC T . PASS FR=0.5;HP=4;NF=4;NR=2;PP=100.0;SC=AAAGTTTTCTTTTTCTTTCTT;TC=29;TR=6 GT:GL:GQ 0/1:-196.61,-29.28,-142.76:100 20 2241427 . AAAAC A . PASS FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=CTTGTCTCTAAAAACAAACAA;TC=19;TR=7 GT:GL:GQ 1/1:-166.73,-37.97,-27.83:84 20 2263098 . TG T . PASS FR=1.0;HP=4;NF=5;NR=5;PP=100.0;SC=TGACGGATGGTGGAGTGAGAA;TC=12;TR=10 GT:GL:GQ 1/1:-115.83,-17.15,-8.29:71 20 2278675 . A ATGAATGGCACT . PASS FR=1.0;HP=4;NF=8;NR=9;PP=100.0;SC=ACTCTGAAAAATGGTCACAGA;TC=18;TR=17 GT:GL:GQ 1/1:-567.99,-218.0,-199.44:100 20 2280081 . C CT . PASS FR=1.0;HP=3;NF=15;NR=9;PP=100.0;SC=TAACTTCATGCGGCTCCACCC;TC=30;TR=24 GT:GL:GQ 1/1:-287.69,-60.5,-41.43:100 20 2280751 . TA T . PASS FR=1.0;HP=10;NF=11;NR=3;PP=100.0;SC=AGACTCCATTTAAAAAAAAAA;TC=22;TR=14 GT:GL:GQ 1/1:-139.24,-88.42,-77.92:88 20 2280882 . A AAAAG . PASS FR=1.0;HP=6;NF=2;NR=2;PP=100.0;SC=AAGAAAGAAAAAAAGAAAGAA;TC=21;TR=4 GT:GL:GQ 1/1:-160.24,-78.2,-70.5:63 20 2285898 . AGTCACTG A . PASS FR=1.0;HP=1;NF=9;NR=3;PP=100.0;SC=CCAAGTCTCTAGTCACTGGTT;TC=19;TR=12 GT:GL:GQ 1/1:-272.68,-30.42,-16.26:99 20 2287002 . TAAG T . PASS FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=GAAAAATCTCTAAGAAGGCTC;TC=24;TR=20 GT:GL:GQ 1/1:-245.61,-20.38,-4.14:100 20 2294297 . A ACT . PASS FR=1.0;HP=2;NF=5;NR=3;PP=100.0;SC=AATCACACACACTCTCTCTCT;TC=24;TR=8 GT:GL:GQ 1/1:-199.54,-41.84,-28.04:100 20 2297084 . AT A . PASS FR=1.0;HP=2;NF=10;NR=7;PP=100.0;SC=GGTGGCACGCATTAACACCAG;TC=18;TR=17 GT:GL:GQ 1/1:-184.14,-27.34,-14.78:100 20 2297605 . CT C . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAATCATGGCCTTTGGCTTCC;TC=24;TR=10 GT:GL:GQ 0/1:-137.24,-29.13,-84.17:100 20 2298589 . C CAT,T . PASS FR=0.5,0.5;HP=1;NF=5,2;NR=2,3;PP=100.0,100.0;SC=ATATATATATCATATATATAT;TC=23;TR=7,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2316853 . G GC . PASS FR=1.0;HP=4;NF=3;NR=6;PP=100.0;SC=TCACCCTGTAGCCCCTGTGCC;TC=15;TR=9 GT:GL:GQ 1/1:-147.72,-38.92,-28.94:83 20 2318317 . GATCACACC G . PASS FR=1.0;HP=2;NF=8;NR=8;PP=100.0;SC=AGTGAGCCGAGATCACACCAC;TC=22;TR=16 GT:GL:GQ 1/1:-356.42,-104.52,-90.96:100 20 2318716 . AG A . PASS FR=1.0;HP=3;NF=13;NR=4;PP=100.0;SC=CACTCAGAGCAGGGCACCGAT;TC=26;TR=17 GT:GL:GQ 1/1:-256.21,-181.8,-170.54:94 20 2323655 . A AT . PASS FR=1.0;HP=8;NF=11;NR=9;PP=100.0;SC=AGGAAAAAAAAACACTGATGT;TC=31;TR=20 GT:GL:GQ 1/1:-290.56,-28.0,-5.91:100 20 2326944 . G GA . PASS FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=AGATACAGAGGAAAAATGAAG;TC=25;TR=18 GT:GL:GQ 1/1:-204.47,-32.24,-15.14:100 20 2329825 . T TC . PASS FR=1.0;HP=1;NF=16;NR=4;PP=100.0;SC=ATATGGGTTGTCTTTGAGACT;TC=22;TR=20 GT:GL:GQ 1/1:-212.37,-32.28,-17.55:100 20 2334719 . CTAT C . PASS FR=1.0;HP=3;NF=14;NR=16;PP=100.0;SC=TTCCCAGGTTCTATTATGTAG;TC=36;TR=30 GT:GL:GQ 1/1:-368.57,-33.34,-9.9:100 20 2335944 . C CTG . PASS FR=1.0;HP=4;NF=10;NR=19;PP=100.0;SC=GCTGAGAAAACTATATCCAAA;TC=34;TR=29 GT:GL:GQ 1/1:-370.96,-31.85,-8.29:100 20 2340299 . TTGTC T . PASS FR=1.0;HP=2;NF=10;NR=15;PP=100.0;SC=ATCCTGTAGGTTGTCTGTTTA;TC=27;TR=25 GT:GL:GQ 1/1:-327.39,-42.17,-22.8:100 20 2342117 . T TG . PASS FR=1.0;HP=5;NF=14;NR=14;PP=100.0;SC=TGCTTATTTTTTCCACTTAAT;TC=32;TR=28 GT:GL:GQ 1/1:-450.6,-326.69,-308.08:100 20 2344369 . TAAG T . PASS FR=1.0;HP=2;NF=13;NR=10;PP=100.0;SC=TGAGAGGTGGTAAGAAGAAGA;TC=36;TR=23 GT:GL:GQ 1/1:-351.7,-76.99,-56.29:100 20 2344451 . G GAGGA . PASS FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=ACACCCAACAGAGGAAGGTTA;TC=20;TR=15 GT:GL:GQ 1/1:-372.02,-158.89,-145.61:100 20 2344539 . T TTTTGTTTG . PASS FR=1.0;HP=3;NF=8;NR=4;PP=100.0;SC=ACTACCCCAGTTTTGTTTGTT;TC=23;TR=12 GT:GL:GQ 1/1:-243.77,-36.7,-24.92:99 20 2345269 . TCCTGGC T . PASS FR=1.0;HP=2;NF=7;NR=13;PP=100.0;SC=ATCGAGACCATCCTGGCTAAC;TC=21;TR=20 GT:GL:GQ 1/1:-260.12,-24.22,-9.67:100 20 2346660 . T TAATAAATAAATAAATA . PASS FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=CAATTCCTTATAATAAATAAA;TC=13;TR=7 GT:GL:GQ 1/1:-305.93,-18.69,-7.6:93 20 2352930 . AC A . PASS FR=1.0;HP=2;NF=10;NR=8;PP=100.0;SC=TTTCAGGCCTACCTCTCAAGC;TC=21;TR=18 GT:GL:GQ 1/1:-216.23,-90.38,-78.46:100 20 2362643 . C CTG . PASS FR=1.0;HP=3;NF=11;NR=8;PP=100.0;SC=AAGAACTTGTCTTAGATGCTG;TC=21;TR=19 GT:GL:GQ 1/1:-259.19,-87.0,-72.75:100 20 2379170 . TC T . PASS FR=0.5;HP=4;NF=1;NR=3;PP=99.0;SC=AGCTTGGGCTTCCCCACAATA;TC=23;TR=4 GT:GL:GQ 0/1:-84.89,-51.93,-137.5:100 20 2401510 . ATGT A . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CATTATATGGATGTACACAGT;TC=23;TR=6 GT:GL:GQ 0/1:-138.83,-80.65,-217.86:100 20 2406090 . AACT A . PASS FR=0.5;HP=3;NF=8;NR=7;PP=100.0;SC=GTTGCCACAAAACTTCAATTT;TC=36;TR=15 GT:GL:GQ 0/1:-277.31,-158.31,-369.27:100 20 2407722 . A AT . PASS FR=0.5;HP=9;NF=4;NR=11;PP=100.0;SC=AATTGCTATAATTTTTTTTTC;TC=38;TR=15 GT:GL:GQ 0/1:-112.13,-34.3,-69.71:100 20 2409340 . C CAATA . PASS FR=0.5;HP=2;NF=4;NR=3;PP=100.0;SC=CATAATAAATCAATCAATAAA;TC=22;TR=7 GT:GL:GQ 0/1:-189.45,-43.56,-132.72:100 20 2409613 . G GCA . PASS FR=0.5;HP=1;NF=6;NR=4;PP=57.0;SC=GGGATTATAGGCACAACACCA;TC=25;TR=10 GT:GL:GQ 0/1:-231.71,-206.44,-319.84:100 20 2411731 . CAG C . PASS FR=0.5;HP=1;NF=1;NR=2;PP=36.0;SC=GTGGATGAGCCAGAGAGAAGT;TC=13;TR=3 GT:GL:GQ 0/1:-55.56,-36.89,-120.4:84 20 2414786 . G GA . PASS FR=1.0;HP=8;NF=8;NR=10;PP=100.0;SC=GAAGCTTTCAGAAAAAAACCC;TC=23;TR=18 GT:GL:GQ 1/1:-173.45,-78.53,-65.46:100 20 2418166 . GTGTT G . PASS FR=0.5;HP=1;NF=1;NR=4;PP=100.0;SC=CACCTGGCTAGTGTTTGTTTG;TC=21;TR=5 GT:GL:GQ 0/1:-134.79,-72.62,-117.78:100 20 2425523 . A ATTTATTTTATTTTAT . PASS FR=0.5;HP=7;NF=3;NR=2;PP=100.0;SC=ATTTTATTTTATTTATTTTAT;TC=23;TR=5 GT:GL:GQ 0/1:-149.61,-12.23,-46.02:100 20 2425934 . T TA . PASS FR=0.5;HP=8;NF=8;NR=4;PP=67.0;SC=TTAATCAATTTAAAAAAAATG;TC=25;TR=12 GT:GL:GQ 0/1:-160.28,-133.72,-162.95:100 20 2430943 . ATGTG A . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=GTGCGTGTGCATGTGTGTGTG;TC=29;TR=2 GT:GL:GQ 0/1:-164.1,-78.49,-99.2:92 20 2433931 . TC T . PASS FR=0.5;HP=5;NF=1;NR=1;PP=26.0;SC=CCCTGGAAGCTCCCCTTTGTG;TC=10;TR=2 GT:GL:GQ 0/1:-34.79,-18.58,-53.81:73 20 2436455 . A AAAAAAG,AAAAAG . PASS FR=0.5,0.5;HP=9;NF=3,3;NR=1,4;PP=50.0,100.0;SC=CTACCAAAAAAAAAAGAAAAG;TC=25;TR=4,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2436835 . A AC . PASS FR=0.5;HP=1;NF=7;NR=8;PP=100.0;SC=ACAATGATGTACATTTTTCAG;TC=37;TR=15 GT:GL:GQ 0/1:-177.52,-36.56,-198.23:100 20 2448573 . CCT C . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CCCATGCCACCCTGTTTTAGC;TC=34;TR=11 GT:GL:GQ 0/1:-159.22,-114.6,-320.68:100 20 2450954 . CA C . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CAAACTTCCGCAAGTCTGAGC;TC=22;TR=5 GT:GL:GQ 0/1:-106.22,-51.15,-126.38:100 20 2452700 . TAAAAAAGAA T . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=TTTCTTGGATTAAAAAAGAAA;TC=32;TR=9 GT:GL:GQ 0/1:-216.2,-29.76,-153.35:100 20 2458350 . G GA . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=CAAGGTGGGAGAATTGCTTGA;TC=27;TR=10 GT:GL:GQ 0/1:-156.97,-38.22,-122.55:100 20 2477736 . A AT . PASS FR=0.5;HP=10;NF=4;NR=3;PP=100.0;SC=AAAAAAAAAAATTTTACCATC;TC=23;TR=7 GT:GL:GQ 0/1:-89.51,-39.15,-127.81:100 20 2498012 . GTA G . PASS FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=GTATATGTGTGTATATATATA;TC=22;TR=9 GT:GL:GQ 0/1:-140.02,-17.32,-103.73:100 20 2516178 . GA G . PASS FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=GTTTAATTGGGAAAAAAAATA;TC=17;TR=8 GT:GL:GQ 0/1:-52.67,-14.95,-45.28:100 20 2520604 . T TAGCA . PASS FR=0.5;HP=4;NF=4;NR=3;PP=100.0;SC=CTCCCGCAAATAGCACACAAG;TC=20;TR=7 GT:GL:GQ 0/1:-194.0,-75.16,-105.67:100 20 2522684 . G GA . PASS FR=0.5;HP=7;NF=5;NR=6;PP=83.0;SC=TTTCTTATTTGAAAAAAACTT;TC=31;TR=11 GT:GL:GQ 0/1:-153.71,-123.52,-187.08:100 20 2523586 . T TA . PASS FR=1.0;HP=4;NF=11;NR=6;PP=100.0;SC=TTTTTCTTTTTAAAACAAAAT;TC=23;TR=17 GT:GL:GQ 1/1:-179.22,-18.0,-3.45:100 20 2526468 . GAAGA G . PASS FR=0.5001;HP=2;NF=2;NR=4;PP=100.0;SC=AGAGGAAGAGGAAGAAAGAAA;TC=25;TR=6 GT:GL:GQ 0/1:-210.76,-128.72,-136.62:37 20 2526552 . A AAG . PASS FR=0.5;HP=6;NF=5;NR=8;PP=100.0;SC=GAAAGAAAGAAAAAAAGAAAG;TC=30;TR=13 GT:GL:GQ 0/1:-215.19,-78.8,-144.35:100 20 2527129 . G GTTGGGCATAAGCTGTAGATC . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=AACCTGCAGAGTTGGGCATAA;TC=18;TR=4 GT:GL:GQ 0/1:-243.57,-136.91,-199.82:100 20 2534184 . T TGTTTTGTGTGAC . PASS FR=0.5;HP=1;NF=5;NR=9;PP=100.0;SC=GATACAGGTCTGTTTTTGTCT;TC=31;TR=14 GT:GL:GQ 0/1:-444.44,-61.75,-181.17:100 20 2546156 . TGG T . PASS FR=0.5;HP=3;NF=4;NR=12;PP=100.0;SC=CCCAAAGTGCTGGGATTACAG;TC=31;TR=16 GT:GL:GQ 0/1:-172.01,-63.37,-146.93:100 20 2568176 . G GT . PASS FR=1.0;HP=10;NF=12;NR=9;PP=100.0;SC=ATTTGGGAATGTTTTTTTTTA;TC=27;TR=21 GT:GL:GQ 1/1:-116.08,-18.72,-6.68:100 20 2577356 . A AAT . PASS FR=0.5;HP=6;NF=1;NR=2;PP=100.0;SC=ATCAGAAAAAAATATATATGT;TC=26;TR=3 GT:GL:GQ 0/1:-199.48,-88.19,-98.9:49 20 2579040 . C CTTTATTTA . PASS FR=0.5;HP=3;NF=1;NR=2;PP=100.0;SC=CTTGCCTCTACTTTATTTATT;TC=16;TR=3 GT:GL:GQ 0/1:-103.59,-10.59,-52.57:100 20 2586119 . GGA G . PASS FR=0.5;HP=1;NF=2;NR=1;PP=30.0;SC=GCATGTGCATGGAGAGAGAGA;TC=23;TR=3 GT:GL:GQ 0/1:-35.49,-18.23,-170.44:77 20 2594696 . A AT . PASS FR=0.5;HP=8;NF=2;NR=7;PP=100.0;SC=TTTCTGTCACATTTTTTTTCG;TC=24;TR=9 GT:GL:GQ 0/1:-70.9,-30.05,-77.99:100 20 2597210 . TAAAG T . PASS FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=GAAAGGAAAATAAAGAAGGAG;TC=20;TR=4 GT:GL:GQ 0/1:-85.33,-27.89,-144.98:100 20 2611781 . A ATATCT . PASS FR=0.5;HP=1;NF=8;NR=8;PP=100.0;SC=ATTATAATTAATATAACAAAC;TC=31;TR=16 GT:GL:GQ 0/1:-408.96,-183.07,-309.58:100 20 2613623 . T TTTG . PASS FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTTCCATGGGTTTGTTGTTGT;TC=18;TR=4 GT:GL:GQ 0/1:-165.53,-112.66,-139.53:100 20 2613971 . TA T . PASS FR=0.5;HP=4;NF=4;NR=7;PP=100.0;SC=CTTGGACACATAAACAGCCCT;TC=27;TR=11 GT:GL:GQ 0/1:-121.36,-29.89,-140.29:100 20 2614405 . T TGGGTAGG . PASS FR=0.5;HP=3;NF=2;NR=2;PP=52.0;SC=ACTACAGAACTGGGTAGGGGA;TC=30;TR=4 GT:GL:GQ 0/1:-185.89,-156.26,-363.71:100 20 2616002 . C CT . PASS FR=0.5;HP=4;NF=5;NR=5;PP=100.0;SC=ACCTCCACCTCCCCCTCTCAG;TC=22;TR=10 GT:GL:GQ 0/1:-182.46,-117.29,-171.16:100 20 2617861 . C CCT . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=ATGGTGAACCCGTCTCTACTA;TC=17;TR=7 GT:GL:GQ 0/1:-111.22,-36.32,-97.76:100 20 2625967 . TGAG T . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CTGAGTAGGCTGAGGAGGAGG;TC=15;TR=5 GT:GL:GQ 0/1:-133.1,-85.47,-137.74:100 20 2627766 . TTTTATTTA T . PASS FR=0.5;HP=3;NF=1;NR=1;PP=86.0;SC=ACTGAATTTATTTTATTTATT;TC=19;TR=2 GT:GL:GQ 0/1:-102.46,-70.95,-132.69:100 20 2630436 . T TACC . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=ACATGCCAGGTACACCATTGT;TC=23;TR=11 GT:GL:GQ 0/1:-159.47,-31.83,-143.4:100 20 2634285 . CTG C . PASS FR=0.5;HP=1;NF=3;NR=15;PP=100.0;SC=CTTGTGGGCACTGTAGTGACA;TC=29;TR=18 GT:GL:GQ 0/1:-229.42,-26.07,-86.72:100 20 2641823 . C CTG . PASS FR=0.5;HP=5;NF=2;NR=2;PP=100.0;SC=ATTGCATTTTCTGTGTGTGTG;TC=21;TR=4 GT:GL:GQ 0/1:-96.78,-48.19,-99.13:100 20 2643833 . G GAAATGCAAT . PASS FR=0.5;HP=4;NF=9;NR=2;PP=100.0;SC=TGGTATTCCAGAAATGCAATG;TC=31;TR=11 GT:GL:GQ 0/1:-379.88,-109.48,-180.95:100 20 2650007 . T TACACACACACACACACAC . PASS FR=1.0;HP=1;NF=3;NR=1;PP=100.0;SC=ACCCTTTTCTTACACACACAC;TC=19;TR=4 GT:GL:GQ 1/1:-231.82,-84.82,-75.66:76 20 2650235 . C CT . PASS FR=1.0;HP=9;NF=12;NR=9;PP=100.0;SC=TTTATTGGGCCTTTTTTTTTG;TC=28;TR=21 GT:GL:GQ 1/1:-325.44,-296.08,-289.77:79 20 2656886 . AT A . PASS FR=1.0;HP=6;NF=17;NR=6;PP=100.0;SC=ATAAATAATAATTTTTTAAAA;TC=29;TR=23 GT:GL:GQ 1/1:-339.94,-246.4,-231.12:100 20 2663020 . G GGAA . PASS FR=1.0;HP=1;NF=8;NR=7;PP=100.0;SC=AAGAGGAAGAGGAAGAAGACA;TC=28;TR=15 GT:GL:GQ 1/1:-408.26,-206.61,-189.41:100 20 2665268 . TA T . PASS FR=1.0;HP=8;NF=2;NR=1;PP=43.0;SC=TATGCAGCCATAAAAAAATGA;TC=4;TR=3 GT:GL:GQ 1/1:-20.74,-4.04,-1.38:43 20 2665956 . AG A . PASS FR=1.0;HP=1;NF=9;NR=5;PP=100.0;SC=CCCAGGCTATAGTGCAGTGGC;TC=16;TR=14 GT:GL:GQ 1/1:-156.94,-33.67,-23.62:84 20 2666401 . TA T . PASS FR=0.5;HP=2;NF=8;NR=7;PP=100.0;SC=ACTTTTCTATTAAGAAACGCA;TC=38;TR=15 GT:GL:GQ 0/1:-158.74,-28.32,-160.06:100 20 2668149 . A ATG . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATATATGTGTGTGTG;TC=17;TR=3 GT:GL:GQ 0/1:-54.4,-18.57,-68.0:100 20 2671350 . GTA G . PASS FR=1.0;HP=2;NF=8;NR=5;PP=100.0;SC=ATATATATGTGTATATATATA;TC=23;TR=13 GT:GL:GQ 1/1:-348.62,-348.37,-348.16:60 20 2676135 . C CAG . PASS FR=0.5;HP=1;NF=6;NR=2;PP=100.0;SC=TGCTGGGATGCAGAGGGCTTC;TC=17;TR=8 GT:GL:GQ 0/1:-189.45,-108.27,-131.01:100 20 2678198 . A AAAAG . PASS FR=1.0;HP=10;NF=1;NR=2;PP=100.0;SC=CTCAAAAAAAAAAAGAAAGAA;TC=16;TR=3 GT:GL:GQ 1/1:-113.89,-62.27,-58.08:51 20 2691794 . AAAT A . PASS FR=1.0;HP=3;NF=2;NR=4;PP=100.0;SC=ACCCTGTCTAAAATAATAATA;TC=12;TR=6 GT:GL:GQ 1/1:-83.97,-10.76,-5.22:69 20 2713483 . C CAG . PASS FR=0.5;HP=2;NF=7;NR=1;PP=100.0;SC=TTTTTTGAGACGGAATTATAA;TC=28;TR=8 GT:GL:GQ 0/1:-114.91,-36.16,-205.08:100 20 2717474 . A ACAAAGGTCTC . PASS FR=1.0;HP=2;NF=9;NR=5;PP=100.0;SC=AGTCATAAGGACAAAGGACCC;TC=17;TR=14 GT:GL:GQ 1/1:-343.26,-32.05,-17.5:94 20 2724519 . AG A . PASS FR=0.5;HP=3;NF=6;NR=7;PP=100.0;SC=CCAGATATTTAGGGTGTCCAT;TC=28;TR=13 GT:GL:GQ 0/1:-149.48,-35.03,-149.61:100 20 2734607 . C CCCCCTTGGTTTTGAAACTTT . PASS FR=1.0;HP=4;NF=2;NR=4;PP=100.0;SC=TCTGTGGGCACCCCCTTGGGC;TC=12;TR=6 GT:GL:GQ 1/1:-301.3,-108.37,-98.31:100 20 2742852 . C CCAGCAATCCTCAGT . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=CTCAATAGCACCTGAGGATGA;TC=16;TR=6 GT:GL:GQ 0/1:-233.59,-35.77,-130.91:100 20 2766949 . C CT . PASS FR=1.0;HP=10;NF=5;NR=10;PP=100.0;SC=ACTTCATTCCCTTTTTTTTTT;TC=28;TR=15 GT:GL:GQ 1/1:-134.68,-37.76,-21.4:100 20 2782855 . AC A . PASS FR=1.0;HP=4;NF=3;NR=8;PP=100.0;SC=AATCACTTGTACCCCGGGGGC;TC=25;TR=11 GT:GL:GQ 1/1:-262.64,-187.36,-174.92:100 20 2789088 . AC A . PASS FR=1.0;HP=9;NF=1;NR=4;PP=100.0;SC=CAAAAAAAAAACCAAAAAACA;TC=13;TR=5 GT:GL:GQ 1/1:-119.81,-36.46,-27.82:89 20 2796485 . C CCTTTT . PASS FR=0.5;HP=4;NF=1;NR=4;PP=100.0;SC=CATCAGGCCCCCTTTTCTCCT;TC=18;TR=5 GT:GL:GQ 0/1:-128.25,-42.55,-123.81:100 20 2797764 . AG A . PASS FR=1.0;HP=3;NF=1;NR=4;PP=100.0;SC=CTGCCTTGGCAGGGCCCAGAC;TC=14;TR=5 GT:GL:GQ 1/1:-134.46,-67.08,-59.42:63 20 2834884 . T TAC . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=ACCCCGTCTCTACACACACAC;TC=22;TR=3 GT:GL:GQ 0/1:-64.62,-28.32,-80.82:100 20 2849974 . AT A . PASS FR=0.5;HP=10;NF=4;NR=6;PP=99.0;SC=TTGGTTTGCAATTTTTTTTTT;TC=36;TR=10 GT:GL:GQ 0/1:-66.95,-34.01,-107.66:100 20 2850721 . ACT A . PASS FR=0.5;HP=1;NF=4;NR=4;PP=100.0;SC=CCAGTGAAAGACTCTTGGGGT;TC=17;TR=8 GT:GL:GQ 0/1:-88.06,-17.99,-74.67:100 20 2858849 . GT G . PASS FR=0.5;HP=8;NF=1;NR=5;PP=52.0;SC=GACAGCTGTAGTTTTTTTTAA;TC=15;TR=6 GT:GL:GQ 0/1:-33.96,-11.94,-50.39:98 20 2867547 . AT A . PASS FR=0.5;HP=6;NF=5;NR=6;PP=100.0;SC=AAATAAAAAAATGTAGTATCT;TC=32;TR=11 GT:GL:GQ 0/1:-115.49,-28.1,-161.94:100 20 2880787 . C CCT . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=GAAAAATCTGCCTCCTTTTTT;TC=27;TR=9 GT:GL:GQ 0/1:-140.77,-68.5,-172.28:100 20 2890657 . C CAT . PASS FR=0.5003;HP=1;NF=2;NR=1;PP=100.0;SC=TATCATATATCATATATAATC;TC=5;TR=3 GT:GL:GQ 0/1:-44.82,-3.47,-10.33:32 20 2890805 . CAT C . PASS FR=0.5017;HP=1;NF=1;NR=6;PP=100.0;SC=TACTATACGTCATATATAATA;TC=9;TR=7 GT:GL:GQ 0/1:-87.98,-14.06,-19.03:24 20 2894312 . CTTATT C . PASS FR=0.5;HP=4;NF=3;NR=5;PP=100.0;SC=GTGCTGTGTTCTTATTTTATC;TC=22;TR=8 GT:GL:GQ 0/1:-141.94,-29.98,-159.98:100 20 2896142 . T TTATC . PASS FR=1.0;HP=2;NF=9;NR=10;PP=100.0;SC=TAAGAGTTCTTTATTCTGATA;TC=30;TR=19 GT:GL:GQ 1/1:-399.17,-94.52,-74.73:100 20 2912364 . T TTG . PASS FR=0.5004;HP=1;NF=1;NR=1;PP=75.0;SC=GGGTCTTGGCTTGTGTGTGTG;TC=20;TR=2 GT:GL:GQ 0/1:-121.99,-92.59,-99.11:31 20 2926228 . GGTGTGTGT G . PASS FR=0.5;HP=1;NF=1;NR=9;PP=100.0;SC=ATAATTGGCAGGTGTGTGTGT;TC=27;TR=10 GT:GL:GQ 0/1:-233.62,-33.54,-77.33:100 20 2937307 . AAAATAAAT A . PASS FR=0.5;HP=4;NF=3;NR=3;PP=100.0;SC=TCAGTAAATAAAAATAAATAA;TC=17;TR=6 GT:GL:GQ 0/1:-165.86,-12.93,-101.78:100 20 2950624 . T TAATA,TAATAAATAAATA . PASS FR=0.5,0.5;HP=5;NF=5,2;NR=2,2;PP=100.0,100.0;SC=TCTAAATAAATAATAAATAAA;TC=24;TR=7,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 2966530 . CTTGTTTGT CTTGT,C . PASS FR=0.5,0.5;HP=2;NF=1,1;NR=2,1;PP=100.0,27.0;SC=CAGCTGTCTCCTTGTTTGTTT;TC=22;TR=3,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:80 20 2973326 . T TTTAGGGTTTTTC . PASS FR=0.5;HP=4;NF=1;NR=5;PP=100.0;SC=CATATCCAAATATTACGATTC;TC=15;TR=6 GT:GL:GQ 0/0:-275.74,-159.4,-213.4:3 20 2977781 . CATAT C . PASS FR=0.5;HP=5;NF=3;NR=6;PP=100.0;SC=TGTGAGAAAACATATGTGGGA;TC=26;TR=9 GT:GL:GQ 0/1:-131.98,-30.22,-206.04:100 20 2979576 . T TTATTA . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TATTTATAATTTATTATATAT;TC=21;TR=7 GT:GL:GQ 0/1:-148.89,-17.32,-97.42:100 20 2982245 . CT C . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=CTGTGGAAATCTTATGTGAAG;TC=27;TR=12 GT:GL:GQ 0/1:-126.56,-21.8,-132.46:100 20 2982823 . CA C . PASS FR=1.0;HP=7;NF=10;NR=9;PP=100.0;SC=TTCCATCTGACAAAAAATTGG;TC=21;TR=19 GT:GL:GQ 1/1:-196.74,-95.2,-82.42:100 20 2989926 . AT A . PASS FR=0.5;HP=10;NF=2;NR=5;PP=29.0;SC=GAGTTGTGTGATTTTTTTTTT;TC=36;TR=7 GT:GL:GQ 0/1:-66.0,-49.11,-118.97:76 20 3005541 . TC T . PASS FR=0.5;HP=5;NF=7;NR=7;PP=100.0;SC=AGCAGTTTTTTCTGTAAGAGC;TC=32;TR=14 GT:GL:GQ 0/1:-167.85,-53.03,-186.47:100 20 3007694 . A AGGT . PASS FR=0.5;HP=3;NF=4;NR=5;PP=100.0;SC=CCAGGGCCTGAGGTGGGAGCA;TC=22;TR=9 GT:GL:GQ 0/1:-162.22,-42.91,-117.4:100 20 3012419 . C CTGTT . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=CCTCCTTACTCTGTGTGTTTT;TC=26;TR=8 GT:GL:GQ 0/1:-154.4,-24.26,-143.38:100 20 3022136 . GAATT G . PASS FR=0.5;HP=7;NF=8;NR=1;PP=100.0;SC=AAAAGAAAAAGAATTAATTAA;TC=20;TR=9 GT:GL:GQ 1/0:-190.17,-78.0,-90.9:100 20 3039218 . GT G . PASS FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=TGTTGTTGTTGTTTGTTTGTT;TC=29;TR=25 GT:GL:GQ 1/1:-226.7,-48.88,-31.11:100 20 3042034 . T TA . PASS FR=1.0;HP=10;NF=5;NR=14;PP=100.0;SC=AAGACACTGATAAAAAAAAAT;TC=25;TR=19 GT:GL:GQ 1/1:-125.74,-31.3,-15.65:100 20 3047853 . A ATTCCCCCATT . PASS FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=ACTCCCTCTCATTCCCCCATT;TC=20;TR=7 GT:GL:GQ 0/1:-258.31,-36.83,-99.91:100 20 3050529 . A AT . PASS FR=0.5;HP=10;NF=4;NR=1;PP=23.0;SC=GCAAAAAAAAAAATTTTTATT;TC=22;TR=5 GT:GL:GQ 0/1:-257.11,-262.46,-292.84:73 20 3050531 . A ATTT,T . PASS FR=0.5,0.5;HP=10;NF=3,13;NR=0,6;PP=97.0,100.0;SC=AAAAAAAAAAATTTTTATTTT;TC=22;TR=3,19 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3051123 . A AT . PASS FR=0.5;HP=6;NF=2;NR=1;PP=69.0;SC=TCAAGAAAAAAATATATATAT;TC=17;TR=3 GT:GL:GQ 0/1:-107.95,-81.12,-160.4:100 20 3058938 . C CTT . PASS FR=1.0;HP=2;NF=19;NR=9;PP=100.0;SC=ACTGGATACTCTGAACTCCTA;TC=30;TR=28 GT:GL:GQ 1/1:-404.4,-115.7,-94.26:100 20 3060201 . C CAAT . PASS FR=0.5;HP=4;NF=13;NR=9;PP=100.0;SC=ACAAAGTCAACAATAATTCAT;TC=44;TR=22 GT:GL:GQ 0/1:-325.42,-43.13,-189.79:100 20 3062903 . T TC . PASS FR=0.5;HP=3;NF=1;NR=5;PP=94.0;SC=TCCAGGCCTTTCCCTCTCTGC;TC=19;TR=6 GT:GL:GQ 0/1:-95.35,-62.58,-147.62:100 20 3072606 . A AAGG . PASS FR=1.0;HP=5;NF=4;NR=4;PP=100.0;SC=CCAAGTAAAAAAGGGCGGGGG;TC=22;TR=8 GT:GL:GQ 1/1:-220.94,-78.12,-65.62:100 20 3126086 . CCT TCT,C . PASS FR=0.5,0.5;HP=7;NF=1,1;NR=3,1;PP=8.0,36.0;SC=GCCTTTTTTTCCTTTTTTTTT;TC=19;TR=4,2 GT:GL:GQ 2/1:-1.0,-1.0,-1.0:42 20 3159346 . C CA . PASS FR=1.0;HP=2;NF=3;NR=12;PP=100.0;SC=GCTGGGACTACGGCATTTACT;TC=15;TR=15 GT:GL:GQ 1/1:-149.15,-11.32,-0.92:87 20 3161722 . C CAGAT,CAGATAGAT . PASS FR=0.5,0.5;HP=2;NF=2,1;NR=2,2;PP=35.0,42.0;SC=GATAGATAGACAGATAGATAG;TC=18;TR=4,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:99 20 3161783 . CTA C . PASS FR=1.0;HP=2;NF=9;NR=7;PP=100.0;SC=TTTTATATATCTATATATATA;TC=25;TR=16 GT:GL:GQ 1/1:-263.89,-139.12,-127.54:97 20 3162560 . CAT C . PASS FR=0.5369;HP=2;NF=1;NR=3;PP=100.0;SC=CACACACACACATGGTCCATG;TC=6;TR=4 GT:GL:GQ 0/1:-84.99,-50.52,-52.5:11 20 3169476 . T TTTG . PASS FR=0.5;HP=3;NF=5;NR=9;PP=100.0;SC=AATGTTTACTTTTAATAAACT;TC=35;TR=14 GT:GL:GQ 0/1:-273.66,-64.07,-202.46:100 20 3169541 . A AT . PASS FR=0.5;HP=7;NF=5;NR=9;PP=100.0;SC=AGGATCATAGATTTTTTTCCT;TC=23;TR=14 GT:GL:GQ 0/1:-204.2,-123.3,-145.94:100 20 3172618 . GACAC G . PASS FR=0.7893;HP=1;NF=3;NR=1;PP=100.0;SC=TTGCTCCCCTGACACACACAC;TC=16;TR=4 GT:GL:GQ 1/1:-154.29,-100.95,-101.25:3 20 3172771 . C CAT . PASS FR=1.0;HP=1;NF=13;NR=6;PP=100.0;SC=CCGAGACACACGAGTGGTAAT;TC=24;TR=19 GT:GL:GQ 1/1:-267.07,-44.87,-28.98:100 20 3177159 . T TA . PASS FR=1.0;HP=5;NF=6;NR=3;PP=87.0;SC=CTGTCTCCACTAAAAATACAA;TC=15;TR=9 GT:GL:GQ 1/1:-169.92,-142.98,-139.57:56 20 3177517 . C CAT . PASS FR=1.0;HP=2;NF=15;NR=10;PP=100.0;SC=TAATAAATAACGTTACTGGAT;TC=26;TR=25 GT:GL:GQ 1/1:-294.64,-37.59,-18.88:100 20 3188342 . A AAACAACAACAACAAC . PASS FR=0.5;HP=3;NF=2;NR=2;PP=100.0;SC=CTCCATCTCAAAACAACAACA;TC=17;TR=4 GT:GL:GQ 0/1:-131.35,-46.51,-82.74:100 20 3192138 . T TTTTGTTTGTTTG . PASS FR=0.5;HP=3;NF=3;NR=1;PP=99.0;SC=TTTTGTTTTGTTTTGTTTGTT;TC=17;TR=4 GT:GL:GQ 0/1:-79.23,-33.31,-124.52:100 20 3192798 . C CAG . PASS FR=0.5;HP=2;NF=2;NR=6;PP=100.0;SC=GCCTGGGTGACAGAGAGAGAG;TC=20;TR=8 GT:GL:GQ 0/1:-108.84,-41.85,-123.5:100 20 3198551 . G GTT . PASS FR=0.5;HP=2;NF=1;NR=2;PP=63.0;SC=AGTTTTTGTGGGTTTTTTTTT;TC=22;TR=3 GT:GL:GQ 0/1:-111.88,-112.41,-193.71:91 20 3202220 . GTGGC G . PASS FR=0.5;HP=2;NF=2;NR=5;PP=100.0;SC=TGTCCCGGGTGTGGCTGGCGA;TC=19;TR=7 GT:GL:GQ 0/1:-150.53,-63.82,-136.14:100 20 3276659 . CT C . PASS FR=1.0;HP=3;NF=5;NR=6;PP=100.0;SC=ACATCGGGAACTTTCGGTTTC;TC=16;TR=11 GT:GL:GQ 1/1:-135.26,-24.21,-14.73:79 20 3290980 . A AAAAG . PASS FR=0.9998;HP=4;NF=1;NR=1;PP=30.0;SC=AAGAGAAAGAAAAAGAAAGAA;TC=7;TR=2 GT:GL:GQ 1/1:-37.89,-18.65,-17.26:34 20 3313547 . G GGTGT . PASS FR=1.0;HP=1;NF=1;NR=3;PP=100.0;SC=GTGTGCGTGTGGTGTGTGTGT;TC=20;TR=4 GT:GL:GQ 1/1:-194.22,-148.74,-144.19:56 20 3314333 . G GT . PASS FR=1.0;HP=10;NF=9;NR=9;PP=100.0;SC=CTTATTAAAGGTTTTTTTTTT;TC=34;TR=18 GT:GL:GQ 1/1:-126.24,-28.85,-19.8:75 20 3317061 . G GT . PASS FR=1.0;HP=10;NF=5;NR=7;PP=100.0;SC=GTTTTGTTCAGTTTTTTTTTT;TC=20;TR=12 GT:GL:GQ 1/1:-81.13,-22.72,-13.12:80 20 3318622 . TATAAAATATATAATAC T . PASS FR=0.5;HP=2;NF=3;NR=5;PP=100.0;SC=ATATATAATATATAAAATATA;TC=21;TR=8 GT:GL:GQ 1/0:-309.41,-50.93,-55.49:45 20 3320964 . AGTTT A . PASS FR=1.0;HP=1;NF=6;NR=12;PP=100.0;SC=AATCATACCTAGTTTGTACTA;TC=22;TR=18 GT:GL:GQ 1/1:-403.07,-167.86,-153.33:100 20 3320971 . A AC . PASS FR=1.0;HP=1;NF=6;NR=13;PP=100.0;SC=CCTAGTTTGTACTATAAAAAA;TC=19;TR=19 GT:GL:GQ 1/1:-403.07,-261.66,-248.63:100 20 3323678 . AT A . PASS FR=1.0;HP=5;NF=3;NR=1;PP=100.0;SC=TCTGATGATTATTTCTATTGC;TC=28;TR=4 GT:GL:GQ 1/1:-575.25,-570.95,-570.67:100 20 3323683 . T TAAA . PASS FR=1.0;HP=1;NF=13;NR=11;PP=100.0;SC=TGATTATTTCTATTGCTGTGC;TC=29;TR=24 GT:GL:GQ 1/1:-597.36,-560.99,-550.34:86 20 3323709 . T TA . PASS FR=1.0;HP=2;NF=16;NR=21;PP=100.0;SC=CATGTTCATTTGTTAGGTCCC;TC=38;TR=37 GT:GL:GQ 1/1:-694.83,-570.91,-558.14:100 20 3325237 . TACACACAC T . PASS FR=1.0;HP=2;NF=4;NR=2;PP=100.0;SC=TACACACACATACACACACAC;TC=33;TR=6 GT:GL:GQ 1/1:-276.44,-185.04,-177.42:63 20 3332481 . TTTTA T . PASS FR=1.0;HP=3;NF=7;NR=10;PP=100.0;SC=GTTTGTGTTATTTTATTTATT;TC=28;TR=17 GT:GL:GQ 1/1:-276.75,-43.8,-27.83:100 20 3333166 . TCA T . PASS FR=1.0;HP=1;NF=9;NR=10;PP=100.0;SC=TGGCTGTCATTCACATTCCAG;TC=22;TR=19 GT:GL:GQ 1/1:-222.99,-23.7,-9.78:100 20 3333493 . T TTA . PASS FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=TTCAAAATATTTATATATATA;TC=27;TR=13 GT:GL:GQ 1/1:-272.96,-96.81,-86.7:65 20 3336192 . G GC . PASS FR=1.0;HP=2;NF=5;NR=10;PP=100.0;SC=CTGCACTCCAGCCTGGGTGAC;TC=18;TR=15 GT:GL:GQ 1/1:-163.64,-31.05,-19.12:100 20 3338276 . G GCTTAT . PASS FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=CACCCATCCAGCTTTATCTTT;TC=23;TR=18 GT:GL:GQ 1/1:-329.33,-26.75,-8.74:100 20 3345587 . C CT . PASS FR=1.0;HP=6;NF=1;NR=10;PP=100.0;SC=CCTTCTTTTCCTTTTTTCTTT;TC=27;TR=11 GT:GL:GQ 1/1:-267.74,-155.91,-141.96:100 20 3346020 . TTTTATTTA T . PASS FR=1.0;HP=3;NF=7;NR=6;PP=100.0;SC=TTTGATAACATTTTATTTATT;TC=29;TR=13 GT:GL:GQ 1/1:-347.46,-36.68,-23.65:100 20 3349612 . T TA . PASS FR=1.0;HP=2;NF=8;NR=3;PP=100.0;SC=ACCCCATTTCTCTAAAAATAC;TC=11;TR=11 GT:GL:GQ 1/1:-135.85,-60.43,-52.97:61 20 3377965 . G GTTTTGTT . PASS FR=1.0;HP=8;NF=3;NR=2;PP=100.0;SC=TTTTTGTTTTGTTTTGTTTTT;TC=16;TR=5 GT:GL:GQ 1/1:-157.49,-62.9,-56.59:79 20 3378366 . TG T . PASS FR=1.0;HP=10;NF=6;NR=4;PP=100.0;SC=AGATTTTTTTTGGGGGGGGGG;TC=22;TR=10 GT:GL:GQ 1/1:-84.99,-30.32,-19.67:66 20 3382249 . T TA . PASS FR=1.0;HP=2;NF=7;NR=9;PP=100.0;SC=AATTATTATCTTTCATTCAAT;TC=19;TR=16 GT:GL:GQ 1/1:-178.1,-44.13,-31.76:100 20 3382515 . TC T . PASS FR=1.0;HP=6;NF=2;NR=10;PP=100.0;SC=TGGGGAGGGCTCCCCCGCCCC;TC=19;TR=12 GT:GL:GQ 1/1:-132.42,-42.62,-32.12:88 20 3398847 . T TAC . PASS FR=0.5;HP=2;NF=2;NR=1;PP=82.0;SC=AATAACAACATACACACACAC;TC=26;TR=3 GT:GL:GQ 0/1:-87.09,-56.01,-103.69:100 20 3418279 . TACACACACAC T . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=CACACGAGGGTACACACACAC;TC=17;TR=3 GT:GL:GQ 0/1:-117.7,-66.19,-77.13:50 20 3419562 . TACAC T . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TCAAAATACATACACACACAC;TC=29;TR=4 GT:GL:GQ 0/1:-141.17,-79.46,-166.16:100 20 3426771 . T TC . PASS FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=TTGCAGAAACTGACAAAATAG;TC=25;TR=23 GT:GL:GQ 1/1:-297.92,-207.29,-192.68:100 20 3439128 . AT A . PASS FR=1.0;HP=4;NF=4;NR=3;PP=100.0;SC=TGTCTCAAAAATATATATATA;TC=13;TR=7 GT:GL:GQ 1/1:-127.06,-48.08,-43.43:57 20 3439712 . CATTTATTTATTT CATTTATTT,C . PASS FR=0.5,0.5;HP=1;NF=2,5;NR=1,1;PP=100.0,100.0;SC=AACATAAAATCATTTATTTAT;TC=23;TR=3,6 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3441674 . G GA . PASS FR=0.5;HP=7;NF=13;NR=3;PP=100.0;SC=TTCTTATTAGGAAAAAAACCA;TC=23;TR=16 GT:GL:GQ 0/1:-122.74,-20.86,-35.93:68 20 3456629 . CA C . PASS FR=0.5;HP=8;NF=3;NR=5;PP=100.0;SC=TCCTCACTACCAAAAAAAAGA;TC=22;TR=8 GT:GL:GQ 0/1:-62.73,-25.03,-67.91:100 20 3462307 . A ATTC . PASS FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=TAAATTTTTAATTAAGTTTTC;TC=17;TR=9 GT:GL:GQ 0/1:-213.54,-117.72,-169.88:100 20 3465413 . G GTTA . PASS FR=0.5;HP=3;NF=4;NR=7;PP=100.0;SC=TATATTTCCAGTTTAGGTCTC;TC=32;TR=11 GT:GL:GQ 0/1:-171.48,-39.39,-198.21:100 20 3465556 . AATT A . PASS FR=0.5;HP=3;NF=3;NR=3;PP=100.0;SC=TGGATTTTAAAATTATTATTA;TC=23;TR=6 GT:GL:GQ 0/1:-128.2,-26.49,-64.94:100 20 3467027 . TTTTCC T . PASS FR=0.5;HP=3;NF=3;NR=10;PP=100.0;SC=GTTGTTTTTCTTTTCCTTTTT;TC=35;TR=13 GT:GL:GQ 0/1:-205.57,-36.22,-212.27:100 20 3468732 . AT A . PASS FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=GTTGGCTAACATGTTCCCTGC;TC=24;TR=10 GT:GL:GQ 0/1:-129.57,-23.07,-107.21:100 20 3472426 . T TA . PASS FR=0.5;HP=1;NF=4;NR=5;PP=100.0;SC=CCCCAAAACTTATCTAAGTAT;TC=30;TR=9 GT:GL:GQ 0/1:-164.9,-36.91,-163.8:100 20 3473769 . TTGTGTGTGTG TTGTGTGTG,T . PASS FR=0.5,0.5;HP=2;NF=3,2;NR=1,0;PP=100.0,100.0;SC=GTACGTTTGTTTGTGTGTGTG;TC=10;TR=4,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3489906 . C CAG . PASS FR=0.5;HP=3;NF=7;NR=5;PP=100.0;SC=TGTAATGAGTCAAATATTGAA;TC=30;TR=12 GT:GL:GQ 0/1:-218.47,-143.39,-285.84:100 20 3495915 . T TG . PASS FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=GTGTTACCATTCTAGAGATGA;TC=24;TR=10 GT:GL:GQ 0/1:-170.31,-150.44,-250.52:100 20 3509359 . CTAAAA C . PASS FR=0.5;HP=1;NF=7;NR=9;PP=100.0;SC=CCCCTTGAACCTAAAATAAAA;TC=36;TR=16 GT:GL:GQ 0/1:-259.32,-75.45,-201.38:100 20 3516100 . GA G . PASS FR=0.5;HP=2;NF=4;NR=5;PP=100.0;SC=AACATTACTTGATAACCTTTC;TC=24;TR=9 GT:GL:GQ 0/1:-89.87,-17.09,-134.48:100 20 3517232 . T TA . PASS FR=0.5;HP=4;NF=5;NR=10;PP=100.0;SC=TTTATTCATTTAAAAGCAACA;TC=33;TR=15 GT:GL:GQ 0/1:-148.46,-23.56,-134.17:100 20 3518135 . TTG T . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TATTTTTTTCTTGTTTTTTTT;TC=24;TR=9 GT:GL:GQ 0/1:-164.48,-76.63,-118.93:100 20 3520111 . TGAGAAACAGAAA T . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=GTCAAATACTTGAGAAACAGA;TC=30;TR=10 GT:GL:GQ 0/1:-291.42,-56.72,-205.51:100 20 3533082 . C CTA . PASS FR=0.5;HP=6;NF=5;NR=7;PP=100.0;SC=CCAGATGTCCCCCCCAGTTAA;TC=28;TR=12 GT:GL:GQ 0/1:-172.54,-164.36,-281.23:100 20 3536203 . CA C . PASS FR=0.5;HP=5;NF=5;NR=1;PP=100.0;SC=TGGTAGACCACAAAACAAAAT;TC=20;TR=6 GT:GL:GQ 0/1:-93.07,-22.5,-78.34:100 20 3549166 . A AT . PASS FR=0.5;HP=7;NF=6;NR=5;PP=100.0;SC=ACTCAAAAAAAATATATTTCA;TC=27;TR=11 GT:GL:GQ 0/1:-132.66,-26.81,-119.92:100 20 3550790 . AT A . PASS FR=0.5;HP=10;NF=9;NR=3;PP=100.0;SC=AATTGTCTCAATTTTTTTTTT;TC=36;TR=12 GT:GL:GQ 0/1:-95.8,-54.46,-109.39:100 20 3554405 . TTTTA T . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=TTTTATTTTATTTTATTTATT;TC=28;TR=8 GT:GL:GQ 0/1:-169.52,-76.02,-126.65:100 20 3557342 . G GTCTATCTATCTATCTATCTA,GTCTGTCTGTCTATCTA . PASS FR=0.5,0.5;HP=2;NF=0,1;NR=2,1;PP=100.0,100.0;SC=CTGTCTGTCTGTCTATCTATC;TC=14;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3577359 . AACTTT A . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GTTCTCTTAAAACTTTACTTT;TC=28;TR=12 GT:GL:GQ 0/1:-187.21,-26.31,-190.0:100 20 3587084 . A ACT . PASS FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=TTCTCTCTTCACTGTTTCCTG;TC=27;TR=7 GT:GL:GQ 0/1:-175.39,-93.87,-225.08:100 20 3587106 . TGTG T . PASS FR=0.5;HP=1;NF=4;NR=3;PP=100.0;SC=ATGTGGGACTTGTGGTGCCAC;TC=26;TR=7 GT:GL:GQ 0/1:-197.29,-142.58,-281.02:100 20 3597598 . AT A . PASS FR=0.5;HP=5;NF=5;NR=7;PP=29.0;SC=CAAGGATCGCATTTTTATCCC;TC=39;TR=12 GT:GL:GQ 0/1:-225.54,-208.64,-370.51:76 20 3599489 . G GGTT . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TGGTGGTGGTGGTTTTGTTTC;TC=28;TR=10 GT:GL:GQ 0/1:-173.69,-38.78,-110.57:100 20 3601166 . T TAC . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTACTGGGATTAGGCGTGAGC;TC=23;TR=6 GT:GL:GQ 0/1:-99.56,-38.65,-114.14:100 20 3607044 . TAAAAA T . PASS FR=0.5;HP=5;NF=6;NR=1;PP=100.0;SC=TTTTCTCTCTTAAAAAGAAAA;TC=23;TR=7 GT:GL:GQ 0/1:-96.17,-24.47,-167.72:100 20 3608928 . A AAG . PASS FR=0.5;HP=2;NF=6;NR=2;PP=100.0;SC=GAAAACTAGAAAGAAACTTCT;TC=32;TR=8 GT:GL:GQ 0/1:-96.19,-24.02,-201.47:100 20 3610589 . G GT . PASS FR=0.5;HP=7;NF=7;NR=8;PP=100.0;SC=ATCATTCTGAGTTTTTTTATT;TC=36;TR=15 GT:GL:GQ 0/1:-148.28,-61.67,-123.51:100 20 3612124 . A AC . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=GTCTGTTGAGACTGTGTCCTA;TC=17;TR=6 GT:GL:GQ 0/1:-86.01,-27.19,-97.39:100 20 3627840 . C CA . PASS FR=0.5;HP=6;NF=4;NR=7;PP=100.0;SC=CTCAACTGTGCAAAAAACAAA;TC=27;TR=11 GT:GL:GQ 0/1:-99.01,-25.59,-91.79:100 20 3627925 . A ATTAAC . PASS FR=0.5;HP=2;NF=2;NR=9;PP=100.0;SC=AGTCAGATGAATTGTTTTCAT;TC=29;TR=11 GT:GL:GQ 0/1:-210.42,-38.37,-176.36:100 20 3635158 . A AT . PASS FR=0.5;HP=2;NF=8;NR=5;PP=100.0;SC=CAAGAAAGCCATAGACCGGAA;TC=23;TR=13 GT:GL:GQ 0/1:-191.76,-111.36,-148.51:100 20 3642221 . TTC T . PASS FR=1.0;HP=2;NF=12;NR=3;PP=100.0;SC=TCGCCACCATTTCTCCAGAAC;TC=20;TR=15 GT:GL:GQ 1/1:-312.08,-172.82,-161.67:43 20 3643129 . TC T . PASS FR=1.0;HP=9;NF=4;NR=4;PP=100.0;SC=CGGGGTGGTATCCCCCCCCCA;TC=20;TR=8 GT:GL:GQ 1/1:-89.01,-45.99,-37.4:71 20 3645120 . AAAAC A . PASS FR=1.0;HP=5;NF=1;NR=4;PP=100.0;SC=TTTTTTTTAAAAAACAAACAA;TC=18;TR=5 GT:GL:GQ 1/1:-88.2,-13.8,-7.58:77 20 3650540 . A ACACCACC . PASS FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CCAGGCTCTGACAGCAGCCTG;TC=12;TR=7 GT:GL:GQ 1/1:-183.63,-21.64,-13.12:68 20 3664603 . AG A . PASS FR=1.0;HP=6;NF=3;NR=9;PP=100.0;SC=TTCTGTAGACAGGGGGGTCTC;TC=16;TR=12 GT:GL:GQ 1/1:-110.02,-26.49,-16.31:85 20 3667748 . C CG . PASS FR=1.0;HP=2;NF=12;NR=5;PP=100.0;SC=AAAGTTCACCCGCCCCCAACT;TC=24;TR=17 GT:GL:GQ 1/1:-221.42,-44.79,-28.21:100 20 3677095 . T TGCTG . PASS FR=1.0;HP=1;NF=4;NR=13;PP=100.0;SC=GGAGGCCTTCTGCTGGCTGGA;TC=22;TR=17 GT:GL:GQ 1/1:-297.16,-58.83,-44.05:100 20 3685444 . A AT . PASS FR=1.0;HP=7;NF=6;NR=4;PP=100.0;SC=TTGTTTTTTAATTTTTTTGTA;TC=15;TR=10 GT:GL:GQ 1/1:-93.4,-15.67,-6.68:75 20 3699376 . AAAAT A . PASS FR=1.0;HP=5;NF=4;NR=2;PP=100.0;SC=CAAAAAATAAAAAATAAATAA;TC=21;TR=6 GT:GL:GQ 1/1:-124.16,-19.34,-11.28:66 20 3700024 . TTTAC T . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=TATTTATTTATTTACTTACTT;TC=22;TR=7 GT:GL:GQ 0/1:-142.54,-24.82,-34.29:44 20 3702676 . C CT . PASS FR=1.0;HP=9;NF=9;NR=6;PP=100.0;SC=ATATGTTGAACTTTTTTTTTA;TC=20;TR=15 GT:GL:GQ 1/1:-102.25,-23.87,-11.51:100 20 3703373 . GAATA G . PASS FR=1.0;HP=3;NF=3;NR=4;PP=100.0;SC=TATACATGGAGAATAAATAAA;TC=24;TR=7 GT:GL:GQ 1/1:-129.84,-26.73,-19.11:63 20 3705235 . G GGAAA . PASS FR=1.0;HP=3;NF=3;NR=2;PP=100.0;SC=AAGAAAGAAAGGAAAGAAATA;TC=24;TR=5 GT:GL:GQ 1/1:-319.51,-157.83,-145.36:98 20 3717704 . AAAATAAATAAATAAAT AAAATAAATAAAT,A . PASS FR=0.5,0.5;HP=4;NF=1,0;NR=1,2;PP=100.0,55.0;SC=CTCTGCCTCAAAAATAAATAA;TC=12;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3719488 . AGT A . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=TCTGTGAGTGAGTGTGTGTGT;TC=28;TR=10 GT:GL:GQ 0/1:-149.53,-25.54,-102.21:100 20 3736407 . CCCCCAGCCCAGTGG C . PASS FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=AGCTGATCGACCCCCAGCCCA;TC=22;TR=4 GT:GL:GQ 0/1:-177.03,-114.74,-207.47:100 20 3740620 . GCA G . PASS FR=1.0;HP=1;NF=4;NR=6;PP=100.0;SC=ACTCACACATGCACACACACA;TC=17;TR=10 GT:GL:GQ 1/1:-154.32,-36.11,-25.75:86 20 3751453 . G GT . PASS FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=CAAACACACGGTTTTTTGTTT;TC=25;TR=2 GT:GL:GQ 1/1:-234.3,-199.49,-191.92:62 20 3752464 . A AACAC,AACACAC . PASS FR=0.5,0.5;HP=3;NF=4,3;NR=3,3;PP=100.0,100.0;SC=AAAAAGAGAAAACACACACAC;TC=29;TR=7,6 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3755004 . G GACA . PASS FR=1.0;HP=2;NF=1;NR=7;PP=100.0;SC=GACAGAGTGAGACATCTCATA;TC=13;TR=8 GT:GL:GQ 1/1:-134.63,-25.28,-17.61:63 20 3768789 . A AAAAG . PASS FR=0.5;HP=8;NF=4;NR=3;PP=100.0;SC=ATCTCAAAAAAAAAGAAAGAA;TC=28;TR=7 GT:GL:GQ 0/1:-141.47,-38.74,-119.72:100 20 3770324 . T TAATAATA . PASS FR=0.5;HP=8;NF=1;NR=2;PP=29.0;SC=GGCCAAAAAATAATAATAAAT;TC=11;TR=3 GT:GL:GQ 0/1:-67.44,-43.02,-52.14:42 20 3774219 . AATTTT A . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=GGTTTTAGAGAATTTTATTTT;TC=20;TR=5 GT:GL:GQ 0/1:-126.4,-91.22,-154.58:100 20 3775162 . GTT G . PASS FR=0.5;HP=10;NF=3;NR=6;PP=100.0;SC=TCTCGGGGCAGTTTTTTTTTT;TC=26;TR=9 GT:GL:GQ 0/1:-103.9,-68.26,-117.09:100 20 3776005 . C CA . PASS FR=0.5;HP=8;NF=1;NR=4;PP=23.0;SC=GACTCCATCCCAAAAAAAACA;TC=14;TR=5 GT:GL:GQ 0/1:-145.51,-129.15,-148.62:73 20 3776021 . AAAC A . PASS FR=0.5;HP=3;NF=3;NR=1;PP=100.0;SC=AAACAAAACAAAACAAAAAGA;TC=21;TR=4 GT:GL:GQ 0/1:-163.41,-119.44,-232.96:100 20 3780857 . T TGGACTGGAGACCTGGTGCTAG . PASS FR=0.5;HP=6;NF=4;NR=1;PP=100.0;SC=TACTCCCCCCTGGACTGGGGG;TC=10;TR=5 GT:GL:GQ 0/1:-153.98,-19.16,-34.72:70 20 3786892 . C CT . PASS FR=1.0;HP=4;NF=10;NR=2;PP=100.0;SC=CTTGTCCCTTCTTCTCCCAAT;TC=16;TR=12 GT:GL:GQ 1/1:-171.33,-64.44,-53.38:92 20 3787614 . CAT C . PASS FR=1.0;HP=2;NF=11;NR=13;PP=100.0;SC=AGTGCACACACATGTCAGGCA;TC=30;TR=24 GT:GL:GQ 1/1:-451.43,-312.17,-297.5:100 20 3789927 . C CCCG . PASS FR=1.0;HP=2;NF=2;NR=10;PP=100.0;SC=AGTTACCACGCGCTCTCTTTC;TC=17;TR=12 GT:GL:GQ 1/1:-241.99,-120.76,-110.7:78 20 3790246 . ATATAT A . PASS FR=1.0;HP=8;NF=5;NR=2;PP=92.0;SC=TCAAAAAAAAATATATATATA;TC=14;TR=7 GT:GL:GQ 1/1:-198.37,-176.0,-172.1:52 20 3795480 . AGGCGTGAGCCACCGCGCCC A . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=CTGGGATTACAGGCGTGAGCC;TC=12;TR=4 GT:GL:GQ 0/1:-109.14,-46.17,-99.46:100 20 3824585 . TTTTAC T . PASS FR=1.0;HP=3;NF=18;NR=4;PP=100.0;SC=AGATGATTTATTTTACTTTAT;TC=28;TR=22 GT:GL:GQ 1/1:-337.35,-36.39,-16.32:100 20 3843259 . A AT . PASS FR=0.5;HP=10;NF=3;NR=7;PP=100.0;SC=AGTTTTCCAAATTTTTTTTTT;TC=31;TR=10 GT:GL:GQ 0/1:-80.23,-37.02,-73.45:100 20 3859483 . TCACACACACA TCA,T . PASS FR=0.5,0.5;HP=1;NF=1,2;NR=1,1;PP=100.0,85.0;SC=TGAGACTCTGTCACACACACA;TC=21;TR=2,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 3860757 . AAAAC A . PASS FR=0.5;HP=4;NF=5;NR=2;PP=100.0;SC=GTCTCTACTAAAAACAAACAA;TC=18;TR=7 GT:GL:GQ 0/1:-108.81,-21.22,-75.5:100 20 3860858 . GC G . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=AACCCAGGAGGCGGAGCTTGT;TC=16;TR=6 GT:GL:GQ 0/1:-84.65,-31.03,-99.29:100 20 3865910 . A AGGC . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=TCTGTCACCCAGGCTCAAGTT;TC=27;TR=12 GT:GL:GQ 0/1:-249.42,-106.14,-180.19:100 20 3873092 . TTTTA T . PASS FR=1.0;HP=5;NF=6;NR=8;PP=100.0;SC=ACTAAATCTTTTTTATTTATT;TC=25;TR=14 GT:GL:GQ 1/1:-225.87,-50.85,-37.99:100 20 3879882 . AGT A . PASS FR=1.0;HP=1;NF=4;NR=4;PP=100.0;SC=GCAGTGATGTAGTGTAGGCTC;TC=17;TR=8 GT:GL:GQ 1/1:-213.63,-128.83,-121.45:61 20 3882311 . TTTTG T . PASS FR=1.0;HP=3;NF=15;NR=11;PP=100.0;SC=AAGTCAGTACTTTTGTTTATT;TC=29;TR=26 GT:GL:GQ 1/1:-341.87,-21.25,-0.46:100 20 3883619 . GACACACACACACACAC G . PASS FR=0.5013;HP=2;NF=4;NR=1;PP=100.0;SC=GATGTGTATAGACACACACAC;TC=14;TR=5 GT:GL:GQ 0/1:-204.43,-28.1,-33.39:25 20 3885810 . GACTGCACC G . PASS FR=1.0;HP=1;NF=4;NR=7;PP=100.0;SC=CATCGCTTGTGACTGCACCAC;TC=19;TR=11 GT:GL:GQ 1/1:-301.58,-43.69,-32.0:95 20 3899973 . T TTGA . PASS FR=1.0;HP=3;NF=18;NR=6;PP=100.0;SC=AGAAAAACCCTTGAACATTCC;TC=30;TR=24 GT:GL:GQ 1/1:-376.13,-29.44,-7.6:100 20 3900864 . T TA . PASS FR=1.0;HP=10;NF=11;NR=11;PP=100.0;SC=AAGTTAACCTTAAAAAAAAAA;TC=30;TR=22 GT:GL:GQ 1/1:-160.94,-53.86,-35.6:100 20 3929292 . G GA . PASS FR=1.0;HP=1;NF=16;NR=6;PP=100.0;SC=TACATACCAGGATAACTGTTG;TC=29;TR=22 GT:GL:GQ 1/1:-330.17,-190.24,-173.09:100 20 3930806 . T TGACTGG . PASS FR=1.0;HP=2;NF=7;NR=14;PP=100.0;SC=CCTTGTATAGTGATGAATGTG;TC=26;TR=21 GT:GL:GQ 1/1:-450.24,-61.65,-40.95:100 20 3945171 . A AT . PASS FR=1.0;HP=10;NF=7;NR=12;PP=100.0;SC=TTTTCAAGTAATTTTTTTTTT;TC=29;TR=19 GT:GL:GQ 1/1:-126.38,-32.45,-22.97:79 20 3956227 . C CA . PASS FR=1.0;HP=5;NF=12;NR=13;PP=100.0;SC=ATTGTGTTCTCAAAAAGATAT;TC=28;TR=25 GT:GL:GQ 1/1:-249.31,-33.1,-13.35:100 20 3965697 . AACC A . PASS FR=1.0;HP=1;NF=9;NR=9;PP=100.0;SC=GAACAACAACAACCACAACAA;TC=26;TR=18 GT:GL:GQ 1/1:-461.94,-340.35,-326.48:100 20 3971557 . G GTTCCATGATAACAT . PASS FR=1.0;HP=2;NF=12;NR=8;PP=100.0;SC=ATTTGGCACAGTTCCATGATA;TC=27;TR=20 GT:GL:GQ 1/1:-553.38,-41.98,-23.08:100 20 3990695 . CACAAACAA C . PASS FR=1.0;HP=1;NF=6;NR=4;PP=100.0;SC=GAGACCCTGTCACAAACAAAC;TC=23;TR=10 GT:GL:GQ 1/1:-176.37,-39.86,-31.94:65 20 3995386 . GCACACA G . PASS FR=1.0;HP=2;NF=1;NR=1;PP=100.0;SC=ACTTGAATGCGCACACACACA;TC=18;TR=2 GT:GL:GQ 1/1:-95.82,-46.66,-41.67:61 20 4008931 . C CTCTT . PASS FR=1.0;HP=2;NF=1;NR=4;PP=100.0;SC=TCTCATCTCTCTGTCTTTCTC;TC=9;TR=5 GT:GL:GQ 1/1:-127.43,-46.42,-40.22:77 20 4021562 . C CGA . PASS FR=1.0;HP=2;NF=8;NR=2;PP=100.0;SC=GAAGAGAAAGCGAGAGAGAGA;TC=21;TR=10 GT:GL:GQ 1/1:-216.37,-85.41,-73.73:98 20 4025709 . TGA T . PASS FR=1.0;HP=2;NF=12;NR=9;PP=100.0;SC=AAATACATAATGAGAGAGAGA;TC=26;TR=21 GT:GL:GQ 1/1:-247.4,-21.57,-4.6:100 20 4035810 . T TGTTTGTATTACA . PASS FR=1.0;HP=2;NF=10;NR=4;PP=100.0;SC=TAGCTGGGCATGGTGGCGGGT;TC=15;TR=14 GT:GL:GQ 1/1:-361.94,-174.62,-163.57:92 20 4042278 . A AT . PASS FR=1.0;HP=2;NF=7;NR=15;PP=100.0;SC=AAACACATAAATCTCTCTCTC;TC=29;TR=22 GT:GL:GQ 1/1:-269.48,-66.17,-47.18:100 20 4044153 . C CA . PASS FR=1.0;HP=6;NF=8;NR=10;PP=100.0;SC=GCCCCAGGGACGGGGGGCTGG;TC=21;TR=18 GT:GL:GQ 1/1:-167.11,-27.75,-13.35:100 20 4048870 . AGAGTTATCTTGCCTGAG A . PASS FR=0.5;HP=4;NF=9;NR=5;PP=100.0;SC=CACGTGCCCCAGAGTTATCTT;TC=24;TR=14 GT:GL:GQ 1/0:-626.63,-331.02,-449.96:74 20 4050067 . A AT . PASS FR=1.0;HP=8;NF=14;NR=11;PP=100.0;SC=TAAGTTTTAAATTTTTTTTGT;TC=36;TR=25 GT:GL:GQ 1/1:-400.71,-316.84,-301.94:100 20 4052527 . A AT . PASS FR=1.0;HP=1;NF=15;NR=9;PP=100.0;SC=CTAAGCATGAAGTGGTCTCAG;TC=27;TR=24 GT:GL:GQ 1/1:-335.51,-240.21,-229.69:88 20 4057207 . G GT . PASS FR=1.0;HP=3;NF=17;NR=11;PP=100.0;SC=TAGATTATTTGGTTTTTTTTT;TC=40;TR=28 GT:GL:GQ 1/1:-398.27,-278.49,-261.61:100 20 4057861 . T TTTCC . PASS FR=1.0;HP=4;NF=8;NR=13;PP=100.0;SC=CTGATGATTTTTATGTTTTCT;TC=33;TR=21 GT:GL:GQ 1/1:-430.04,-131.81,-113.85:100 20 4058335 . T TATTA . PASS FR=1.0;HP=2;NF=14;NR=5;PP=100.0;SC=TTAATATGTTTATTATACATA;TC=19;TR=19 GT:GL:GQ 1/1:-424.99,-369.88,-364.34:69 20 4060198 . CTCTT C . PASS FR=0.5;HP=3;NF=8;NR=6;PP=100.0;SC=TTCTATTGTTCTCTTTGTTTT;TC=37;TR=14 GT:GL:GQ 0/1:-273.47,-128.98,-306.0:100 20 4060592 . C CTTTA . PASS FR=0.5;HP=3;NF=4;NR=8;PP=100.0;SC=ATAATTTTTGCTTTATTTATT;TC=31;TR=12 GT:GL:GQ 0/1:-163.9,-38.86,-129.26:100 20 4070170 . GTA G . PASS FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTGTGTGTGTATATATATA;TC=25;TR=5 GT:GL:GQ 0/1:-276.88,-237.9,-267.79:100 20 4070252 . A ATGTATATATG . PASS FR=1.0;HP=2;NF=3;NR=1;PP=100.0;SC=GTGTGTATATATGTATATATG;TC=16;TR=4 GT:GL:GQ 1/1:-231.61,-30.38,-18.61:81 20 4070382 . ATATGTGTGTGTG A . PASS FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=ATGTGTATATATATGTGTGTG;TC=25;TR=3 GT:GL:GQ 1/1:-347.8,-231.66,-223.35:51 20 4070396 . GTGTGTGTGTGTGTATATATATATATA G . PASS FR=0.5;HP=2;NF=4;NR=4;PP=100.0;SC=GTGTGTGTGTGTGTGTGTGTG;TC=18;TR=8 GT:GL:GQ 1/0:-384.34,-235.32,-225.8:62 20 4071341 . CA C . PASS FR=0.5026;HP=9;NF=5;NR=5;PP=100.0;SC=CTGATTATGGCAAAAAAAAAC;TC=20;TR=10 GT:GL:GQ 0/1:-155.5,-119.13,-123.71:22 20 4071895 . G GT . PASS FR=0.5;HP=8;NF=3;NR=3;PP=72.0;SC=TGGGACCTTTGTTTTTGCAAA;TC=22;TR=6 GT:GL:GQ 0/1:-127.95,-100.32,-170.75:100 20 4074739 . G GA . PASS FR=0.5;HP=9;NF=2;NR=4;PP=75.0;SC=ACTACATCTCGAAAAAAAAAG;TC=16;TR=6 GT:GL:GQ 0/1:-104.75,-76.46,-99.49:100 20 4077346 . ATATTAT A . PASS FR=0.5;HP=1;NF=2;NR=2;PP=100.0;SC=TATGAGGACAATATTATTATT;TC=23;TR=4 GT:GL:GQ 0/1:-62.56,-10.62,-98.18:100 20 4092195 . G GTCAGCCAGAGAGGCTC . PASS FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=AGGTAAGACAGTCAGCCAGAG;TC=21;TR=12 GT:GL:GQ 1/1:-408.88,-45.59,-29.88:100 20 4092421 . A AT . PASS FR=0.5;HP=4;NF=5;NR=6;PP=100.0;SC=CTGGCAGCAGATTTTCCCTTA;TC=31;TR=11 GT:GL:GQ 0/1:-137.54,-52.61,-154.29:100 20 4095639 . T TATAC . PASS FR=0.5;HP=2;NF=3;NR=6;PP=100.0;SC=TATATATATATACACACACAT;TC=30;TR=9 GT:GL:GQ 0/1:-239.61,-67.33,-166.02:100 20 4096614 . T TG . PASS FR=0.5;HP=1;NF=3;NR=8;PP=100.0;SC=TTTGATGGCTTGTGAAGCCCA;TC=42;TR=11 GT:GL:GQ 0/1:-166.13,-48.49,-243.23:100 20 4099234 . C CTCT . PASS FR=1.0;HP=1;NF=2;NR=7;PP=100.0;SC=CTTCTTCTTCCTCTTCTTCCT;TC=17;TR=9 GT:GL:GQ 1/1:-213.81,-121.18,-113.85:91 20 4106279 . C CA . PASS FR=1.0;HP=4;NF=9;NR=14;PP=100.0;SC=ATGATCCACCCCCTTGGCCTC;TC=27;TR=23 GT:GL:GQ 1/1:-261.7,-33.57,-14.72:100 20 4106498 . AC A . PASS FR=0.5;HP=3;NF=4;NR=6;PP=100.0;SC=ACCCGCCACCACGTCAAGCTA;TC=17;TR=10 GT:GL:GQ 0/1:-151.03,-63.2,-86.55:100 20 4107003 . T TCTAA . PASS FR=0.5;HP=2;NF=4;NR=9;PP=100.0;SC=TGGAGGTAACTCTAGGACATA;TC=28;TR=13 GT:GL:GQ 0/1:-216.14,-60.6,-196.15:100 20 4108348 . A AC . PASS FR=1.0;HP=3;NF=9;NR=6;PP=100.0;SC=TTCTATGGAAAAGAGCAGTCA;TC=22;TR=15 GT:GL:GQ 1/1:-263.65,-164.58,-152.76:96 20 4111438 . CA C . PASS FR=1.0;HP=2;NF=13;NR=9;PP=100.0;SC=GGTGATCACACAGGGGCATGG;TC=27;TR=22 GT:GL:GQ 1/1:-393.14,-310.63,-301.96:68 20 4111530 . T TG . PASS FR=1.0;HP=1;NF=13;NR=14;PP=100.0;SC=CATCAAAACTTGCAGAAGTAT;TC=30;TR=27 GT:GL:GQ 1/1:-576.34,-531.28,-526.81:55 20 4112367 . TA T . PASS FR=0.5;HP=2;NF=7;NR=2;PP=100.0;SC=AGACTTTAGTTAATAATAATA;TC=25;TR=9 GT:GL:GQ 0/1:-105.53,-48.17,-185.05:100 20 4124037 . TACAC TAC,T . PASS FR=0.5,0.5;HP=2;NF=0,1;NR=6,6;PP=100.0,100.0;SC=TGTATGTGTATACACACACAC;TC=29;TR=6,7 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4165244 . C CAG . PASS FR=0.5;HP=3;NF=9;NR=7;PP=100.0;SC=TAAAACTCAACAGTTATATTT;TC=28;TR=16 GT:GL:GQ 0/1:-164.36,-34.34,-133.84:100 20 4189405 . A AGTGTTCT . PASS FR=1.0;HP=1;NF=8;NR=19;PP=100.0;SC=TGATCACAGAAGTGTTGAATG;TC=31;TR=27 GT:GL:GQ 1/1:-510.65,-52.94,-31.94:100 20 4193006 . T TA . PASS FR=1.0;HP=9;NF=5;NR=11;PP=100.0;SC=TGTGTTTGATTAAAAAAAAAT;TC=25;TR=16 GT:GL:GQ 1/1:-189.06,-113.86,-103.2:89 20 4204545 . CAACAGGTTT C . PASS FR=0.5;HP=3;NF=5;NR=5;PP=100.0;SC=TTTCAATTTACAACAGGTTTA;TC=29;TR=10 GT:GL:GQ 0/1:-264.93,-66.16,-208.86:100 20 4210072 . T TA . PASS FR=0.5;HP=5;NF=7;NR=3;PP=100.0;SC=GGAAGGAAGATGGGGGCGAGT;TC=33;TR=10 GT:GL:GQ 0/1:-169.78,-122.55,-232.56:100 20 4211685 . T TTTTCTTTC . PASS FR=1.0;HP=4;NF=3;NR=1;PP=100.0;SC=CTTTCTTTCTTTTTCTTTCTT;TC=17;TR=4 GT:GL:GQ 1/1:-163.69,-62.85,-59.76:50 20 4222606 . TG T,AG . PASS FR=0.5,0.5;HP=2;NF=14,3;NR=8,0;PP=72.0,7.0;SC=CAGCACAGCCTGATGGCTCTG;TC=29;TR=22,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:41 20 4223993 . CG C . PASS FR=1.0;HP=4;NF=10;NR=1;PP=100.0;SC=CTGGGCTCCTCGGGGCATCCG;TC=14;TR=11 GT:GL:GQ 1/1:-180.73,-119.68,-111.91:64 20 4255571 . TGAAA T . PASS FR=1.0;HP=1;NF=5;NR=4;PP=100.0;SC=AGGTATGCTCTGAAAGGAAGA;TC=15;TR=9 GT:GL:GQ 1/1:-155.75,-66.2,-58.38:79 20 4260218 . C CA . PASS FR=0.5;HP=3;NF=1;NR=9;PP=100.0;SC=CTGGTCTCCCCAGCATCTAGT;TC=27;TR=10 GT:GL:GQ 0/1:-138.73,-38.26,-150.01:100 20 4280077 . G GTGA . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=GATGTCTTTGGTGATGATGAT;TC=23;TR=6 GT:GL:GQ 0/1:-118.58,-26.45,-67.22:100 20 4300671 . G GT . PASS FR=1.0;HP=9;NF=9;NR=7;PP=100.0;SC=TATTTTTTAAGTTTTTTTTTC;TC=22;TR=16 GT:GL:GQ 1/1:-112.49,-30.96,-17.5:100 20 4305010 . C CCTGT . PASS FR=1.0;HP=1;NF=9;NR=14;PP=100.0;SC=AGGTTTGGCTCCTGTCTGACA;TC=27;TR=23 GT:GL:GQ 1/1:-478.98,-124.12,-105.32:100 20 4306264 . GT G . PASS FR=0.5;HP=3;NF=7;NR=4;PP=100.0;SC=ACAATATAAGGTTTACTTCAA;TC=24;TR=11 GT:GL:GQ 0/1:-115.0,-27.63,-111.62:100 20 4310291 . T TC . PASS FR=1.0;HP=1;NF=20;NR=9;PP=100.0;SC=CTCCTACGTGTCATGCCAGCT;TC=32;TR=29 GT:GL:GQ 1/1:-333.81,-66.33,-44.4:100 20 4310977 . GC G . PASS FR=0.5;HP=1;NF=14;NR=6;PP=100.0;SC=CCTGAAACTGGCGTAATTTAT;TC=41;TR=20 GT:GL:GQ 0/1:-231.9,-39.91,-159.66:100 20 4321071 . A AG . PASS FR=0.5;HP=5;NF=3;NR=2;PP=100.0;SC=AAGTCAAATCAGGGGGAGGAA;TC=19;TR=5 GT:GL:GQ 0/1:-50.11,-15.88,-71.26:100 20 4322091 . CA C . PASS FR=0.5;HP=1;NF=11;NR=7;PP=100.0;SC=GCCGTGTGTCCAGCCAAAACT;TC=33;TR=18 GT:GL:GQ 0/1:-210.17,-46.06,-156.61:100 20 4329185 . TC T . PASS FR=0.5;HP=1;NF=8;NR=2;PP=100.0;SC=AATTCTAGGTTCTTTCTCTCA;TC=28;TR=10 GT:GL:GQ 0/1:-148.46,-71.81,-182.2:100 20 4330761 . GGTGTGTGT G . PASS FR=1.0;HP=3;NF=1;NR=3;PP=100.0;SC=TAATTCATGGGGTGTGTGTGT;TC=30;TR=4 GT:GL:GQ 1/1:-224.07,-44.24,-35.58:72 20 4332044 . TG T . PASS FR=1.0;HP=6;NF=5;NR=2;PP=57.0;SC=TTTGTTTTTTTGTTTTTTTTT;TC=24;TR=7 GT:GL:GQ 1/1:-226.96,-113.86,-100.61:42 20 4343821 . TA T . PASS FR=0.5;HP=8;NF=5;NR=8;PP=100.0;SC=CATTTTTTTTTAAAATTTTTG;TC=35;TR=13 GT:GL:GQ 1/0:-274.8,-111.87,-90.41:100 20 4349378 . A AT . PASS FR=0.5;HP=3;NF=11;NR=7;PP=100.0;SC=TTTTGAAGGCATTTCCAGGGT;TC=27;TR=18 GT:GL:GQ 0/1:-181.47,-28.52,-69.89:100 20 4366637 . AAAAC A . PASS FR=1.0;HP=3;NF=8;NR=10;PP=100.0;SC=AAAACAAAACAAAACAAACAA;TC=29;TR=18 GT:GL:GQ 1/1:-255.42,-38.69,-23.59:100 20 4378952 . A AAAC . PASS FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=CAAAACAAACAAACAACAACA;TC=26;TR=13 GT:GL:GQ 1/1:-242.03,-34.58,-19.38:100 20 4380979 . CACAT C . PASS FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CACACACACACACATACAAGC;TC=29;TR=12 GT:GL:GQ 1/1:-310.99,-41.83,-21.18:100 20 4381267 . T TGTGTATTGTGGA . PASS FR=1.0;HP=2;NF=4;NR=9;PP=100.0;SC=GACAGCCTCCTTCAACAAAAA;TC=23;TR=13 GT:GL:GQ 1/1:-573.3,-462.6,-447.82:96 20 4381268 . TC T . PASS FR=1.0;HP=1;NF=4;NR=9;PP=100.0;SC=ACAGCCTCCTTCAACAAAAAA;TC=27;TR=13 GT:GL:GQ 1/1:-573.3,-567.48,-566.42:96 20 4384878 . TAGAC T . PASS FR=0.5;HP=4;NF=7;NR=6;PP=100.0;SC=ATGGAAGAAATAGACAGAGAG;TC=32;TR=13 GT:GL:GQ 0/1:-215.18,-58.15,-186.03:100 20 4390996 . ACT A . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AACACTCGAGACTCTCCAGCT;TC=25;TR=9 GT:GL:GQ 0/1:-160.6,-43.63,-115.25:100 20 4392384 . T TTG . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=GGGAATATAGTTGTGTGTGTG;TC=26;TR=3 GT:GL:GQ 0/1:-141.31,-92.22,-156.97:100 20 4403198 . CGT CGTGT,C . PASS FR=0.5,0.5;HP=2;NF=3,3;NR=2,0;PP=100.0,91.0;SC=TGTGTGTGTGCGTGTGTGTGT;TC=16;TR=5,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4418283 . TCC T . PASS FR=1.0;HP=5;NF=9;NR=17;PP=100.0;SC=TGAAAAATGCTCCCCAGGTTT;TC=26;TR=26 GT:GL:GQ 1/1:-235.22,-17.92,0.0:100 20 4422138 . A AAGAGGCAAGGCTTCCCCACATGCTCAGAATGG,G . PASS FR=0.5,0.5;HP=1;NF=2,3;NR=0,5;PP=100.0,87.0;SC=CTACAGAAAGATGATGGAGGT;TC=14;TR=2,8 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:23 20 4422142 . T TG . PASS FR=1.0;HP=2;NF=8;NR=6;PP=100.0;SC=AGAAAGATGATGGAGGTACTA;TC=19;TR=14 GT:GL:GQ 1/1:-319.37,-289.62,-286.77:23 20 4427312 . A AGCTTCTAT . PASS FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=TGTATAATAGAGTCCAGAGTC;TC=11;TR=2 GT:GL:GQ 1/0:-513.43,-441.06,-437.62:42 20 4431651 . TA T . PASS FR=0.5;HP=5;NF=9;NR=13;PP=100.0;SC=TCTAGACCCTTAAAAATAACA;TC=34;TR=22 GT:GL:GQ 0/1:-196.04,-30.01,-107.67:100 20 4438168 . T TTACACAAATGTAACCTATGTAACAA . PASS FR=0.5;HP=1;NF=2;NR=3;PP=100.0;SC=CCTGCACATGTACCCTTGAAC;TC=16;TR=5 GT:GL:GQ 0/1:-418.07,-256.53,-367.22:100 20 4439599 . GT G . PASS FR=0.5;HP=2;NF=11;NR=12;PP=100.0;SC=TGTGGGGAGAGTTAGCAAGAG;TC=36;TR=23 GT:GL:GQ 0/1:-329.81,-228.22,-300.4:100 20 4442338 . CTTTATTTTATTTTAT CTTTATTTTAT,C . PASS FR=0.5,0.5;HP=3;NF=2,1;NR=0,3;PP=100.0,100.0;SC=AAGTATCTAACTTTATTTTAT;TC=21;TR=2,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4445547 . T TAA . PASS FR=1.0;HP=1;NF=18;NR=22;PP=100.0;SC=TGTTTCCAGTTGTTATACTTT;TC=39;TR=40 GT:GL:GQ 1/1:-459.22,-244.89,-221.84:100 20 4452980 . TACAC T . PASS FR=1.0;HP=2;NF=1;NR=2;PP=100.0;SC=TTAATTCTTATACACACACAC;TC=21;TR=3 GT:GL:GQ 1/1:-75.87,-32.41,-30.31:43 20 4460649 . G GA . PASS FR=0.5;HP=9;NF=5;NR=8;PP=100.0;SC=TTTCCTCGGAGAAAAAAAACA;TC=39;TR=13 GT:GL:GQ 0/1:-191.57,-119.31,-159.65:100 20 4462152 . GGTCAATGTTATAAACTTTGC G . PASS FR=0.5;HP=2;NF=6;NR=5;PP=100.0;SC=CTACTTCTTGGGTCAATGTTA;TC=18;TR=11 GT:GL:GQ 1/0:-501.72,-174.1,-171.31:67 20 4462516 . T TTC . PASS FR=0.5;HP=1;NF=16;NR=1;PP=100.0;SC=GGGTTTAAAGTTCTCTAATGA;TC=41;TR=17 GT:GL:GQ 0/1:-181.56,-38.08,-223.18:100 20 4462799 . C CTT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=TCTTCTTCGTCCTTTTTTTTT;TC=36;TR=2 GT:GL:GQ 0/1:-520.7,-504.74,-499.84:81 20 4465737 . TG T . PASS FR=1.0;HP=2;NF=9;NR=18;PP=100.0;SC=CTCCTTGACATGGACTGAGAA;TC=27;TR=27 GT:GL:GQ 1/1:-258.03,-34.15,-15.14:100 20 4468340 . TA T . PASS FR=0.5;HP=10;NF=5;NR=2;PP=57.0;SC=ATATATATATTAAAAAAAAAA;TC=21;TR=7 GT:GL:GQ 0/1:-41.89,-18.73,-52.45:100 20 4469569 . C CT . PASS FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=CAAGTAAAGACTTTTGATTGT;TC=23;TR=9 GT:GL:GQ 0/1:-113.7,-24.95,-84.55:100 20 4474613 . GA G . PASS FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=ATTAGGAACAGAAAAAAATTA;TC=37;TR=10 GT:GL:GQ 0/1:-311.99,-245.02,-353.92:100 20 4474629 . A AAAT . PASS FR=0.5;HP=9;NF=11;NR=5;PP=100.0;SC=AATTAAAAAAAAAATATACAC;TC=32;TR=16 GT:GL:GQ 0/1:-322.36,-111.27,-187.62:100 20 4475883 . AT A . PASS FR=0.5;HP=5;NF=1;NR=3;PP=100.0;SC=AAATATATATATTTTAATATA;TC=14;TR=4 GT:GL:GQ 0/1:-74.26,-40.07,-92.44:100 20 4481373 . A AG . PASS FR=1.0;HP=1;NF=5;NR=6;PP=100.0;SC=TCTTTTTTCAAGTTTTTAGCT;TC=13;TR=11 GT:GL:GQ 1/1:-84.43,-9.42,-0.46:74 20 4484587 . T TA . PASS FR=0.5;HP=9;NF=4;NR=9;PP=100.0;SC=TCTCTGATTTTAAAAAAAAAG;TC=46;TR=13 GT:GL:GQ 0/1:-163.36,-92.55,-141.98:100 20 4487527 . TG T . PASS FR=0.5006;HP=5;NF=8;NR=7;PP=100.0;SC=TACTAGGGGCTGGGGGCAGGG;TC=34;TR=15 GT:GL:GQ 0/1:-421.09,-350.88,-356.92:29 20 4492336 . C CA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATTCTTGCCACCTTTGGTA;TC=27;TR=25 GT:GL:GQ 1/1:-281.59,-90.33,-72.03:100 20 4493592 . C CG . PASS FR=1.0;HP=2;NF=20;NR=17;PP=100.0;SC=GCATTTTGGACATCTCACCCT;TC=39;TR=37 GT:GL:GQ 1/1:-454.89,-182.56,-157.87:100 20 4497462 . TTA T . PASS FR=0.5;HP=2;NF=2;NR=2;PP=88.0;SC=TAAATCAACTTTATATATATA;TC=14;TR=4 GT:GL:GQ 1/0:-149.41,-117.69,-112.45:46 20 4500613 . G GC . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATGCCCAAGGGTGTCCCAGAG;TC=29;TR=25 GT:GL:GQ 1/1:-293.02,-49.83,-29.64:100 20 4502874 . CT C . PASS FR=1.0;HP=4;NF=11;NR=7;PP=100.0;SC=TACAGCCCTTCTTGGGAGCCC;TC=24;TR=18 GT:GL:GQ 1/1:-204.97,-36.44,-20.43:100 20 4512447 . AAAACAAAC AAAAC,A . PASS FR=0.5,0.5;HP=3;NF=3,4;NR=0,1;PP=100.0,100.0;SC=ACTCCATCTCAAAACAAACAA;TC=20;TR=3,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4519983 . GA G . PASS FR=0.5;HP=3;NF=7;NR=13;PP=100.0;SC=TCCAAACTAAGACAGGTATTA;TC=36;TR=20 GT:GL:GQ 0/1:-201.76,-27.24,-148.43:100 20 4524299 . AGTGTGT A . PASS FR=0.5;HP=3;NF=2;NR=1;PP=100.0;SC=TCTGTGCTTTAGTGTGTGTGT;TC=28;TR=3 GT:GL:GQ 0/1:-144.55,-75.64,-138.78:100 20 4530940 . CTT C . PASS FR=0.5002;HP=6;NF=2;NR=9;PP=80.0;SC=TTCTTTCTTTCTTTCTCTCTC;TC=25;TR=11 GT:GL:GQ 0/1:-323.77,-294.9,-301.87:33 20 4541935 . A AGAG . PASS FR=0.5;HP=2;NF=8;NR=4;PP=100.0;SC=GTGGCAGATTAGAGGAGACAT;TC=32;TR=12 GT:GL:GQ 0/1:-211.5,-48.19,-198.54:100 20 4547067 . G GA . PASS FR=0.5116;HP=10;NF=5;NR=1;PP=100.0;SC=TATAGAGAGAGAAAAAAAAAC;TC=18;TR=6 GT:GL:GQ 0/1:-156.12,-119.31,-122.4:16 20 4553580 . GT G . PASS FR=0.5;HP=10;NF=1;NR=1;PP=71.0;SC=TTTTGTTTTTGTTTTTGTTTT;TC=17;TR=2 GT:GL:GQ 1/0:-197.42,-152.57,-154.01:100 20 4553925 . T TC . PASS FR=1.0;HP=1;NF=7;NR=5;PP=100.0;SC=CGGCCCCTCTTCACTTTTAAG;TC=16;TR=12 GT:GL:GQ 1/1:-135.25,-18.29,-7.82:87 20 4560578 . C CCTTA . PASS FR=1.0;HP=1;NF=11;NR=12;PP=100.0;SC=ATGTTATATACCTTTTAGAGA;TC=32;TR=23 GT:GL:GQ 1/1:-416.23,-42.65,-19.11:100 20 4566007 . G GC . PASS FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=AGCTGGGGCTGACTCATCTGA;TC=27;TR=12 GT:GL:GQ 0/1:-150.18,-87.47,-213.89:100 20 4572622 . T TA . PASS FR=0.5;HP=1;NF=5;NR=4;PP=100.0;SC=AAAGGGGTGCTAGGAATTCCA;TC=21;TR=9 GT:GL:GQ 0/1:-105.47,-33.77,-107.56:100 20 4580659 . ATTG A . PASS FR=0.5;HP=3;NF=9;NR=11;PP=100.0;SC=AATAATTTATATTGTTATTAT;TC=41;TR=20 GT:GL:GQ 0/1:-343.69,-136.17,-313.1:100 20 4580822 . AAC A . PASS FR=0.5;HP=1;NF=7;NR=7;PP=100.0;SC=TATCTTACATAACAGTGTATC;TC=27;TR=14 GT:GL:GQ 0/1:-159.59,-31.47,-183.78:100 20 4589159 . TAC T . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CACACACACGTACACACACAC;TC=25;TR=10 GT:GL:GQ 0/1:-134.67,-33.29,-88.29:100 20 4590266 . T TCTGGCC . PASS FR=0.5;HP=3;NF=3;NR=4;PP=100.0;SC=GCTGGCAGCCTCTGGCCCTGG;TC=20;TR=7 GT:GL:GQ 0/1:-180.62,-56.12,-103.3:100 20 4613873 . T TATA . PASS FR=0.5;HP=3;NF=6;NR=2;PP=100.0;SC=CTCTTTCTTTTATAATAATAA;TC=26;TR=8 GT:GL:GQ 0/1:-121.23,-16.51,-65.45:100 20 4616453 . G GAGTAGA . PASS FR=0.5;HP=3;NF=5;NR=7;PP=100.0;SC=CACAGAGTAGGGGTTCAATAA;TC=22;TR=12 GT:GL:GQ 0/1:-211.56,-25.38,-113.94:100 20 4617264 . G GAGAA . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=GAAAGCAAGAGAGAAAGAAGA;TC=22;TR=4 GT:GL:GQ 0/1:-126.22,-46.88,-138.67:100 20 4617272 . AG A . PASS FR=0.5;HP=1;NF=1;NR=3;PP=20.0;SC=GAGAGAAAGAAGAGAAGAGAA;TC=22;TR=4 GT:GL:GQ 0/1:-134.04,-119.35,-223.11:66 20 4617303 . G GAGGA . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=GGGAGGGAGAGAGGAAGGAAG;TC=19;TR=5 GT:GL:GQ 0/1:-154.78,-90.63,-135.29:100 20 4655424 . G GA . PASS FR=0.5;HP=8;NF=13;NR=4;PP=100.0;SC=GTTCTTTAGAGAAAAAAAGAT;TC=30;TR=17 GT:GL:GQ 0/1:-186.33,-114.25,-152.75:100 20 4668235 . AT A . PASS FR=0.5;HP=10;NF=12;NR=5;PP=100.0;SC=TAGGAAATAGATTTTTTTTTT;TC=33;TR=17 GT:GL:GQ 0/1:-91.71,-31.87,-60.05:100 20 4673330 . C CTTT . PASS FR=0.5;HP=5;NF=6;NR=8;PP=100.0;SC=TGAAGAAAATCTTTTCTTCCT;TC=24;TR=14 GT:GL:GQ 0/1:-183.35,-23.94,-71.42:100 20 4684173 . TG T . PASS FR=0.5;HP=1;NF=5;NR=1;PP=100.0;SC=CAGGCACAGTTGCTCACGCCT;TC=17;TR=6 GT:GL:GQ 0/1:-81.87,-25.35,-94.89:100 20 4691383 . CA C . PASS FR=1.0;HP=2;NF=14;NR=12;PP=100.0;SC=TGGGGTCATCCAAGCATGGCT;TC=29;TR=26 GT:GL:GQ 1/1:-259.65,-39.57,-19.54:100 20 4692075 . C CA . PASS FR=0.5;HP=9;NF=5;NR=3;PP=95.0;SC=AGTAATTGGACAAAAAAAACA;TC=26;TR=8 GT:GL:GQ 0/1:-67.83,-34.9,-96.78:100 20 4704696 . A ATG . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=ATATGTATATATGTGTGTGTA;TC=30;TR=8 GT:GL:GQ 0/1:-168.25,-105.64,-257.19:100 20 4706654 . GTGCCATCA G . PASS FR=1.0;HP=2;NF=7;NR=4;PP=100.0;SC=TTACAGGTGTGTGCCATCATG;TC=17;TR=11 GT:GL:GQ 1/1:-236.92,-30.58,-21.39:67 20 4727159 . C CATTTTATTTT . PASS FR=1.0;HP=1;NF=2;NR=4;PP=100.0;SC=ATAGCATTTGCATTTTATTTT;TC=27;TR=6 GT:GL:GQ 1/1:-510.26,-402.24,-397.15:63 20 4735780 . T TTTCTTTCTTTCTTTCTTTCTTTCTTTC,C . PASS FR=0.5,0.5;HP=3;NF=0,5;NR=3,16;PP=100.0,100.0;SC=CCTTTCTTTCTTTTCTTTCTT;TC=27;TR=3,21 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 4737530 . T TA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=TTAAATGTATTGAGGCTCATT;TC=26;TR=25 GT:GL:GQ 1/1:-245.38,-21.97,-3.97:100 20 4737701 . T TTGA . PASS FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=ACTTTCTGTCTTGACCTGTCT;TC=19;TR=19 GT:GL:GQ 1/1:-227.02,-18.69,-5.52:100 20 4741155 . G GGA . PASS FR=1.0;HP=1;NF=5;NR=11;PP=100.0;SC=AACACACCAGGTGTGTCAAAA;TC=22;TR=16 GT:GL:GQ 1/1:-218.41,-31.08,-15.98:100 20 4743693 . G GTTAA . PASS FR=1.0;HP=2;NF=6;NR=7;PP=100.0;SC=AGCCCAGGAGGTTAAGTCTGC;TC=16;TR=13 GT:GL:GQ 1/1:-225.23,-59.89,-50.88:75 20 4743774 . A AAAATAAAT . PASS FR=1.0;HP=5;NF=4;NR=3;PP=100.0;SC=AAAAGGAGAAAAAATAAATAA;TC=16;TR=7 GT:GL:GQ 1/1:-319.93,-209.77,-203.54:78 20 4748739 . A ACTAT . PASS FR=1.0;HP=1;NF=12;NR=7;PP=100.0;SC=TCTTTCACCAACTATTTTCAC;TC=23;TR=19 GT:GL:GQ 1/1:-501.66,-334.66,-319.16:100 20 4761877 . T TG . PASS FR=0.5;HP=8;NF=1;NR=4;PP=100.0;SC=ACAGATATTTTGGGGGGGGCA;TC=23;TR=5 GT:GL:GQ 0/1:-97.23,-58.4,-90.76:100 20 4768475 . A AAGGGACT . PASS FR=1.0;HP=2;NF=7;NR=8;PP=100.0;SC=CAGGGGTCCAAAGGCACCTTA;TC=23;TR=15 GT:GL:GQ 1/1:-372.13,-36.56,-17.94:100 20 4783543 . CATAT C . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=TATATATATACATATATATAT;TC=23;TR=3 GT:GL:GQ 0/1:-115.71,-29.18,-62.14:100 20 4794428 . CGT C . PASS FR=0.5;HP=3;NF=3;NR=2;PP=100.0;SC=CAGTGTGTGGCGTGTGTGTGT;TC=28;TR=5 GT:GL:GQ 0/1:-119.46,-68.74,-106.78:100 20 4796034 . TACC T . PASS FR=0.5;HP=1;NF=7;NR=5;PP=100.0;SC=TATCTGAGGCTACCACCACCC;TC=27;TR=12 GT:GL:GQ 0/1:-222.6,-98.55,-189.77:100 20 4802486 . G GCC . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=GACTGCCACAGCCTAGGCATC;TC=24;TR=9 GT:GL:GQ 0/1:-135.36,-38.11,-126.44:100 20 4803072 . CT C . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GTGCACGCAGCTGTTGAGAGG;TC=15;TR=6 GT:GL:GQ 0/1:-82.81,-37.85,-91.55:100 20 4823348 . AT A . PASS FR=1.0;HP=8;NF=17;NR=7;PP=100.0;SC=AATATTTTCCATTTTTTTTGA;TC=32;TR=24 GT:GL:GQ 1/1:-298.64,-180.3,-160.97:100 20 4850186 . GAC G . PASS FR=0.5;HP=1;NF=3;NR=2;PP=49.0;SC=ATCTCCAAATGACACACACAC;TC=34;TR=5 GT:GL:GQ 0/1:-186.75,-165.14,-349.63:96 20 4880132 . AGCTCAATGCCTTCTGC A . PASS FR=1.0;HP=1;NF=3;NR=4;PP=100.0;SC=CAAACGGCGCAGCTCAATGCC;TC=17;TR=7 GT:GL:GQ 1/1:-255.52,-55.88,-53.61:44 20 4883735 . G GGA . PASS FR=1.0;HP=1;NF=13;NR=18;PP=100.0;SC=GGTGAAAAGAGTAATTCTAAA;TC=34;TR=31 GT:GL:GQ 1/1:-361.9,-346.05,-342.67:97 20 4886527 . GA G . PASS FR=0.5;HP=3;NF=5;NR=6;PP=100.0;SC=ACTCTACTGAGAAGAACAGAT;TC=19;TR=11 GT:GL:GQ 0/1:-166.67,-86.72,-123.24:100 20 4892485 . AATTT A . PASS FR=0.5;HP=1;NF=2;NR=7;PP=100.0;SC=TTTATTTATGAATTTATTTAT;TC=34;TR=9 GT:GL:GQ 0/1:-148.07,-23.75,-121.86:100 20 4922648 . CTAAACTAACT C . PASS FR=0.5;HP=5;NF=1;NR=10;PP=100.0;SC=TCTATATTTTCTAAACTAACT;TC=33;TR=11 GT:GL:GQ 0/1:-284.06,-37.14,-228.78:100 20 4942899 . C CA . PASS FR=0.5;HP=7;NF=4;NR=3;PP=100.0;SC=ACCCCCGCCCCAAAAAAACAG;TC=28;TR=7 GT:GL:GQ 0/1:-99.42,-46.78,-95.55:100 20 4947451 . G GTTTGA . PASS FR=0.5;HP=4;NF=4;NR=4;PP=100.0;SC=ACTTTTGATAGTTTTACACAC;TC=18;TR=8 GT:GL:GQ 0/1:-283.81,-185.62,-217.52:100 20 4947582 . TG T . PASS FR=0.5;HP=4;NF=9;NR=4;PP=100.0;SC=GATTACATGATGGGGAGCAGG;TC=22;TR=13 GT:GL:GQ 0/1:-139.84,-55.72,-119.49:100 20 4947775 . T TA . PASS FR=0.5;HP=6;NF=8;NR=4;PP=100.0;SC=GAAATCTAAATAAACACAGGG;TC=24;TR=12 GT:GL:GQ 0/1:-128.76,-21.0,-91.02:100 20 4949766 . CTT C . PASS FR=0.5;HP=3;NF=8;NR=4;PP=100.0;SC=GAGTTTCCCTCTTGTTACCCA;TC=25;TR=12 GT:GL:GQ 0/1:-147.72,-32.95,-112.56:100 20 4954109 . G GGACTT . PASS FR=0.5;HP=2;NF=4;NR=8;PP=100.0;SC=ATGGCTGGAAGGACTTAACTA;TC=30;TR=12 GT:GL:GQ 0/1:-203.74,-23.32,-169.48:100 20 4965192 . C CT . PASS FR=0.5;HP=2;NF=5;NR=3;PP=100.0;SC=GAGCAAGACTCTGTCTCAAAA;TC=26;TR=8 GT:GL:GQ 0/1:-134.47,-59.87,-111.38:100 20 4969015 . AG A . PASS FR=1.0;HP=8;NF=4;NR=5;PP=100.0;SC=TGGGAAACCGAGGGGGGGCCA;TC=12;TR=9 GT:GL:GQ 1/1:-67.79,-12.99,-5.52:61 20 4970270 . C CTTAATAT . PASS FR=0.5;HP=1;NF=4;NR=1;PP=100.0;SC=TGCAGTGAGCCATGATCTTGC;TC=22;TR=5 GT:GL:GQ 0/1:-247.44,-164.56,-281.24:100 20 4972366 . TCA TCACACA,T . PASS FR=0.5,0.5;HP=2;NF=1,0;NR=1,2;PP=100.0,49.0;SC=AGACTCCGTTTCACACACACA;TC=15;TR=2,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:97 20 4979252 . ATGAGG A . PASS FR=0.5;HP=1;NF=5;NR=2;PP=100.0;SC=AAATGAATTAATGAGGTGAGG;TC=24;TR=7 GT:GL:GQ 0/1:-146.48,-63.04,-172.38:100 20 4985646 . A AAAAT . PASS FR=0.5;HP=4;NF=2;NR=1;PP=100.0;SC=CTCCGTCTCAAAAATAAATAA;TC=22;TR=3 GT:GL:GQ 0/1:-69.57,-20.73,-73.7:100 20 4987193 . T TTTTA . PASS FR=1.0;HP=3;NF=5;NR=7;PP=100.0;SC=GTAAAAGCCATTTTATTTATT;TC=33;TR=12 GT:GL:GQ 1/1:-198.93,-19.38,-8.29:93 20 5003823 . C CA . PASS FR=1.0;HP=2;NF=2;NR=1;PP=69.0;SC=CTCAGCCTCCCAGTAGCTGGG;TC=5;TR=3 GT:GL:GQ 1/1:-35.46,-12.52,-9.15:55 20 5006924 . GTATATATATGTGTA G . PASS FR=0.5;HP=2;NF=3;NR=1;PP=100.0;SC=ATGTATATATGTATATATATG;TC=17;TR=4 GT:GL:GQ 0/1:-102.23,-17.74,-69.04:100 20 5019857 . C CT . PASS FR=1.0;HP=1;NF=5;NR=1;PP=100.0;SC=CACCCCTGCACTCCAGCCTGG;TC=10;TR=6 GT:GL:GQ 1/1:-78.84,-38.79,-34.59:51 20 5021323 . T TC . PASS FR=1.0;HP=10;NF=8;NR=5;PP=100.0;SC=CTTTTTTTTTTTCAATGGCAA;TC=18;TR=13 GT:GL:GQ 1/1:-164.3,-19.64,-6.44:82 20 5021471 . G GA . PASS FR=1.0;HP=1;NF=11;NR=14;PP=100.0;SC=ACATAATGCTGGTTAAAGAGG;TC=33;TR=25 GT:GL:GQ 1/1:-406.51,-306.39,-293.23:100 20 5033824 . G GTATA . PASS FR=1.0;HP=8;NF=6;NR=6;PP=100.0;SC=CCAAAAAAAAGTATATATATA;TC=19;TR=12 GT:GL:GQ 1/1:-293.31,-92.78,-80.65:100 20 5034013 . GGCAT G . PASS FR=1.0;HP=1;NF=8;NR=10;PP=100.0;SC=ATGACAGCCAGGCATGGGGGC;TC=24;TR=18 GT:GL:GQ 1/1:-275.61,-34.13,-17.26:100 20 5044461 . A AAATTTTTAT . PASS FR=1.0;HP=4;NF=13;NR=12;PP=100.0;SC=GTTAACTTGGAAAAATTTCTA;TC=29;TR=25 GT:GL:GQ 1/1:-660.59,-158.53,-137.22:100 20 5058110 . G GGGGGCT . PASS FR=1.0;HP=2;NF=6;NR=6;PP=100.0;SC=CAACATTTTGGGAGGTGGGTG;TC=14;TR=12 GT:GL:GQ 1/1:-206.1,-87.92,-82.33:69 20 5062840 . AAAG A . PASS FR=1.0;HP=4;NF=12;NR=4;PP=100.0;SC=AATTTTTTAAAAAGAAGAAGA;TC=21;TR=16 GT:GL:GQ 1/1:-217.23,-55.74,-43.97:99 20 5079870 . AAATAAATAAATCAATC A . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=ATAAATAAATAAATAAATAAA;TC=24;TR=10 GT:GL:GQ 1/0:-419.18,-202.82,-208.38:27 20 5094493 . T TA . PASS FR=1.0;HP=1;NF=7;NR=16;PP=100.0;SC=AAAATGAACTTACTACTGGAC;TC=26;TR=23 GT:GL:GQ 1/1:-300.98,-148.38,-131.87:100 20 5097837 . AC A . PASS FR=1.0;HP=1;NF=15;NR=5;PP=100.0;SC=TAAAGGTTATACGCCTAACTT;TC=25;TR=20 GT:GL:GQ 1/1:-243.65,-32.97,-15.65:100 20 5100990 . AAG A . PASS FR=1.0;HP=1;NF=10;NR=6;PP=100.0;SC=TTGCAGCCTGAAGAGAGTACA;TC=18;TR=16 GT:GL:GQ 1/1:-198.64,-18.46,-5.29:100 20 5105482 . C CATTTTAGG . PASS FR=1.0;HP=2;NF=6;NR=11;PP=100.0;SC=GTTCAGACCACATGTTATCCA;TC=22;TR=17 GT:GL:GQ 1/1:-471.45,-181.5,-164.38:100 20 5118209 . A AT . PASS FR=0.5;HP=8;NF=3;NR=2;PP=100.0;SC=TTTAAGTCTTATTTTTTCAAA;TC=16;TR=5 GT:GL:GQ 0/1:-55.51,-21.15,-68.35:100 20 5145860 . A AC . PASS FR=0.5;HP=5;NF=6;NR=2;PP=100.0;SC=TTTTTTGGAAACCCCCGTATT;TC=29;TR=8 GT:GL:GQ 0/1:-81.29,-28.9,-130.37:100 20 5150896 . G GC . PASS FR=0.5;HP=3;NF=2;NR=5;PP=100.0;SC=ACCTCGCTGTGCCCAGAGGAG;TC=17;TR=7 GT:GL:GQ 0/1:-79.22,-17.13,-53.13:100 20 5156258 . CCT C . PASS FR=0.5093;HP=2;NF=6;NR=6;PP=100.0;SC=ATGGTGAAACCCTGTCTCTAC;TC=16;TR=12 GT:GL:GQ 0/1:-101.9,-26.13,-29.44:17 20 5156432 . AAAAC A . PASS FR=0.5;HP=3;NF=5;NR=3;PP=100.0;SC=ACTCCATCTCAAAACAAACAA;TC=23;TR=8 GT:GL:GQ 0/1:-98.71,-15.69,-97.38:100 20 5173014 . C CA . PASS FR=1.0;HP=2;NF=8;NR=13;PP=100.0;SC=GAAGGGGGGTCTAGGAAGCCG;TC=22;TR=21 GT:GL:GQ 1/1:-250.84,-61.97,-47.15:100 20 5178081 . C CCT . PASS FR=0.5;HP=1;NF=5;NR=6;PP=100.0;SC=AGAGGTCAGCCGTGTCTGCCC;TC=22;TR=11 GT:GL:GQ 0/1:-193.35,-72.27,-102.13:100 20 5181165 . C CA . PASS FR=0.5;HP=8;NF=1;NR=6;PP=91.0;SC=TTAGACACAACAAAAAAGAGA;TC=22;TR=7 GT:GL:GQ 0/1:-61.45,-29.38,-90.08:100 20 5187401 . A AC . PASS FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TTTTCATGTCACCCCCGAGGT;TC=17;TR=7 GT:GL:GQ 0/1:-139.03,-104.99,-121.15:73 20 5187831 . G GAATC . PASS FR=0.5;HP=5;NF=5;NR=3;PP=100.0;SC=TGAAAGGAAAGAAGCATGTTT;TC=22;TR=8 GT:GL:GQ 0/1:-144.73,-26.29,-132.63:100 20 5192127 . A AATT . PASS FR=0.5;HP=3;NF=2;NR=7;PP=100.0;SC=AATGTGTTAAAATTATATAAG;TC=32;TR=9 GT:GL:GQ 0/1:-228.5,-119.37,-283.27:100 20 5212592 . TA T . PASS FR=1.0;HP=9;NF=20;NR=10;PP=100.0;SC=CCTGCCATATTAAAAAAAAAC;TC=39;TR=30 GT:GL:GQ 1/1:-191.03,-64.37,-41.93:100 20 5223122 . TA T . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=GAATAAGACCTAGTATTTGCT;TC=11;TR=6 GT:GL:GQ 0/1:-63.8,-25.4,-69.29:100 20 5234499 . AAC A . PASS FR=0.5;HP=1;NF=1;NR=1;PP=25.0;SC=GTGCCTTCACAACACACACAC;TC=26;TR=2 GT:GL:GQ 0/1:-75.14,-59.09,-216.84:72 20 5236854 . A AATTAT . PASS FR=1.0;HP=1;NF=17;NR=9;PP=100.0;SC=AAAAGACATGAATTATCATTA;TC=29;TR=26 GT:GL:GQ 1/1:-427.74,-26.55,-5.07:100 20 5240296 . CT C . PASS FR=0.5;HP=1;NF=7;NR=6;PP=100.0;SC=AATTGATACACTACAATGGCC;TC=39;TR=13 GT:GL:GQ 0/1:-220.75,-129.27,-297.86:100 20 5242946 . A AC . PASS FR=0.5;HP=3;NF=6;NR=5;PP=100.0;SC=AGCTGGAACCACTGTTGTGGA;TC=22;TR=11 GT:GL:GQ 0/1:-141.29,-37.29,-109.65:100 20 5246342 . GC G . PASS FR=0.5;HP=7;NF=6;NR=8;PP=100.0;SC=AACCGAGACAGCCCCCCCTTT;TC=21;TR=14 GT:GL:GQ 0/1:-107.74,-25.34,-35.96:49 20 5247531 . T TTGCAGTAGAGAAACTCCC . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TTGCAGGTTATTGCAGTAGAG;TC=31;TR=8 GT:GL:GQ 0/1:-296.8,-101.13,-189.63:100 20 5251109 . ACTCTCTCTCTCTCTCTCT A . PASS FR=0.5;HP=1;NF=3;NR=2;PP=37.0;SC=CATCCAGTGTACTCTCTCTCT;TC=27;TR=5 GT:GL:GQ 0/1:-322.05,-299.54,-356.33:100 20 5251154 . G GTGTA . PASS FR=0.5;HP=2;NF=1;NR=4;PP=100.0;SC=CTCTGTGTGTGTGTATGTGTG;TC=19;TR=5 GT:GL:GQ 0/1:-297.98,-257.24,-280.47:100 20 5256228 . GAAAAAC G . PASS FR=0.5;HP=5;NF=8;NR=3;PP=100.0;SC=CAAATGTTTTGAAAAACAAAA;TC=29;TR=11 GT:GL:GQ 0/1:-159.47,-21.9,-134.38:100 20 5256836 . CT C . PASS FR=0.5;HP=10;NF=4;NR=7;PP=58.0;SC=TCTCAACTCACTTTTTTTTTT;TC=23;TR=11 GT:GL:GQ 0/1:-145.3,-121.72,-154.45:100 20 5260631 . G GA . PASS FR=0.5;HP=9;NF=6;NR=2;PP=100.0;SC=TTTAATGAAGGAAAAAAAAAT;TC=25;TR=8 GT:GL:GQ 0/1:-133.97,-86.93,-109.55:100 20 5261161 . ACT A . PASS FR=0.5;HP=2;NF=9;NR=8;PP=100.0;SC=CTTGAATGAAACTTATCTAAC;TC=33;TR=17 GT:GL:GQ 0/1:-246.04,-189.54,-319.81:100 20 5275657 . CAAAATAACTATTACAAATAACA C . PASS FR=0.5;HP=6;NF=2;NR=1;PP=100.0;SC=TCAAACATAACAAAATAACTA;TC=27;TR=3 GT:GL:GQ 0/1:-135.83,-52.75,-276.31:100 20 5277471 . C CCTT . PASS FR=0.5;HP=1;NF=11;NR=5;PP=100.0;SC=GTATCCATGTCCTAGGGTACA;TC=27;TR=16 GT:GL:GQ 0/1:-278.16,-87.4,-130.16:100 20 5278336 . TA T . PASS FR=0.5;HP=4;NF=3;NR=6;PP=100.0;SC=TTGAACTCTTTAAAAGTTTGA;TC=24;TR=9 GT:GL:GQ 0/1:-132.29,-83.79,-178.99:100 20 5280465 . TTG T . PASS FR=0.5;HP=4;NF=6;NR=8;PP=100.0;SC=GATGGGGTTTTTGGCCATGTT;TC=30;TR=14 GT:GL:GQ 0/1:-161.14,-49.68,-168.09:100 20 5280839 . T TATA . PASS FR=0.5;HP=1;NF=9;NR=3;PP=100.0;SC=ACCACAAATGTATAATACAAA;TC=30;TR=12 GT:GL:GQ 0/1:-228.47,-89.38,-201.59:100 20 5285786 . T TG . PASS FR=0.5;HP=1;NF=3;NR=2;PP=21.0;SC=GGCTAATCAGTTCACTCTAAG;TC=24;TR=5 GT:GL:GQ 0/1:-80.46,-64.62,-184.45:71 20 5289619 . GA G . PASS FR=0.5;HP=1;NF=9;NR=5;PP=100.0;SC=GAAGATCTAGGATGAAGCTGG;TC=22;TR=14 GT:GL:GQ 0/1:-219.59,-148.82,-190.02:100 20 5291220 . TGATCA T . PASS FR=0.5;HP=2;NF=6;NR=6;PP=100.0;SC=GTTTAGAACCTGATCAGAGAA;TC=27;TR=12 GT:GL:GQ 0/1:-284.71,-179.16,-294.64:100 20 5291304 . G GACTTATGGGGAGCTGGGGTATAAATACCCCAGCTCCCTCCT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=CCTCATCAATGACCTCCCACC;TC=8;TR=2 GT:GL:GQ 0/1:-488.84,-441.13,-506.41:71 20 5293792 . ATG A . PASS FR=0.5;HP=3;NF=6;NR=12;PP=100.0;SC=TACAATTATTATGTGTCAATT;TC=42;TR=18 GT:GL:GQ 0/1:-201.09,-30.39,-231.82:100 20 5303337 . CAGCT C . PASS FR=0.5;HP=2;NF=7;NR=7;PP=100.0;SC=AAATGTCACACAGCTAGCTGG;TC=32;TR=14 GT:GL:GQ 0/1:-273.85,-111.21,-258.62:100 20 5313928 . TA T . PASS FR=0.5;HP=10;NF=9;NR=8;PP=100.0;SC=ATACAGTTGATAAAAAAAAAC;TC=39;TR=17 GT:GL:GQ 0/1:-100.8,-36.94,-107.23:100 20 5316589 . GT G . PASS FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=GAATATCTGGGTAAAATTTAA;TC=22;TR=18 GT:GL:GQ 1/1:-227.4,-66.98,-52.55:100 20 5320851 . AT A . PASS FR=0.5;HP=6;NF=5;NR=10;PP=100.0;SC=ATCTCAATAGATTTTTTAAAA;TC=39;TR=15 GT:GL:GQ 0/1:-177.77,-103.88,-250.39:100 20 5323468 . GA G . PASS FR=0.5;HP=10;NF=2;NR=4;PP=85.0;SC=GGCAACAAAAGAAAAAATAGA;TC=23;TR=6 GT:GL:GQ 0/1:-61.27,-31.53,-121.44:100 20 5326511 . G GT . PASS FR=0.5;HP=9;NF=11;NR=2;PP=100.0;SC=TTGATTCAAAGTTTTTTTTTA;TC=29;TR=13 GT:GL:GQ 0/1:-178.07,-139.61,-153.82:64 20 5326660 . T TA . PASS FR=0.5;HP=8;NF=4;NR=6;PP=100.0;SC=CTTTATCCTTTAAAAAAAATC;TC=26;TR=10 GT:GL:GQ 0/1:-181.43,-128.15,-159.02:100 20 5328799 . CA C . PASS FR=1.0;HP=4;NF=10;NR=6;PP=100.0;SC=AACCACCTTCCAAAATGTGGA;TC=20;TR=16 GT:GL:GQ 1/1:-179.33,-21.23,-7.37:100 20 5351875 . T TACACACAC . PASS FR=0.5;HP=6;NF=1;NR=1;PP=38.0;SC=ATCTTAAAAATACACACACAC;TC=12;TR=2 GT:GL:GQ 0/1:-48.31,-20.86,-63.23:100 20 5354510 . G GGC . PASS FR=0.5;HP=1;NF=5;NR=5;PP=100.0;SC=CCTCCTCCCTGCAGAGCTCCT;TC=28;TR=10 GT:GL:GQ 0/1:-148.18,-38.3,-173.54:100 20 5373349 . A AATTT . PASS FR=0.5;HP=6;NF=1;NR=2;PP=96.0;SC=CTAATTTTTTAATTTTTTTTT;TC=20;TR=3 GT:GL:GQ 0/1:-100.6,-64.12,-96.6:100 20 5390447 . C CA . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=CATTAGCATACAAAAACCATC;TC=26;TR=9 GT:GL:GQ 0/1:-88.65,-28.46,-120.44:100 20 5408475 . AAAAC A . PASS FR=0.5;HP=4;NF=4;NR=5;PP=100.0;SC=CTCTGTCTCAAAAACAAACAA;TC=29;TR=9 GT:GL:GQ 0/1:-128.94,-29.02,-144.52:100 20 5410361 . G GA . PASS FR=1.0;HP=9;NF=6;NR=7;PP=100.0;SC=CTGGGTTGGGGAAAAAAAAAG;TC=25;TR=13 GT:GL:GQ 1/1:-119.78,-34.18,-19.33:100 20 5419440 . CTCCCTGTG C . PASS FR=0.5;HP=3;NF=1;NR=4;PP=100.0;SC=TGTTGTTCCCCTCCCTGTGTC;TC=19;TR=5 GT:GL:GQ 0/1:-128.97,-30.52,-125.82:100 20 5432204 . A AG . PASS FR=0.5;HP=8;NF=2;NR=3;PP=100.0;SC=AAAGAAAGAGAAAAAAAAAGG;TC=19;TR=5 GT:GL:GQ 0/1:-83.51,-76.05,-116.49:100 20 5432394 . G GT . PASS FR=1.0;HP=5;NF=9;NR=14;PP=100.0;SC=TTCCTCAATTGAAAAATCTTA;TC=26;TR=23 GT:GL:GQ 1/1:-328.05,-211.91,-196.14:100 20 5435136 . GAGAAAA G . PASS FR=0.5;HP=3;NF=3;NR=6;PP=44.0;SC=AAAAAAAGGGGAGAAAAAGAA;TC=24;TR=9 GT:GL:GQ 0/1:-190.59,-169.15,-271.82:96 20 5435153 . A ATTT . PASS FR=0.5;HP=8;NF=4;NR=10;PP=100.0;SC=AGAAAAAAAAATTTTAATGTT;TC=22;TR=14 GT:GL:GQ 0/1:-325.96,-275.2,-333.88:100 20 5435908 . G GTTAAT . PASS FR=0.5;HP=2;NF=5;NR=2;PP=100.0;SC=ACCAGGCCCAGTTATTTTTTG;TC=16;TR=7 GT:GL:GQ 0/1:-176.12,-112.78,-176.63:100 20 5443418 . A ACAGGGGCAC . PASS FR=0.5;HP=4;NF=3;NR=1;PP=100.0;SC=GCTTTGTCCCACAGCCTGATG;TC=15;TR=4 GT:GL:GQ 0/1:-94.87,-42.4,-160.11:100 20 5443724 . C CT . PASS FR=0.5;HP=3;NF=6;NR=4;PP=38.0;SC=GTTACCTTTCCCCTGAGATGC;TC=20;TR=10 GT:GL:GQ 0/1:-163.73,-143.91,-199.73:89 20 5452897 . G GA . PASS FR=0.5;HP=10;NF=2;NR=2;PP=26.0;SC=TCAGTCAGAAGAAAAAAAATT;TC=15;TR=4 GT:GL:GQ 0/1:-34.37,-17.3,-53.75:77 20 5460271 . C CA . PASS FR=0.5;HP=10;NF=2;NR=2;PP=67.0;SC=ACCCCTGTCTCAAAAAAAAAA;TC=21;TR=4 GT:GL:GQ 0/1:-56.83,-30.33,-56.83:100 20 5473577 . A AGT . PASS FR=0.5;HP=2;NF=2;NR=8;PP=100.0;SC=AACTGAGCAGAGTTCCTTTTT;TC=29;TR=10 GT:GL:GQ 0/1:-165.26,-86.94,-217.65:100 20 5475853 . CTTATTTAT CTTATTTATTTAT,C . PASS FR=0.5,0.5;HP=4;NF=1,1;NR=2,2;PP=100.0,100.0;SC=GAAGGCTCTTCTTATTTATTT;TC=18;TR=3,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5485434 . C CT . PASS FR=0.5001;HP=10;NF=4;NR=1;PP=63.0;SC=TTTTTATCTTCTTTTTTTTCC;TC=9;TR=5 GT:GL:GQ 0/1:-37.99,-12.58,-20.26:36 20 5518456 . C CG . PASS FR=0.5;HP=7;NF=7;NR=6;PP=100.0;SC=GTGACAAATGCGGGGGGTCTT;TC=27;TR=13 GT:GL:GQ 0/1:-115.32,-28.55,-76.08:100 20 5546352 . A AAG . PASS FR=1.0;HP=1;NF=13;NR=12;PP=100.0;SC=AAGTAGTCACAAGCTGTGATT;TC=26;TR=25 GT:GL:GQ 1/1:-322.1,-20.79,0.0:100 20 5596481 . TTATG T . PASS FR=1.0;HP=2;NF=4;NR=4;PP=100.0;SC=TGCTACTGGTTTATGTATGTA;TC=20;TR=8 GT:GL:GQ 1/1:-167.17,-32.77,-22.47:86 20 5596891 . ATGTGTGTG A . PASS FR=1.0;HP=2;NF=3;NR=4;PP=100.0;SC=AATTTGGGGTATGTGTGTGTG;TC=23;TR=7 GT:GL:GQ 1/1:-241.36,-45.12,-34.38:90 20 5600458 . A AG . PASS FR=1.0;HP=2;NF=3;NR=3;PP=100.0;SC=TCTTGACCTGAGTGATACACC;TC=16;TR=6 GT:GL:GQ 1/1:-146.08,-65.05,-55.59:79 20 5613790 . GA G . PASS FR=1.0;HP=4;NF=11;NR=9;PP=100.0;SC=CATGATTTCTGAAAACAAGCT;TC=26;TR=20 GT:GL:GQ 1/1:-222.44,-43.9,-26.57:100 20 5624959 . C CCTCCTTACCCT . PASS FR=0.5;HP=1;NF=1;NR=1;PP=100.0;SC=AACTTGTCCACCTCCATTACC;TC=28;TR=2 GT:GL:GQ 0/1:-225.26,-176.16,-303.27:100 20 5627592 . AT A . PASS FR=0.5;HP=6;NF=4;NR=3;PP=100.0;SC=TCTCAAAAAAATAATAAAGTT;TC=19;TR=7 GT:GL:GQ 0/1:-112.89,-28.55,-78.51:100 20 5629324 . T TTAC . PASS FR=0.5;HP=1;NF=3;NR=3;PP=100.0;SC=ATTATTACTATTATTATTATT;TC=26;TR=6 GT:GL:GQ 1/0:-227.05,-75.82,-72.8:100 20 5635153 . TGGAATATGAAAGAG T . PASS FR=1.0;HP=2;NF=7;NR=11;PP=100.0;SC=CAAGCCTGTTTGGAATATGAA;TC=27;TR=18 GT:GL:GQ 1/1:-490.0,-56.65,-38.89:100 20 5635246 . T TTGTGTG,TTGTGTGTG . PASS FR=0.5,0.5;HP=1;NF=2,0;NR=2,3;PP=100.0,100.0;SC=AAAATGAATATTGTGTGTGTG;TC=22;TR=4,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5644716 . GTCTCTCTCTCTC G . PASS FR=1.0;HP=1;NF=1;NR=6;PP=100.0;SC=ATGAGACCTCGTCTCTCTCTC;TC=22;TR=7 GT:GL:GQ 1/1:-261.18,-61.24,-58.02:52 20 5654462 . C CGTGTGTGTGTGTGT . PASS FR=0.5;HP=1;NF=3;NR=1;PP=100.0;SC=TATACATATACGTGTGTGTGT;TC=16;TR=4 GT:GL:GQ 0/1:-129.11,-28.26,-136.2:100 20 5654661 . AAAAAAATTTTTTTTGCTT A . PASS FR=0.5;HP=6;NF=7;NR=3;PP=100.0;SC=ATTTTTTGCCAAAAAAATTTT;TC=21;TR=10 GT:GL:GQ 0/1:-264.68,-158.41,-268.38:100 20 5655925 . ACG A . PASS FR=0.5047;HP=2;NF=4;NR=3;PP=100.0;SC=TTGCATGCGCACGCGCGCACA;TC=34;TR=7 GT:GL:GQ 0/1:-234.34,-106.46,-110.43:20 20 5674501 . T TTTTG . PASS FR=0.5;HP=4;NF=2;NR=2;PP=100.0;SC=AGATTTAGATTTTTGTTTGTT;TC=22;TR=4 GT:GL:GQ 0/1:-64.3,-21.33,-64.69:100 20 5691054 . A AC . PASS FR=0.5;HP=6;NF=4;NR=5;PP=100.0;SC=GTATAGTGAGACCCCCCATCT;TC=18;TR=9 GT:GL:GQ 0/1:-137.75,-89.82,-120.86:100 20 5696589 . AAAG A . PASS FR=0.5;HP=2;NF=3;NR=9;PP=100.0;SC=AGAAAACCATAAAGAAGAGAA;TC=35;TR=12 GT:GL:GQ 0/1:-142.07,-32.31,-238.04:100 20 5706639 . T TA . PASS FR=0.5;HP=9;NF=5;NR=2;PP=98.0;SC=TTGTCTCAATTAAAAAAAAAT;TC=31;TR=7 GT:GL:GQ 0/1:-60.75,-27.2,-75.24:100 20 5707109 . A ATTTTTCCC . PASS FR=0.5;HP=7;NF=2;NR=2;PP=100.0;SC=TGCCCAGCTGATTTTTTTAAA;TC=15;TR=4 GT:GL:GQ 0/1:-95.63,-40.43,-104.52:100 20 5740635 . T TAC,TACAC . PASS FR=0.5,0.5;HP=2;NF=3,1;NR=7,4;PP=100.0,100.0;SC=TGTATTTTTATACACACACAC;TC=23;TR=10,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5747768 . ATTTTC ATTTTCTTTTC,A . PASS FR=0.5,0.5;HP=4;NF=1,4;NR=1,1;PP=100.0,100.0;SC=CTCCATTCACATTTTCTTTTC;TC=17;TR=2,5 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5754003 . A AT . PASS FR=0.5;HP=9;NF=6;NR=4;PP=100.0;SC=AGAGAGTGGAATTTTTTTTTG;TC=33;TR=10 GT:GL:GQ 0/1:-69.42,-30.04,-87.94:100 20 5762289 . A AT . PASS FR=0.5;HP=8;NF=2;NR=3;PP=95.0;SC=CTGCCCAGCTATTTTTTTGTA;TC=13;TR=5 GT:GL:GQ 0/1:-43.82,-10.94,-28.53:79 20 5767540 . AGATCATTT A . PASS FR=1.0;HP=2;NF=5;NR=6;PP=100.0;SC=TTCTCAAGCCAGATCATTTGA;TC=16;TR=11 GT:GL:GQ 1/1:-333.85,-224.08,-215.75:69 20 5768941 . AGTT A . PASS FR=0.5;HP=1;NF=4;NR=9;PP=100.0;SC=TATATTCAGTAGTTGTTGTTT;TC=21;TR=13 GT:GL:GQ 0/1:-159.07,-13.83,-29.97:73 20 5771896 . CAAATAAATA C . PASS FR=1.0;HP=3;NF=11;NR=5;PP=100.0;SC=AAAATCTTAGCAAATAAATAA;TC=26;TR=16 GT:GL:GQ 1/1:-433.86,-58.29,-43.98:62 20 5778212 . AAAG A . PASS FR=1.0;HP=5;NF=6;NR=12;PP=100.0;SC=CCATCTCAAAAAAGAAGAAGA;TC=23;TR=18 GT:GL:GQ 1/1:-251.53,-37.12,-21.87:100 20 5781503 . GCGTA G . PASS FR=1.0;HP=1;NF=9;NR=6;PP=100.0;SC=GTGTGTGTGTGCGTATGTCTA;TC=23;TR=15 GT:GL:GQ 1/1:-450.31,-256.77,-243.2:93 20 5788895 . C CAGCCTGGGTGACAG . PASS FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=CACTGCACTCCAGCAAGACTC;TC=11;TR=9 GT:GL:GQ 1/1:-304.26,-23.03,-12.43:73 20 5798352 . CTGGCATTA C . PASS FR=0.5;HP=1;NF=1;NR=3;PP=100.0;SC=CTGGCTGTGCCTGGCATTATG;TC=29;TR=4 GT:GL:GQ 1/0:-390.33,-302.72,-305.99:100 20 5798359 . T TGC . PASS FR=0.5;HP=1;NF=6;NR=6;PP=100.0;SC=TGCCTGGCATTATGACTTAGT;TC=26;TR=12 GT:GL:GQ 0/1:-390.33,-366.98,-362.46:100 20 5807781 . T TG . PASS FR=1.0;HP=3;NF=7;NR=3;PP=100.0;SC=TGAGTGGGCGTGGCACCCACA;TC=10;TR=10 GT:GL:GQ 1/1:-98.15,-11.06,-4.14:57 20 5808542 . C CT . PASS FR=1.0;HP=3;NF=16;NR=16;PP=100.0;SC=ATCATTCACTCTTGTGGGTAG;TC=33;TR=32 GT:GL:GQ 1/1:-408.08,-203.57,-182.32:100 20 5808967 . T TGTGTAGTAG . PASS FR=1.0;HP=2;NF=7;NR=18;PP=100.0;SC=CTTAGAACAGTGTGATAGGTC;TC=28;TR=25 GT:GL:GQ 1/1:-678.96,-93.79,-70.92:100 20 5809144 . TTGA T . PASS FR=1.0;HP=1;NF=10;NR=16;PP=100.0;SC=GAGTCATTTCTTGATGACTCC;TC=34;TR=26 GT:GL:GQ 1/1:-408.43,-70.02,-46.73:100 20 5809747 . CCTGGGCTCA C . PASS FR=1.0;HP=1;NF=13;NR=15;PP=100.0;SC=GGTCTCAACTCCTGGGCTCAA;TC=33;TR=28 GT:GL:GQ 1/1:-583.71,-71.8,-56.82:48 20 5810527 . G GA . PASS FR=1.0;HP=9;NF=9;NR=9;PP=100.0;SC=TCTTCTTTAGGAAAAAAAAAC;TC=26;TR=18 GT:GL:GQ 1/1:-296.92,-216.99,-203.12:100 20 5820132 . A AAGATAGAT,AAGATAGATAGAT . PASS FR=0.5,0.5;HP=2;NF=4,2;NR=2,6;PP=100.0,100.0;SC=ATTAGATAGAAAGATAGATAG;TC=36;TR=6,8 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5822610 . A AAAG . PASS FR=0.5;HP=2;NF=4;NR=6;PP=100.0;SC=GACTATGGAGAAAGAGAACAT;TC=30;TR=10 GT:GL:GQ 0/1:-160.25,-33.5,-176.54:100 20 5830758 . C CAATAATAAT . PASS FR=1.0;HP=2;NF=2;NR=2;PP=100.0;SC=GACCCCGTCTCAATAATAATA;TC=8;TR=4 GT:GL:GQ 1/1:-112.77,-19.78,-14.93:60 20 5848219 . C CAAAAT . PASS FR=1.0;HP=7;NF=10;NR=13;PP=100.0;SC=ATTAAACACTCAAAAAAATAA;TC=29;TR=23 GT:GL:GQ 1/1:-431.75,-125.0,-103.09:100 20 5848530 . A AAT . PASS FR=1.0;HP=1;NF=13;NR=10;PP=100.0;SC=ATATATATAGAATATATATAT;TC=33;TR=23 GT:GL:GQ 1/1:-409.72,-328.74,-317.3:96 20 5850230 . A AT . PASS FR=1.0;HP=6;NF=1;NR=1;PP=100.0;SC=TAATTTTTGCATTTTTTGTTT;TC=22;TR=2 GT:GL:GQ 1/1:-134.01,-105.23,-98.33:86 20 5854908 . A AATTTTATTTT . PASS FR=1.0;HP=3;NF=3;NR=7;PP=100.0;SC=CATATACTTTAATTTTATTTT;TC=28;TR=10 GT:GL:GQ 1/1:-352.01,-27.1,-12.2:100 20 5856355 . CTAAA C . PASS FR=1.0;HP=4;NF=2;NR=2;PP=100.0;SC=GACCCTATTTCTAAATAAATA;TC=15;TR=4 GT:GL:GQ 1/1:-57.0,-6.23,-2.76:42 20 5860647 . TGAG T . PASS FR=1.0;HP=4;NF=8;NR=6;PP=100.0;SC=AGAAAGAAAATGAGGAGCGAA;TC=18;TR=14 GT:GL:GQ 1/1:-182.28,-15.91,-4.13:99 20 5879792 . CAA C . PASS FR=1.0;HP=10;NF=14;NR=15;PP=100.0;SC=ACAATAACATCAAAAAAAAAA;TC=39;TR=29 GT:GL:GQ 1/1:-170.66,-28.34,-5.76:100 20 5898748 . GAA G . PASS FR=1.0;HP=2;NF=5;NR=5;PP=100.0;SC=AGCCAAGATTGAACTCCATTG;TC=13;TR=10 GT:GL:GQ 1/1:-132.95,-97.25,-91.93:66 20 5900669 . G GC . PASS FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CATGACAGATGCATTTCCCTG;TC=15;TR=6 GT:GL:GQ 0/1:-72.42,-12.46,-72.17:100 20 5911588 . TCA T . PASS FR=0.5;HP=2;NF=6;NR=1;PP=100.0;SC=CTGGCAAATCTCACACACACA;TC=19;TR=7 GT:GL:GQ 0/1:-115.11,-26.04,-76.51:100 20 5923828 . CAGAGAGAATACATGCTTA C . PASS FR=0.5;HP=1;NF=3;NR=5;PP=100.0;SC=TGTATTCTTCCAGAGAGAATA;TC=22;TR=8 GT:GL:GQ 0/1:-297.99,-115.43,-361.46:100 20 5928403 . T TA . PASS FR=0.5;HP=2;NF=3;NR=2;PP=100.0;SC=ACCTAGGTGCTTTGAAACACT;TC=18;TR=5 GT:GL:GQ 0/1:-52.7,-18.59,-121.61:100 20 5930573 . A AG . PASS FR=0.5;HP=3;NF=4;NR=4;PP=100.0;SC=ACAGGTGATTAGGGTGTGGAG;TC=26;TR=8 GT:GL:GQ 0/1:-121.38,-46.04,-144.61:100 20 5932104 . C CT . PASS FR=0.5;HP=2;NF=5;NR=6;PP=100.0;SC=TCTTTATTTACTTGTATACTT;TC=20;TR=11 GT:GL:GQ 0/1:-138.34,-48.83,-107.16:100 20 5934084 . GGTGT GGT,G . PASS FR=0.5,0.5;HP=3;NF=1,2;NR=3,2;PP=100.0,100.0;SC=TCTCATGAGGGGTGTGTGTGT;TC=32;TR=4,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 5938650 . A AT . PASS FR=0.5;HP=3;NF=3;NR=6;PP=100.0;SC=TTTTCCTTAAATTTCTTTTTT;TC=36;TR=9 GT:GL:GQ 0/1:-182.01,-137.8,-289.15:100 20 5939638 . G GT . PASS FR=0.5;HP=7;NF=8;NR=7;PP=100.0;SC=ATTAGTGTCTGTTTTTTACCT;TC=37;TR=15 GT:GL:GQ 0/1:-244.24,-166.31,-240.23:100 20 5946414 . TTTTACTTCTTAGAGTATGC T . PASS FR=0.5;HP=3;NF=2;NR=4;PP=100.0;SC=TAAGTGCTGGTTTTACTTCTT;TC=34;TR=6 GT:GL:GQ 0/1:-213.07,-102.23,-466.92:100 20 5948421 . CATT C . PASS FR=0.5;HP=1;NF=6;NR=8;PP=100.0;SC=CTAGTTGAGTCATTGTAGGGA;TC=25;TR=14 GT:GL:GQ 0/1:-180.5,-26.28,-114.93:100 20 5958367 . TATA T . PASS FR=0.5;HP=2;NF=1;NR=12;PP=100.0;SC=TAAATCAGGATATAATAATAC;TC=28;TR=13 GT:GL:GQ 0/1:-168.03,-21.02,-138.69:100 20 5958971 . AT A . PASS FR=0.5;HP=8;NF=7;NR=10;PP=100.0;SC=ATTTGTGATCATTTTTTTTAA;TC=36;TR=17 GT:GL:GQ 0/1:-190.15,-122.85,-187.1:100 20 5972522 . TC T . PASS FR=0.5;HP=2;NF=3;NR=8;PP=100.0;SC=AGTTTTCATCTCTTCAGCTTC;TC=35;TR=11 GT:GL:GQ 0/1:-138.05,-67.95,-261.75:100 20 5974701 . T TTTTG . PASS FR=0.5;HP=6;NF=12;NR=8;PP=100.0;SC=TTAGCTTGATTTTTTTCAGCT;TC=40;TR=20 GT:GL:GQ 0/1:-282.01,-46.13,-199.33:100 20 5979818 . CTA C . PASS FR=0.5;HP=1;NF=4;NR=2;PP=100.0;SC=CACACACACACTATATAGAGT;TC=23;TR=6 GT:GL:GQ 0/1:-148.54,-97.12,-217.3:100 20 5979861 . T TAG . PASS FR=0.5;HP=1;NF=1;NR=6;PP=100.0;SC=GTATATATACTAGTGTGTATA;TC=23;TR=7 GT:GL:GQ 0/1:-206.33,-148.87,-246.11:100 20 5979921 . ATATATATTATATATAC A . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TCTATAAAGTATATATATTAT;TC=15;TR=5 GT:GL:GQ 0/1:-143.6,-52.22,-114.36:100 20 5980041 . CTATA C . PASS FR=0.5;HP=1;NF=6;NR=4;PP=100.0;SC=TATATATACACTATATATAGT;TC=35;TR=10 GT:GL:GQ 0/1:-130.29,-26.74,-240.87:100 20 5982833 . CTT C . PASS FR=0.5;HP=5;NF=2;NR=5;PP=100.0;SC=GCAATGCACTCTTTTGCTTAC;TC=22;TR=7 GT:GL:GQ 0/1:-154.07,-87.47,-142.2:100 20 5984269 . CTT C . PASS FR=0.5;HP=5;NF=6;NR=7;PP=100.0;SC=AATCCTTTCTCTTTTCACGTT;TC=31;TR=13 GT:GL:GQ 0/1:-161.92,-47.17,-162.99:100 20 5986173 . A ATAATT . PASS FR=0.5;HP=3;NF=9;NR=5;PP=100.0;SC=AAAATTTAAAATAAAAACTAT;TC=31;TR=14 GT:GL:GQ 0/1:-275.95,-89.41,-205.85:100 20 5997120 . T TGTGTGA . PASS FR=0.5;HP=2;NF=2;NR=2;PP=100.0;SC=TGTGTGTGTGTGAGTTTTCTT;TC=20;TR=4 GT:GL:GQ 0/1:-128.89,-41.21,-139.69:100 20 5999929 . G GTTA . PASS FR=0.5;HP=5;NF=7;NR=6;PP=100.0;SC=CTTTTGACCAGTTTTTAAGTT;TC=34;TR=13 GT:GL:GQ 0/1:-145.72,-26.46,-192.55:100 20 6013970 . C CG . PASS FR=0.5;HP=4;NF=4;NR=1;PP=100.0;SC=TTAGTAGAGACGGGGTTTCAC;TC=18;TR=5 GT:GL:GQ 0/1:-76.07,-30.4,-70.18:100 20 6019907 . TTGTGTGTGTGTGTGTG T . PASS FR=0.5;HP=2;NF=1;NR=1;PP=100.0;SC=GCAGTTTTGTTTGTGTGTGTG;TC=27;TR=2 GT:GL:GQ 0/1:-146.39,-89.3,-170.65:100 20 6052252 . CT C . PASS FR=1.0;HP=2;NF=5;NR=9;PP=100.0;SC=ATCCCCAGCCCTTCCTGGCTT;TC=21;TR=14 GT:GL:GQ 1/1:-166.42,-15.59,-2.3:100 20 6054897 . T TG . PASS FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TGGGCAAGGCTGGGAAGGAAG;TC=16;TR=11 GT:GL:GQ 1/1:-170.6,-33.42,-22.33:90 20 6056042 . T TA . PASS FR=1.0;HP=2;NF=8;NR=17;PP=100.0;SC=ACATCAAGTATATACGGTACA;TC=29;TR=25 GT:GL:GQ 1/1:-301.61,-48.56,-28.73:100 20 6163149 . CATTT C . PASS FR=1.0;HP=1;NF=11;NR=10;PP=100.0;SC=AACCTCTGAGCATTTATTTCA;TC=24;TR=21 GT:GL:GQ 1/1:-265.47,-16.86,-0.92:100 20 6169158 . C CT . PASS FR=1.0;HP=1;NF=11;NR=21;PP=100.0;SC=AATTGCAAGACCTTAAGAACC;TC=38;TR=32 GT:GL:GQ 1/1:-377.27,-55.22,-28.98:100 20 6186522 . G GC . PASS FR=1.0;HP=6;NF=10;NR=10;PP=100.0;SC=TAAAAAATGTGTTTTTAATCA;TC=21;TR=20 GT:GL:GQ 1/1:-309.42,-177.87,-163.8:100 20 6186628 . C CA . PASS FR=0.5;HP=3;NF=5;NR=12;PP=100.0;SC=TTCATCACCTCAAACATTTAT;TC=33;TR=17 GT:GL:GQ 0/1:-173.72,-30.0,-131.16:100 20 6189872 . C CCTT . PASS FR=0.5;HP=1;NF=1;NR=10;PP=100.0;SC=CTTCCTCCCTCCTTTCCCTCT;TC=26;TR=11 GT:GL:GQ 0/1:-217.8,-111.28,-184.18:100 20 6190124 . C CTT . PASS FR=0.5;HP=2;NF=2;NR=4;PP=92.0;SC=TCCTGCCTCTCTCTTTCCTCC;TC=16;TR=6 GT:GL:GQ 0/1:-129.79,-96.5,-151.55:100 20 6190921 . A AT . PASS FR=0.5;HP=2;NF=5;NR=4;PP=100.0;SC=CCATAAGTACATTAAAAAAAA;TC=24;TR=9 GT:GL:GQ 0/1:-121.19,-85.53,-104.7:86 20 6202427 . C CT . PASS FR=1.0;HP=6;NF=6;NR=13;PP=100.0;SC=GAAATCCTTTCTTTCCCCCTA;TC=20;TR=19 GT:GL:GQ 1/1:-165.74,-14.09,-0.92:100 20 6211244 . GT G . PASS FR=0.5;HP=10;NF=5;NR=6;PP=100.0;SC=TTGATTTCCAGTTTTTTTTTT;TC=33;TR=11 GT:GL:GQ 0/1:-97.67,-63.78,-117.4:100 20 6217057 . T TA . PASS FR=0.5;HP=2;NF=4;NR=7;PP=100.0;SC=TCTCTACAACTAACCATCAAC;TC=33;TR=11 GT:GL:GQ 0/1:-151.16,-56.84,-189.09:100 20 6227811 . TTTTTCTTTTC T . PASS FR=0.5;HP=6;NF=3;NR=2;PP=100.0;SC=TATACTGCTTTTTTTCTTTTC;TC=28;TR=5 GT:GL:GQ 0/1:-171.28,-80.47,-279.48:100 20 6228139 . TA T . PASS FR=0.5;HP=8;NF=6;NR=7;PP=100.0;SC=ACTGGTTGTTTAAAAAAAACA;TC=27;TR=13 GT:GL:GQ 0/1:-101.53,-37.68,-71.46:100 20 6229361 . G GTA . PASS FR=0.5;HP=2;NF=7;NR=5;PP=100.0;SC=TGCTTTTGAAGTATACCTTTA;TC=28;TR=12 GT:GL:GQ 0/1:-168.24,-128.05,-263.48:100 20 6232719 . T TA . PASS FR=1.0;HP=4;NF=10;NR=14;PP=100.0;SC=CGTACCTCAATAAGTACTGTT;TC=26;TR=24 GT:GL:GQ 1/1:-246.13,-19.86,-1.84:100 20 6235756 . T TA . PASS FR=0.5;HP=10;NF=4;NR=2;PP=51.0;SC=ATATAAAAGTTAAAAAAAAAA;TC=22;TR=6 GT:GL:GQ 0/1:-59.89,-37.16,-67.02:100 20 6242610 . GCAGACC G . PASS FR=0.5;HP=1;NF=7;NR=3;PP=100.0;SC=ACTGGGAGAGGCAGACCCACC;TC=27;TR=10 GT:GL:GQ 0/1:-180.6,-46.65,-174.85:100 20 6245977 . A AT . PASS FR=0.5;HP=6;NF=7;NR=5;PP=100.0;SC=CTTAGTTTTCATTTTTTAGCA;TC=29;TR=12 GT:GL:GQ 0/1:-149.75,-66.4,-136.45:100 20 6258987 . CT C . PASS FR=0.5;HP=6;NF=4;NR=10;PP=100.0;SC=GTATGTTCTTCTTTTGTCCCC;TC=34;TR=14 GT:GL:GQ 0/1:-185.84,-121.45,-268.81:100 20 6272029 . T TA . PASS FR=0.5;HP=3;NF=4;NR=9;PP=100.0;SC=TAATAGCTGGTAAACCCAACC;TC=39;TR=13 GT:GL:GQ 0/1:-151.49,-56.11,-226.05:100 20 6293812 . G GA . PASS FR=1.0;HP=7;NF=15;NR=12;PP=100.0;SC=GGAAAAGAAAGAAAAGAAAAA;TC=35;TR=27 GT:GL:GQ 1/1:-393.29,-260.24,-242.04:100 20 6296458 . T TA . PASS FR=1.0;HP=8;NF=5;NR=17;PP=100.0;SC=GAAAGCACAATTTTTTTTTCT;TC=39;TR=22 GT:GL:GQ 1/1:-284.36,-128.48,-104.71:100 20 6304002 . A ATG . PASS FR=1.0;HP=2;NF=6;NR=5;PP=100.0;SC=ATATATATATATATGTGTGTG;TC=30;TR=11 GT:GL:GQ 1/1:-328.64,-256.07,-245.8:100 20 6307745 . GTA G . PASS FR=1.0;HP=3;NF=4;NR=7;PP=100.0;SC=TATATATGTTGTATATATATA;TC=16;TR=11 GT:GL:GQ 1/1:-114.94,-15.25,-6.19:75 20 6307849 . TATATATATGGTATATATATC T . PASS FR=0.5034;HP=1;NF=2;NR=2;PP=100.0;SC=ATATATGGTGTATATATATGG;TC=11;TR=4 GT:GL:GQ 0/1:-108.24,-70.67,-74.96:21 20 6307908 . TG T . PASS FR=0.5;HP=2;NF=3;NR=4;PP=100.0;SC=ATATCATATATGGTGTATATA;TC=21;TR=7 GT:GL:GQ 0/1:-127.13,-92.55,-148.07:100 20 6308166 . G GTA,GTATA . PASS FR=0.5,0.5;HP=2;NF=2,1;NR=0,3;PP=86.0,100.0;SC=GTGTGTGTGTGTATATATATA;TC=16;TR=2,4 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6308279 . G GTA . PASS FR=1.0;HP=2;NF=5;NR=4;PP=100.0;SC=TATATATGGTGTATATATATA;TC=12;TR=9 GT:GL:GQ 1/1:-129.24,-92.18,-87.75:54 20 6308322 . GTGTGTGTATATATATATATATATA G . PASS FR=1.0;HP=2;NF=1;NR=2;PP=88.0;SC=ATGTATGTGTGTGTGTGTATA;TC=16;TR=3 GT:GL:GQ 1/1:-227.62,-141.11,-132.99:40 20 6319701 . G GGT . PASS FR=0.5;HP=1;NF=1;NR=5;PP=100.0;SC=GAGTCTATGTGGTGTGTGTGT;TC=19;TR=6 GT:GL:GQ 0/1:-99.44,-38.84,-115.36:100 20 6345189 . G GT . PASS FR=0.5;HP=8;NF=8;NR=3;PP=100.0;SC=ATTGTTTTCAGTTTTTTTTCT;TC=31;TR=11 GT:GL:GQ 0/1:-92.31,-34.03,-73.88:100 20 6346428 . C CTCTGTATG . PASS FR=0.5;HP=4;NF=5;NR=1;PP=45.0;SC=TATTCTCTATCTTTAATTTAA;TC=31;TR=6 GT:GL:GQ 0/1:-234.84,-191.03,-405.18:86 20 6349738 . TAC T . PASS FR=0.5;HP=1;NF=2;NR=1;PP=86.0;SC=GACACATACGTACACACACAC;TC=15;TR=3 GT:GL:GQ 0/1:-95.85,-65.71,-99.67:100 20 6364214 . ACTCTT A . PASS FR=0.5;HP=3;NF=5;NR=10;PP=100.0;SC=TCTTTACAAAACTCTTCTAGA;TC=36;TR=15 GT:GL:GQ 0/1:-210.3,-34.68,-236.21:100 20 6373382 . TCTACCTAC T . PASS FR=1.0;HP=1;NF=9;NR=8;PP=100.0;SC=ATTTCCTCTATCTACCTACCT;TC=38;TR=17 GT:GL:GQ 1/1:-510.97,-41.39,-20.72:100 20 6384835 . TACACACAC TAC,T . PASS FR=0.5,0.5;HP=2;NF=2,2;NR=7,1;PP=100.0,51.0;SC=GGATGACACATACACACACAC;TC=32;TR=9,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6390974 . TAA T . PASS FR=1.0;HP=3;NF=19;NR=16;PP=100.0;SC=CTGCCTACCTTAAACACATAA;TC=42;TR=35 GT:GL:GQ 1/1:-376.88,-34.87,-5.52:100 20 6401100 . A AT . PASS FR=1.0;HP=9;NF=15;NR=9;PP=100.0;SC=TTCAAAAAGCATTTTTTTTTG;TC=34;TR=24 GT:GL:GQ 1/1:-148.27,-28.49,-8.51:100 20 6406758 . C CT . PASS FR=1.0;HP=7;NF=4;NR=16;PP=100.0;SC=TCTCTCCCCTCTTTTTTCTCC;TC=31;TR=20 GT:GL:GQ 1/1:-235.73,-83.65,-66.42:100 20 6410888 . CAGGGCTTGGCCCTGGAGT C . PASS FR=0.5;HP=1;NF=2;NR=4;PP=100.0;SC=TTCTCCACTCCAGGGCTTGGC;TC=24;TR=6 GT:GL:GQ 0/1:-188.53,-25.15,-199.92:100 20 6426272 . T TCTC,TTTC . PASS FR=0.5,0.5;HP=1;NF=11,6;NR=5,5;PP=100.0,100.0;SC=TTAAAAATTATCTCATTTCCT;TC=28;TR=16,11 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6428681 . CA C . PASS FR=0.5009;HP=2;NF=4;NR=5;PP=100.0;SC=GGTGGGCCACCAACAGTGTCT;TC=20;TR=9 GT:GL:GQ 0/1:-312.7,-243.18,-248.77:27 20 6430456 . A AT . PASS FR=0.5;HP=10;NF=10;NR=6;PP=100.0;SC=TAATATTTAAATTTTTTTTTT;TC=35;TR=16 GT:GL:GQ 0/1:-143.54,-83.39,-119.6:100 20 6438083 . TA T . PASS FR=0.5;HP=7;NF=2;NR=8;PP=100.0;SC=AACAGATATATAAAAAATGCT;TC=21;TR=10 GT:GL:GQ 0/1:-86.86,-14.54,-78.87:100 20 6441903 . C CT . PASS FR=0.5;HP=9;NF=10;NR=11;PP=100.0;SC=AAATTAAATACTTTTTTTTTA;TC=43;TR=21 GT:GL:GQ 0/1:-221.48,-121.14,-137.31:73 20 6443155 . TTA T . PASS FR=0.5005;HP=5;NF=2;NR=2;PP=100.0;SC=AAACAGTTTTTTATATATATA;TC=14;TR=4 GT:GL:GQ 0/1:-162.1,-119.94,-126.23:30 20 6443546 . G GTA . PASS FR=0.5;HP=2;NF=1;NR=2;PP=100.0;SC=ATATATATGTGTATATATATA;TC=14;TR=3 GT:GL:GQ 0/1:-156.72,-103.24,-116.61:61 20 6447485 . C CA . PASS FR=0.5;HP=3;NF=4;NR=13;PP=100.0;SC=TTTTGAATTTCAAATATTTTC;TC=38;TR=17 GT:GL:GQ 0/1:-255.09,-105.01,-200.26:100 20 6448179 . TAATAA T . PASS FR=0.5;HP=5;NF=3;NR=4;PP=100.0;SC=TATCTCGAAATAATAAAATAA;TC=36;TR=7 GT:GL:GQ 0/1:-185.97,-96.1,-256.82:100 20 6456952 . ATT AT,A . PASS FR=0.5,0.5;HP=10;NF=7,8;NR=4,5;PP=100.0,100.0;SC=CAATGATGTCATTTTTTTTTT;TC=27;TR=11,13 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6458185 . GA G . PASS FR=0.5;HP=10;NF=11;NR=4;PP=100.0;SC=AAATAAAAATGAAAAAAAAAA;TC=48;TR=15 GT:GL:GQ 0/1:-255.96,-202.85,-273.91:100 20 6459292 . G GA . PASS FR=0.5;HP=10;NF=2;NR=6;PP=49.0;SC=TATCCTATCAGAAAAAAAAAC;TC=30;TR=8 GT:GL:GQ 0/1:-83.74,-61.52,-111.1:99 20 6473904 . TAGGTGAAATTTTCTTTTCTGTTTTTTTAA T . PASS FR=0.5;HP=1;NF=2;NR=1;PP=100.0;SC=TCCCTAATTCTAGGTGAAATT;TC=25;TR=3 GT:GL:GQ 0/1:-202.85,-99.33,-502.66:100 20 6481086 . T TTGTC . PASS FR=1.0;HP=2;NF=7;NR=5;PP=100.0;SC=TTGTTCCTCTTTGTCAGAGCA;TC=21;TR=12 GT:GL:GQ 1/1:-268.34,-19.84,-4.6:100 20 6488178 . CTTG C . PASS FR=1.0;HP=2;NF=13;NR=13;PP=100.0;SC=AAGCTACTTGCTTGTTGTTGA;TC=32;TR=26 GT:GL:GQ 1/1:-335.98,-26.27,-4.81:100 20 6520175 . C CTT . PASS FR=1.0;HP=3;NF=12;NR=17;PP=100.0;SC=TTACTTAAGACTTTCTATTGA;TC=35;TR=29 GT:GL:GQ 1/1:-362.42,-32.47,-7.59:100 20 6524976 . GACTAC G . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=CTATGAAATTGACTACACTAC;TC=32;TR=25 GT:GL:GQ 1/1:-403.49,-65.81,-45.47:100 20 6531643 . GT G . PASS FR=1.0;HP=4;NF=17;NR=11;PP=100.0;SC=CAGATAAAGTGTTTAATTCAT;TC=31;TR=28 GT:GL:GQ 1/1:-281.56,-58.08,-38.11:100 20 6544912 . CAGAT CAGATAGATAGATAGAT,C . PASS FR=0.5,0.5;HP=1;NF=1,1;NR=4,1;PP=100.0,100.0;SC=TATTCACTGCCAGATAGATAG;TC=24;TR=5,2 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6548435 . A AAGAG . PASS FR=1.0;HP=2;NF=5;NR=8;PP=100.0;SC=GAGAAACAGAAAGAGAGAGAG;TC=33;TR=13 GT:GL:GQ 1/1:-316.58,-47.12,-29.98:100 20 6549783 . C CTT . PASS FR=1.0;HP=9;NF=3;NR=10;PP=100.0;SC=TGGTCCAGGCCTTTTTTTTTG;TC=24;TR=13 GT:GL:GQ 1/1:-145.52,-61.65,-53.62:66 20 6553955 . TTATA T . PASS FR=1.0;HP=3;NF=12;NR=6;PP=100.0;SC=ATTTTACATTTTATATATATA;TC=30;TR=18 GT:GL:GQ 1/1:-272.92,-35.6,-20.34:100 20 6563467 . CTAGGTAGGTAGG C . PASS FR=1.0;HP=1;NF=3;NR=6;PP=100.0;SC=ACATGCATTCCTAGGTAGGTA;TC=22;TR=9 GT:GL:GQ 1/1:-367.98,-150.14,-139.95:85 20 6565618 . CGTGT C . PASS FR=1.0;HP=2;NF=4;NR=3;PP=100.0;SC=TGTGTGTGTTCGTGTGTGTGT;TC=19;TR=7 GT:GL:GQ 1/1:-220.73,-126.68,-119.85:85 20 6565651 . G GTA . PASS FR=0.5286;HP=2;NF=3;NR=2;PP=100.0;SC=GTGTATATGTGTATATATATA;TC=16;TR=5 GT:GL:GQ 0/1:-258.66,-193.34,-195.57:12 20 6585232 . C CT . PASS FR=1.0;HP=2;NF=15;NR=16;PP=100.0;SC=ACAAACCCATCTCCTAAAATC;TC=33;TR=31 GT:GL:GQ 1/1:-314.24,-29.76,-6.91:100 20 6590623 . C CCTGCTT . PASS FR=1.0;HP=1;NF=17;NR=14;PP=100.0;SC=AGAGTTATCTCCTGCTGTCAT;TC=32;TR=31 GT:GL:GQ 1/1:-527.33,-38.07,-14.51:100 20 6603635 . C CA . PASS FR=1.0;HP=4;NF=12;NR=8;PP=100.0;SC=TTAGTCAAGCCAAAATCACAT;TC=27;TR=20 GT:GL:GQ 1/1:-325.58,-214.53,-199.34:100 20 6609608 . CTT C . PASS FR=1.0;HP=3;NF=10;NR=9;PP=100.0;SC=TGTTTTGATGCTTTCTGGCTT;TC=27;TR=19 GT:GL:GQ 1/1:-576.75,-576.47,-576.51:100 20 6609611 . T TGGAGGAGGA . PASS FR=1.0;HP=2;NF=9;NR=9;PP=100.0;SC=TTTGATGCTTTCTGGCTTGGA;TC=23;TR=18 GT:GL:GQ 1/1:-576.75,-311.9,-294.35:100 20 6644452 . C CTGTAG . PASS FR=1.0;HP=1;NF=14;NR=16;PP=100.0;SC=ATAAAAGGCACTGTAGCATAG;TC=35;TR=30 GT:GL:GQ 1/1:-563.91,-35.77,-9.44:100 20 6647434 . A ATC . PASS FR=1.0;HP=2;NF=4;NR=14;PP=100.0;SC=GGATACTGAGATTCTAAGTAG;TC=21;TR=18 GT:GL:GQ 1/1:-241.28,-23.07,-7.83:100 20 6655343 . T TG . PASS FR=1.0;HP=6;NF=6;NR=9;PP=100.0;SC=AGTCTAAAGATTTTTTTCTGG;TC=18;TR=15 GT:GL:GQ 1/1:-141.83,-27.31,-14.91:95 20 6655876 . GTATATA GTA,G . PASS FR=0.5,0.5;HP=1;NF=8,2;NR=11,1;PP=100.0,58.0;SC=TACATATATAGTATATATATA;TC=31;TR=19,3 GT:GL:GQ 1/2:-1.0,-1.0,-1.0:100 20 6664331 . C CTG . PASS FR=1.0;HP=5;NF=5;NR=10;PP=100.0;SC=GGTTTAAAAACTGTGTGTGTG;TC=30;TR=15 GT:GL:GQ 1/1:-232.49,-35.13,-29.16:74 20 6668238 . CT C . PASS FR=1.0;HP=10;NF=7;NR=15;PP=100.0;SC=ACTGGAGAAACTTTTTTTTTT;TC=30;TR=22 GT:GL:GQ 1/1:-332.94,-279.88,-269.29:89 20 6677392 . CTGTGTG C . PASS FR=0.5;HP=2;NF=1;NR=6;PP=100.0;SC=GTGTGTGGCCCTGTGTGTGTG;TC=24;TR=7 GT:GL:GQ 0/1:-156.67,-56.12,-128.5:100 20 6687137 . CAT C . PASS FR=1.0;HP=2;NF=12;NR=13;PP=100.0;SC=ATAAGATCCACATGAGACAAT;TC=26;TR=25 GT:GL:GQ 1/1:-279.85,-22.16,-4.14:100 20 6690400 . T TG . PASS FR=1.0;HP=2;NF=22;NR=8;PP=100.0;SC=TTAATACATTTGTATGCCCTG;TC=31;TR=30 GT:GL:GQ 1/1:-315.1,-40.57,-19.1:100 20 6694813 . GAA G . PASS FR=1.0;HP=6;NF=5;NR=4;PP=100.0;SC=AAGAAAGAAAGAAAGAGAAAG;TC=13;TR=9 GT:GL:GQ 1/1:-119.78,-18.28,-9.43:64 20 6717401 . G GA . PASS FR=1.0;HP=10;NF=14;NR=6;PP=100.0;SC=CTCTCTTAAGGAAAAAAAAAA;TC=27;TR=20 GT:GL:GQ 1/1:-134.21,-33.86,-20.0:100 20 6723994 . A AAC . PASS FR=1.0;HP=4;NF=10;NR=3;PP=100.0;SC=CACATACAAAAACACACACAC;TC=23;TR=13 GT:GL:GQ 1/1:-174.48,-22.71,-13.76:74 20 6746236 . C CTTAT . PASS FR=0.5;HP=2;NF=2;NR=4;PP=100.0;SC=CTGGAGACTACTTATTTATTT;TC=23;TR=6 GT:GL:GQ 0/1:-115.46,-26.87,-109.86:100 20 6759758 . A AAT . PASS FR=0.5;HP=2;NF=2;NR=3;PP=100.0;SC=TAAATACATAAATATATATAT;TC=21;TR=5 GT:GL:GQ 0/1:-98.2,-23.97,-51.3:100 20 6765134 . A AACAC . PASS FR=0.5;HP=1;NF=2;NR=5;PP=100.0;SC=TTGAGAATCTAACACACACAC;TC=25;TR=7 GT:GL:GQ 0/1:-145.56,-56.64,-151.12:100 pysam-0.7.7/tests/vcf-examples/6.vcf0000664000076400007650000153665011754437212017134 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##fileDate=20110531 ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGertonLunterValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 669442 . TG T 99 PASS SEQUENCING.AC=101;CallSetAC=116,128,155,72,71;CallSetAC2=2,2,2,2,2;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=7;HU=G;IH=1;TR=7;TU=G;Set=SAMTOOLS;SEQUENOM.AC=54 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 676148 . 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C CT 99 PASS SEQUENCING.AC=28;CallSetAC=32,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=2;HU=T;IH=0;TR=2;TU=T;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1655540 . AT A 99 PASS SEQUENCING.AC=4;CallSetAC=7,5,4,4,4;CallSetAC2=1,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=DINDEL;SEQUENOM.AC=4 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2889034 . AAAAT A 99 PASS SEQUENCING.AC=8;CallSetAC=10,9,10,7,8;CallSetAC2=1,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=5;HU=A;IH=0;TR=5;TU=A;Set=BC;SEQUENOM.AC=6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . CT C 99 PASS SEQUENCING.AC=5;CallSetAC=12,5,9,6,6;CallSetAC2=2,1,0,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=7;HU=C;IH=1;TR=7;TU=C;Set=SAMTOOLS;SEQUENOM.AC=4 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3700705 . CTTTGGG C 99 PASS SEQUENCING.AC=3;CallSetAC=4,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=T;IH=0;TR=7;TU=CTT;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 4037626 . 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C CT 99 PASS SEQUENCING.AC=6;CallSetAC=14,3,9,6,7;CallSetAC2=1,0,0,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=6;HU=T;IH=1;TR=6;TU=T;Set=OX;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 8233352 . 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AAAGT A 99 PASS SEQUENCING.AC=10;CallSetAC=12,15,22,11,12;CallSetAC2=0,1,0,0,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=DINDEL;SEQUENOM.AC=11 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 9925738 . 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TA T 99 PASS SEQUENCING.AC=7;CallSetAC=0,0,7,0,0;CallSetAC2=0,0,1,0,0;Groups=DINDEL;HR=2;HU=A;IH=0;TR=2;TU=A;Set=DINDEL;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13960028 . TC T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=8;CallSetAC=10,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=T;IH=0;TR=3;TU=T;Set=BC;SEQUENOM.AC=188 GT 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 . 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 . . 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 20 14159734 . 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TG T 99 PASS SEQUENCING.AC=50;CallSetAC=58,58,56,47,53;CallSetAC2=2,2,2,1,2;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=T;IH=0;TR=7;TU=GTT;Set=BC;SEQUENOM.AC=34 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15703503 . TG T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=9;CallSetAC=11,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=4;HU=T;IH=0;TR=4;TU=T;Set=BC;SEQUENOM.AC=87 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 . 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15871330 . AG A 99 PASS SEQUENCING.AC=1;CallSetAC=2,2,2,2,2;CallSetAC2=0,0,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=BC;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16016504 . TA T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=17;CallSetAC=4,36,0,18,0;CallSetAC2=0,1,0,0,0;Groups=BC,BI,OX;HR=1;HU=A;IH=0;TR=1;TU=A;Set=OX;SEQUENOM.AC=578 GT 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 20 16192114 . AT A 99 INCORRECT_SEQUENOM_CALLS SEQUENCING.AC=45;CallSetAC=52,49,48,42,48;CallSetAC2=3,2,3,2,3;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=4;TU=CT;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16259934 . 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TA T 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=18;CallSetAC=0,0,0,19,0;CallSetAC2=0,0,0,1,0;Groups=OX;HR=2;HU=T;IH=0;TR=2;TU=T;Set=OX;SEQUENOM.AC=682 GT 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 . 0/1 . 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 20 17473782 . 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CA C 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=13;CallSetAC=12,49,0,14,0;CallSetAC2=1,0,0,0,0;Groups=BC,BI,OX;HR=2;HU=C;IH=0;TR=2;TU=C;Set=OX;SEQUENOM.AC=432 GT 0/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/1 0/0 1/1 0/0 1/1 1/1 1/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 . 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/0 1/1 0/1 1/1 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 . 1/1 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/0 1/1 20 21968507 . AC A 99 PASS SEQUENCING.AC=10;CallSetAC=0,12,10,12,7;CallSetAC2=0,1,0,0,0;Groups=BI,DINDEL,OX,SAMTOOLS;HR=5;HU=C;IH=0;TR=5;TU=C;Set=DINDEL;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22434333 . 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TATC T 99 PASS SEQUENCING.AC=12;CallSetAC=14,15,18,11,14;CallSetAC2=1,1,0,0,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=4;TU=AT;Set=OX;SEQUENOM.AC=6 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23200197 . ATT A 99 PASS SEQUENCING.AC=1;CallSetAC=0,0,0,0,1;CallSetAC2=0,0,0,0,1;Groups=SAMTOOLS;HR=4;HU=T;IH=0;TR=4;TU=T;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . 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CATA C 99 PASS SEQUENCING.AC=1;CallSetAC=0,1,2,1,1;CallSetAC2=0,1,2,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=7;TU=AAT;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25905250 . GT G 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=56;CallSetAC=0,58,57,0,0;CallSetAC2=0,1,1,0,0;Groups=BI,DINDEL;HR=6;HU=T;IH=1;TR=6;TU=T;Set=DINDEL;SEQUENOM.AC=764 GT 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 20 29589873 . 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CAT C 99 PASS SEQUENCING.AC=8;CallSetAC=8,13,12,9,10;CallSetAC2=0,1,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=1;HU=A;IH=0;TR=5;TU=AC;Set=SAMTOOLS;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37678954 . 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AAG A 99 PASS SEQUENCING.AC=44;CallSetAC=52,57,44,21,47;CallSetAC2=1,1,2,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=6;TU=AG;Set=SAMTOOLS;SEQUENOM.AC=29 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37836124 . AAAT A 99 PASS SEQUENCING.AC=3;CallSetAC=4,4,6,3,3;CallSetAC2=1,1,1,0,0;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=4;HU=A;IH=0;TR=4;TU=A;Set=BC;SEQUENOM.AC=3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37954797 . A AGT 99 PASS SEQUENCING.AC=110;CallSetAC=126,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=1;HU=T;IH=0;TR=5;TU=AT;Set=BC;SEQUENOM.AC=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37962643 . T TAA 99 PASS SEQUENCING.AC=370;CallSetAC=395,424,394,367,423;CallSetAC2=4,4,4,3,3;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=4;TU=AT;Set=DINDEL;SEQUENOM.AC=178 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 20 38336199 . TA T 99 PASS SEQUENCING.AC=1;CallSetAC=0,2,4,2,2;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=2;HU=T;IH=0;TR=2;TU=T;Set=SAMTOOLS;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38495835 . T TA 99 AMBIGUOUS_SEQUENOM_CALLS SEQUENCING.AC=147;CallSetAC=0,0,0,153,0;CallSetAC2=0,0,0,1,0;Groups=OX;HR=3;HU=A;IH=0;TR=4;TU=AT;Set=OX;SEQUENOM.AC=14 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38696054 . GAAGA G 99 PASS SEQUENCING.AC=2;CallSetAC=0,3,5,3,3;CallSetAC2=0,1,1,1,1;Groups=BI,DINDEL,OX,SAMTOOLS;HR=2;HU=A;IH=0;TR=6;TU=AAG;Set=SAMTOOLS;SEQUENOM.AC=3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 38784318 . CCTT C 99 PASS SEQUENCING.AC=17;CallSetAC=20,19,19,15,17;CallSetAC2=2,1,1,1,1;Groups=BC,BI,DINDEL,OX,SAMTOOLS;HR=2;HU=C;IH=0;TR=7;TU=CTT;Set=SAMTOOLS;SEQUENOM.AC=7 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 39042026 . 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AG A 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=24;CallSetAC=3,51,0,25,0;CallSetAC2=0,2,0,1,0;Groups=BC,BI,OX;HR=2;HU=A;IH=0;TR=4;TU=GT;Set=OX;SEQUENOM.AC=688 GT 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 0/1 1/1 1/1 . 1/1 . 1/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 0/0 0/0 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 . 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 20 39607037 . 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AC A 99 PASS SEQUENCING.AC=1;CallSetAC=0,1,14,1,1;CallSetAC2=0,0,2,0,0;Groups=BI,DINDEL,OX,SAMTOOLS;HR=3;HU=A;IH=0;TR=3;TU=A;Set=OX;SEQUENOM.AC=1 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51838824 . GA G 99 PASS SEQUENCING.AC=1;CallSetAC=2,0,0,0,0;CallSetAC2=1,0,0,0,0;Groups=BC;HR=3;HU=G;IH=0;TR=4;TU=AC;Set=BC;SEQUENOM.AC=4 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 51961394 . 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GT G 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=8;CallSetAC=4,15,0,0,0;CallSetAC2=0,1,0,0,0;Groups=BC,BI;HR=1;HU=T;IH=0;TR=1;TU=T;Set=BC;SEQUENOM.AC=172 GT 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 1/1 1/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 20 55264363 . AG A 99 TOO_MANY_ALT_ALLELES SEQUENCING.AC=12;CallSetAC=7,0,0,19,0;CallSetAC2=1,0,0,0,0;Groups=BC,OX;HR=1;HU=G;IH=0;TR=5;TU=AG;Set=OX;SEQUENOM.AC=530 GT 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 1/1 0/0 1/1 0/0 1/1 0/0 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/0 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 1/1 0/0 0/0 1/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/0 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 1/1 0/1 0/0 0/1 1/1 1/1 1/1 0/0 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 . 1/1 . 1/1 1/1 0/1 1/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 1/1 1/1 0/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 1/1 1/1 1/1 1/1 0/0 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 1/1 0/1 0/1 0/1 1/1 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 20 55608811 . 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##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= pysam-0.7.7/tests/vcf-examples/11.vcf0000664000076400007650000117065711754437212017211 0ustar andreasandreas##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 669442 . TG T . PASS AC=54;AN=766;HW=6.74;HetPct=12.0;HomRefPct=86.9;HomVarPct=1.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 719486 . C CT . PASS AC=1;AN=760;HW=0.00;HetPct=0.3;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 890696 . C CAT . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1102516 . CT C . PASS AC=3;AN=760;HW=0.00;HetPct=0.8;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1149576 . CT C . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1195706 . AAG A . PASS AC=334;AN=764;HW=9.47;HetPct=44.9;HomRefPct=33.7;HomVarPct=21.1;NoCallPct=0.3 GT 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 1/1 1/1 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/0 1/1 0/0 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 1/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/0 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 1/1 1/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/0 0/0 1/1 0/1 1/1 0/1 1/1 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 1/1 0/0 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 1/1 0/0 1/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 1/1 20 1655540 . AT A . PASS AC=4;AN=764;HW=0.00;HetPct=1.0;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2889034 . AAAAT A . PASS AC=6;AN=762;HW=0.00;HetPct=1.6;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3203741 . CT C . PASS AC=4;AN=762;HW=0.00;HetPct=1.0;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 4037626 . TC T . 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G GA . PASS AC=197;AN=762;HW=14.95;HetPct=33.7;HomRefPct=56.9;HomVarPct=8.9;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 1/1 0/1 0/0 1/1 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 1/1 1/1 0/0 0/1 0/0 0/1 1/1 0/1 0/1 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 . 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 . 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 20 4363519 . CATT C . PASS AC=7;AN=764;HW=0.00;HetPct=1.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 4366806 . CAAAT C . 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CCTTGA C . PASS AC=3;AN=766;HW=0.00;HetPct=0.8;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5105482 . C CATTTTAGG . 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GA G . PASS AC=377;AN=764;HW=5.70;HetPct=53.0;HomRefPct=24.0;HomVarPct=22.7;NoCallPct=0.3 GT 0/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/0 1/1 0/0 0/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 0/0 1/1 0/1 0/1 0/0 1/1 0/1 1/1 0/1 1/1 1/1 1/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/0 1/1 1/1 0/0 1/1 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/0 1/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 1/1 1/1 0/1 1/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 . 0/0 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 0/1 1/1 0/0 1/1 0/1 0/0 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/0 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/0 1/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 20 5416109 . CA C . PASS AC=2;AN=752;HW=0.00;HetPct=0.5;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=1.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 5432262 . AGT A . 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CA C . 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CAAAGAAT C . 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T TA . 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AG A . 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C CT . 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C CT . 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TACTC T . 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TAG T . 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T TG . 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T TA . PASS AC=3;AN=756;HW=0.00;HetPct=0.8;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 11511920 . AC A . 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ATTAG A . PASS AC=1;AN=764;HW=0.00;HetPct=0.3;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 12021825 . A AG . 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CTT C . 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CTA C . 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TTATC T . 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GGGA G . 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CT C . PASS AC=10;AN=764;HW=0.00;HetPct=2.6;HomRefPct=97.1;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 20 13287841 . CAT C . PASS AC=134;AN=760;HW=0.21;HetPct=29.2;HomRefPct=67.1;HomVarPct=2.9;NoCallPct=0.8 GT 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 1/1 0/1 0/1 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/0 1/1 0/1 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 . 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 20 13566260 . AAATTG A . PASS AC=374;AN=764;HW=3.95;HetPct=47.5;HomRefPct=27.2;HomVarPct=25.1;NoCallPct=0.3 GT 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/1 0/1 0/0 0/1 0/0 1/1 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 1/1 1/1 1/1 0/0 0/1 0/0 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 0/1 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/1 0/1 1/1 0/0 0/1 0/1 0/1 0/0 1/1 0/0 0/1 0/0 0/1 0/1 1/1 0/1 1/1 0/1 0/1 1/1 1/1 1/1 1/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/1 1/1 1/1 0/1 0/0 0/1 0/1 1/1 0/0 0/1 0/1 1/1 0/1 1/1 0/0 1/1 0/0 0/1 0/1 0/1 1/1 1/1 0/1 1/1 0/0 1/1 1/1 1/1 1/1 0/0 0/1 . 0/1 0/0 1/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/1 0/1 0/1 1/1 0/1 0/1 0/1 1/1 1/1 0/0 0/1 1/1 0/1 0/1 0/1 1/1 0/0 0/1 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/1 0/0 0/1 1/1 0/1 0/1 1/1 1/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 1/1 1/1 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/1 0/0 1/1 0/0 1/1 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 0/0 0/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 1/1 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 1/1 0/1 0/0 1/1 0/1 0/0 1/1 0/0 0/0 0/1 0/1 1/1 0/1 0/1 0/0 0/0 0/0 1/1 1/1 0/1 0/0 0/1 1/1 1/1 20 13685184 . AT A . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 13716193 . GAGAA G . 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TC T . 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TA T . 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GA G . 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TG T . 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TGA T . 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AG A . 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TG T . 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TG T . PASS AC=87;AN=750;HW=3.63;HetPct=19.1;HomRefPct=77.0;HomVarPct=1.8;NoCallPct=2.1 GT 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 . 0/0 0/0 0/1 0/0 0/0 0/0 . 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/1 0/0 0/1 0/0 . 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 . 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 15871330 . AG A . 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TA T . PASS AC=186;AN=764;HW=15.27;HetPct=32.4;HomRefPct=59.3;HomVarPct=8.1;NoCallPct=0.3 GT 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/0 0/1 1/1 0/1 1/1 0/1 1/1 0/1 0/0 0/1 0/1 0/1 0/1 0/1 0/1 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/1 0/1 0/1 1/1 1/1 0/0 1/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0/1 0/0 0/0 0/1 1/1 0/1 0/0 0/0 0/0 0/0 0/0 1/1 1/1 0/1 0/1 1/1 0/1 0/1 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 1/1 0/0 0/1 1/1 1/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/1 0/1 1/1 0/1 1/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/1 0/1 0/1 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 1/1 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 1/1 0/0 0/1 0/0 0/1 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/1 0/0 0/0 0/0 0/1 0/1 0/0 0/1 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 1/1 0/1 0/0 1/1 0/1 0/0 0/0 0/0 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 20 16312599 . CTA C . PASS AC=2;AN=764;HW=0.00;HetPct=0.5;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 16723642 . GGTT G . 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CA C . 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C CA . 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TA T . 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TGC T . 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A AGT . 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AC A . 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AAG A . 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TAA T . 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C CT . 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CCTT C . 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CT C . 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A AC . 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ATTACAGACT A . 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CA C . 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TG T . 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T TC . 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ACTT A . 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AG A . 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CA C . 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AC A . PASS AC=7;AN=762;HW=12.61;HetPct=1.3;HomRefPct=97.9;HomVarPct=0.3;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 22434333 . C CA . PASS AC=8;AN=766;HW=0.00;HetPct=2.1;HomRefPct=97.9;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 20 22637424 . C CAGCCA . 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TATC T . PASS AC=6;AN=766;HW=0.00;HetPct=1.6;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23200197 . ATT A . PASS AC=1;AN=766;HW=0.00;HetPct=0.3;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23293728 . CA C . 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CT C . 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CT C . PASS AC=1;AN=762;HW=0.00;HetPct=0.3;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 23889003 . GA G . 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CT C . 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CATA C . 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TATATC T . 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TTATACTA T . 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CT C . 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CT C . 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CAG C . 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A AG . 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GGCGTCTGA G . 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A AAG . 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C CA . 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CT C . 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GA G . 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TG T . 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TC T . 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TAAAG T . 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ATAC A . 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CAG C . 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CAG C . 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TG T . 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CAT C . 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C CTGG . PASS AC=7;AN=762;HW=0.00;HetPct=1.8;HomRefPct=97.7;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 37712193 . AAG A . 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AAAT A . 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T TAA . 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TA T . 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T TA . 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GAAGA G . 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CCTT C . 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T TG . 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AG A . 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TG T . 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T TG . 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T TATCA . 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C CATTT . 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CACTT C . 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T TA . 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CT C . 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T TGGGTC . 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AG A . 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CA C . 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C CT . 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T TC . 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AACAG A . 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T TA . 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GA G . 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T TAAGC . 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TC T . 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CTG C . 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GC G . 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A AGTC . 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GC G . 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CA C . 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CCTA C . 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G GT . 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AG A . 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TTTTC T . 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A AT . 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G GAA . 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G GT . 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AC A . 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GA G . 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ATTTG A . 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CATGA C . 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T TA . 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T TC . 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CAG C . 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AC A . 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CAT C . 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TGAGC T . 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GT G . 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AG A . 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CT C . 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CAA C . 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CA C . 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T TGAGG . 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T TG . 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TG T . 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TC T . 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CTG C . 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CCT C . 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TG T . 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C CT . 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AC A . 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GC G . 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GC G . 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TCTGC T . 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G GA . PASS AC=2;AN=760;HW=0.00;HetPct=0.5;HomRefPct=98.7;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62310426 . CTT C . PASS AC=1;AN=756;HW=0.00;HetPct=0.3;HomRefPct=98.4;HomVarPct=0.0;NoCallPct=1.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 62871860 . C CCCGCA . PASS AC=27;AN=764;HW=17.87;HetPct=5.5;HomRefPct=93.5;HomVarPct=0.8;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/vcf-examples/2.vcf0000664000076400007650000065605712007614323017123 0ustar andreasandreas##fileformat=VCFv4.0 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-scr1/delangel/VQSRIndels/data/trainMills75_truthMills75_p15_12_12_pctb0.05_std12.0_mG8_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=93.0 ignore_filter=null mode=INDEL" ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR/AFR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN/ASN.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR/AMR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR/EUR.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AFR.admix/AFR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/ASN.admix/ASN.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/AMR.admix/AMR.admix.phase1.chr20.42.raw.indels.vcf, /humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110608VQSRConsensus/calls/chr20/EUR.admix/EUR.admix.phase1.chr20.42.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" ##FILTER= ##FILTER== 4 && (MQ0 / (1.0 * DP)) > 0.1"> ##FILTER=10)"> ##FILTER=20.0"> ##FILTER= 7500"> ##FILTER==15"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER==-1.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/ebanks/ALL.chr20.Oxford.20110407.indels.genotypes.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" ##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false discordance= concordance= family_structure= mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 selectSNPs=false selectIndels=true" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/delangel/calls/chr20/CHB.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CHS.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/CLM.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/JPT.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/MXL.phase1.chr20.42.cleaned.bam, /broad/shptmp/delangel/calls/chr20/PUR.phase1.chr20.42.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:41000001-42000000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=8 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_ALL_SITES standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[MappingQualityZeroFraction]" ##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./ALL.chr20.vqsr_2of5_union_sites_for_validation_boosted.vcf] rodToIntervalTrackName=variant BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sampleName=null annotation=[IndelType] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/1kg/processing/pipeline_test_bams/chr22_chunked.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/broad/shptmp/rpoplin/ALL.phase1.chr22.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1, QUAL<30.0, SB>=-1.0, QD<1.0, HRun>=15, HaplotypeScore>20.0] filterName=[HARD_TO_VALIDATE, LowQual, StrandBias, QualByDepth, HomopolymerRun, HaplotypeScore] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false" ##commandline="/share/software/freebayes/bin/freebayes --stdin --min-alternate-count 2 --genotype-combo-step-max 20 --genotype-variant-threshold 4 --no-marginals --pvar 0.0001 --indels --mnps --no-filters --binomial-obs-priors --allele-balance-priors --region 20:0..100000 --vcf /d1/data/1000G/20101123/populations/finalised.phase1/integrated/including454/wg/ALL/Pipeline/none//freebayes/freebayes.20:0-100000.baq.20110328.vcf --fasta-reference /d2/data/references/build_37/human_reference_v37.fa" ##fileDate=2011-03-28 ##filedate=2011-02-08 ##filter="( SNP | MNP ) & ( MQM > 65 | QUAL > 1 ) & ABP < 30 & AB < 0.9 | ( INS | DEL ) & QUAL > 500" ##phasing=none ##platypusOptions={'bamFiles': ['/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06984', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06985', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06986', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06989', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA06994', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07000', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07037', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07048', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07051', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07056', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07346', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07347', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA07357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10847', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA10851', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11829', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11830', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11831', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/NA11832', 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'/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01354', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01356', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01357', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01359', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01360', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01365', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01366', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01374', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01375', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01377', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01378', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01383', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01384', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01389', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01390', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01437', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01440', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01441', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01455', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01456', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01461', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01462', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01464', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01465', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01488', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01489', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01491', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01492', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01494', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01495', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01497', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01498', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01515', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01516', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01518', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01519', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01521', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01522', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01550', '/scratch/rimmer/ThousandGenomes/PhaseOneBAMs/HG01551'], 'minReads': 2, 'refFile': '/scratch/rimmer/Genomes/human_g1k_v37_ebv.fa', 'maxHaplotypes': 64, 'maxSize': 100, 'ploidy': 2, 'maxRegionSize': 10000, 'nCPU': 1, 'minFlank': 3, 'logFileName': 'LogsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.log', 'regions': ['20:1-100001'], 'maxVariants': 6, 'genIndels': 1, 'labels': None, 'dataType': 'population', 'minMapQual': 20, 'rlen': 100, 'nInd': 994, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'minReadQual': 20, 'maxCoverage': 1000000.0, 'verbosity': 2, 'sourceFile': None, 'callOnlyIndels': 1, 'output': 'VariantCallsAllPhaseOne/ThousandGenomesPhaseOneCalls_20:1-100001.vcf'} 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freebayes.20:57600000-57700000.baq.20110328.vcf, freebayes.20:57700000-57800000.baq.20110328.vcf, freebayes.20:57800000-57900000.baq.20110328.vcf, freebayes.20:57900000-58000000.baq.20110328.vcf, freebayes.20:58000000-58100000.baq.20110328.vcf, freebayes.20:58100000-58200000.baq.20110328.vcf, freebayes.20:58200000-58300000.baq.20110328.vcf, freebayes.20:58300000-58400000.baq.20110328.vcf, freebayes.20:58400000-58500000.baq.20110328.vcf, freebayes.20:58500000-58600000.baq.20110328.vcf, freebayes.20:58600000-58700000.baq.20110328.vcf, freebayes.20:58700000-58800000.baq.20110328.vcf, freebayes.20:58800000-58900000.baq.20110328.vcf, freebayes.20:58900000-59000000.baq.20110328.vcf, freebayes.20:59000000-59100000.baq.20110328.vcf, freebayes.20:59100000-59200000.baq.20110328.vcf, freebayes.20:59200000-59300000.baq.20110328.vcf, freebayes.20:59300000-59400000.baq.20110328.vcf, freebayes.20:59400000-59500000.baq.20110328.vcf, freebayes.20:59500000-59600000.baq.20110328.vcf, freebayes.20:59600000-59700000.baq.20110328.vcf, freebayes.20:59700000-59800000.baq.20110328.vcf, freebayes.20:59800000-59900000.baq.20110328.vcf, freebayes.20:59900000-60000000.baq.20110328.vcf, freebayes.20:60000000-60100000.baq.20110328.vcf, freebayes.20:60100000-60200000.baq.20110328.vcf, freebayes.20:60200000-60300000.baq.20110328.vcf, freebayes.20:60300000-60400000.baq.20110328.vcf, freebayes.20:60400000-60500000.baq.20110328.vcf, freebayes.20:60500000-60600000.baq.20110328.vcf, freebayes.20:60600000-60700000.baq.20110328.vcf, freebayes.20:60700000-60800000.baq.20110328.vcf, freebayes.20:60800000-60900000.baq.20110328.vcf, freebayes.20:60900000-61000000.baq.20110328.vcf, freebayes.20:61000000-61100000.baq.20110328.vcf, freebayes.20:61100000-61200000.baq.20110328.vcf, freebayes.20:61200000-61300000.baq.20110328.vcf, freebayes.20:61300000-61400000.baq.20110328.vcf, freebayes.20:61400000-61500000.baq.20110328.vcf, freebayes.20:61500000-61600000.baq.20110328.vcf, freebayes.20:61600000-61700000.baq.20110328.vcf, freebayes.20:61700000-61800000.baq.20110328.vcf, freebayes.20:61800000-61900000.baq.20110328.vcf, freebayes.20:61900000-62000000.baq.20110328.vcf, freebayes.20:62000000-62100000.baq.20110328.vcf, freebayes.20:62100000-62200000.baq.20110328.vcf, freebayes.20:62200000-62300000.baq.20110328.vcf, freebayes.20:62300000-62400000.baq.20110328.vcf, freebayes.20:62400000-62500000.baq.20110328.vcf, freebayes.20:62500000-62600000.baq.20110328.vcf, freebayes.20:62600000-62700000.baq.20110328.vcf, freebayes.20:62700000-62800000.baq.20110328.vcf, freebayes.20:62800000-62900000.baq.20110328.vcf, freebayes.20:62900000-63000000.baq.20110328.vcf, freebayes.20:63000000-63025520.baq.20110328.vcf #CHROM POS ID REF ALT QUAL FILTER INFO 20 458502 . G GA 4567.01 PASS AA=20;AB=0.61111;ABA=14;ABP=6.8707;ABR=22;AC=38;AF=0.0544;AN=698;BL=374;BR=1129;BVAR;BaseQRankSum=13.364;DP=15979;DP4=1882,2188,45,37;Dels=0.00;EL=5;EPP=13.868;ER=15;FR;FS=6.503;HETAR=11;HOMA=2;HOMR=985;HP=1;HPLen=2;HR=2;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0157;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.50233;LRBP=826.56;MQ=66.16;MQ0Fraction=0.0110;MQM=70.5;MQRankSum=-3.158;NF;NR;NS=998;PP;PV4=0.15,1,0.42,0.15;RA=3173;RL=1;RPP=38.188;RR=19;RUN=1;ReadPosRankSum=-2.346;SAB=0.7;SAF=14;SAP=9.959;SAR=6;SC=GGGCGTGGTGGTGCATGTAAT;SRB=0.50047;SRF=1588;SRP=3.0165;SRR=1585;TC;TR=9;TU=GGT;VQSLOD=10.0079;set=Intersection;sumGLbyD=23.94 20 573764 . TA T 591.51 PASS AC=91;AF=0.1987;AN=458;BaseQRankSum=0.137;DP=519;FS=3.153;HRun=1;HaplotypeScore=14.0744;InbreedingCoeff=0.1460;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ=48.16;MQ0=26;MQ0Fraction=0.0501;MQRankSum=-1.636;QD=3.63;ReadPosRankSum=-4.140;SB=-408.14;VQSLOD=5.2458;set=VQSR 20 766143 . C CATCTGGTA 5521.70 PASS AA=24;AB=0.5;ABA=18;ABP=3.0103;ABR=18;AC=14;AF=0.0289;AF1=0.02038;AN=484;BL=655;BR=1542;BVAR;BaseQRankSum=3.801;CI95=0.01549,0.02655;DP=11749;DP4=2222,1998,14,8;Dels=0.00;EL=9;EPP=6.2675;ER=15;FQ=999;FR;FS=2.941;HETAR=9;HOMA=4;HOMR=901;HP=2;HPLen=2;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0515;IndelType=INS.NumRepetitions_1.EventLength_8.;LEN=8;LRB=0.40373;LRBP=780.64;MQ=56.81;MQ0Fraction=0.0253;MQM=22.167;MQRankSum=-4.809;NF;NR;NS=914;PP;PV4=0.39,1,5.8e-07,1;RA=3093;RL=6;RPP=16.039;RR=18;RUN=1;ReadPosRankSum=-2.827;SAB=0.625;SAF=15;SAP=6.2675;SAR=9;SC=GCTTTAAATTCATCTGGTACT;SRB=0.61623;SRF=1906;SRP=365.95;SRR=1187;TC;TR=1;TU=A;VQSLOD=7.0268;set=Intersection;sumGLbyD=50.23 20 997076 rs11467490 CTG C 15379.78 PASS AA=195;AB=0.59878;ABA=132;ABP=30.896;ABR=197;AC=173;AF=0.14562;AN=1188;BL=7664;BR=7309;BVAR;BaseQRankSum=21.853;DB;DEL;DP=27127;DP4=1801,2002,241,282;Dels=0.13;EL=100;EPP=3.2887;ER=95;FQ=999;FR;FS=6.591;HETAR=77;HOMA=42;HOMR=815;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1284;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TG.;LEN=2;LRB=0.023709;LRBP=21.287;MQ=61.18;MQ0Fraction=0.0214;MQM=43.041;MQRankSum=6.886;NF;NR;NS=934;PP;PV4=0.61,1.5e-78,1,1;RA=2800;RL=120;RPP=25.56;RR=75;RUN=1;ReadPosRankSum=4.504;SAB=0.62051;SAF=121;SAP=27.609;SAR=74;SC=CAGCTAATTACTGTATTTTTA;SRB=0.49821;SRF=1395;SRP=3.0879;SRR=1405;TC;TR=1;TU=T;VQSLOD=8.9396;set=Intersection;sumGLbyD=16.76 20 1042261 rs10597473 CCCTG C 168658.05 PASS AA=4481;AB=0.29043;ABA=2128;ABP=1147.1;ABR=871;AC=1172;AF=0.97830;AN=1198;BL=169975;BR=194027;BVAR;BaseQRankSum=4.599;DB;DEL;DP=29418;DP4=29,47,1441,2403;Dels=0.84;EL=2358;EPP=29.772;ER=2123;FR;FS=9.122;HETAR=482;HOMA=559;HOMR=30;HP=2;HPLen=3;HR=3;HRun=0;HU=C;INDEL;InbreedingCoeff=0.0470;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.066077;LRBP=3454.1;MQ=104.58;MQ0=4;MQ0Fraction=0.0014;MQM=58.257;MQRankSum=-3.368;NF;NR;NS=1071;PP;PV4=0.91,6.8e-09,2.8e-05,1;RA=1039;RL=2088;RPP=48.09;RR=2393;RUN=1;ReadPosRankSum=5.288;SAB=0.41442;SAF=1857;SAP=288.09;SAR=2624;SC=CCAAACCCAACCCTGCCTGGC;SRB=0.48893;SRF=508;SRP=4.1159;SRR=531;TC;TR=8;TU=CCTG;VQSLOD=8.5148;dbSNP=120;set=Intersection;sumGLbyD=59.79 20 1046297 rs33956316 C CT,CTT,CTTT 17698 PASS ABR=408;AC=432,79,230;AF=0.39779,0.07274,0.21179;BVAR;BaseQRankSum=-8.413;DB;DP=15649;DP4=147,199,534,436;FR;FS=11.580;HOMA=97;HOMR=457;HP=20;HR=16;HU=T;HaplotypeScore=16.0590;INDEL;INS;InbreedingCoeff=0.6018;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ0=19;MQ0Fraction=0.0093;MQRankSum=7.992;NF;NR;NS=767;PP;PV4=6e-05,1,1,1;QD=8.18;RA=1183;RUN=1;ReadPosRankSum=2.684;SB=-6384.08;SC=GGAAAATTTTCTTTTTTTTTT;SRB=0.40913;SRF=484;SRP=87.859;SRR=699;TC;TR=16;TU=T;VQSLOD=8.4941;dbSNP=132;set=Intersection 20 1405740 . T TA 257.28 PASS AF=0.0188;BaseQRankSum=-0.745;DP=3769;Dels=0.00;FS=0.742;HPLen=9;HRun=9;InbreedingCoeff=0.0462;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0151;MQRankSum=-0.090;ReadPosRankSum=-1.582;VQSLOD=5.6502;set=Intersection;sumGLbyD=6.94 20 1690501 . TC T 27928 PASS AA=108;AB=0.91372;ABA=100;ABP=1726.1;ABR=1059;AC=35;AF=0.02966;AN=1180;BL=593;BR=6973;BVAR;BaseQRankSum=7.567;DEL;DP=10612;Dels=0.01;EL=50;EPP=4.2971;ER=58;FS=0.000;HETAR=378;HOMA=184;HOMR=477;HRun=1;InbreedingCoeff=0.0495;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.84325;LRBP=11685;MQ0=0;MQ0Fraction=0.0000;MQM=87.361;MQRankSum=4.088;NS=1045;RA=3125;RL=3;RPP=212.2;RR=105;RUN=1;ReadPosRankSum=-13.096;SAB=0.56481;SAF=61;SAP=6.9511;SAR=47;SRB=0.51776;SRF=1618;SRP=11.572;SRR=1507;VQSLOD=3.9824;set=filterInVQSR-2of5;sumGLbyD=4.07 20 1991285 rs113891396 TAA T,TA,TAAA,TAAAAA,TAAAAAA,TAAAAAAA,TAAAAAAAA 39235.36 PASS AC=5,251,20,39,188,52,79;AF=0.0056,0.2789,0.0222,0.0433,0.2089,0.0578,0.0878;AN=900;BVAR;BaseQRankSum=1.124;DB;DEL;DP=54393;DP4=906,772,824,579;Dels=0.21;FR;FS=37.525;HP=12;HR=12;HRun=12;HU=A;INDEL;INS;InbreedingCoeff=0.6891;IndelType=MULTIALLELIC_INDEL;MQ=76.81;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-6.593;NF;NR;PP;PV4=0.0087,1,6.3e-19,1;RUN=1;ReadPosRankSum=-2.184;SC=ATCTGCCACTTAAAAAAAAAA;TC;TR=12;TU=A;VQSLOD=9.0007;dbSNP=132;set=Intersection;sumGLbyD=11.45 20 2355911 . TA T 11723 PASS AA=79;AB=0.9393;ABA=57;ABP=1577;ABR=882;AC=38;AF=0.0411;AN=924;BL=644;BR=5536;BVAR;BaseQRankSum=2.434;DEL;DP=9687;Dels=0.00;EL=45;EPP=6.3362;ER=34;FS=3.043;HETAR=321;HOMA=182;HOMR=555;HRun=5;InbreedingCoeff=0.0412;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.79159;LRBP=8411.9;MQ0=0;MQ0Fraction=0.0000;MQM=70.848;MQRankSum=0.137;NS=1058;RA=3415;RL=3;RPP=149.49;RR=76;RUN=1;ReadPosRankSum=-12.116;SAB=0.44304;SAF=35;SAP=5.2367;SAR=44;SRB=0.43572;SRF=1488;SRP=125.55;SRR=1927;VQSLOD=3.8910;set=filterInVQSR-2of5;sumGLbyD=4.88 20 2771621 rs11479849 GT G,GTT 1605.60 PASS AA=80;AB=0.79825;ABA=69;ABP=267.24;ABR=273;AC=79,91;AF=0.06551,0.07546;AN=1206;BL=2593;BR=3805;BVAR;BaseQRankSum=7.825;DB;DP=9790;Dels=0.04;EL=37;EPP=3.9875;ER=43;FR;FS=4.751;HETAR=62;HOMA=5;HOMR=958;HP=11;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2646;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.18943;LRBP=501.57;MQ0=0;MQ0Fraction=0.0000;MQM=52.45;MQRankSum=-0.560;NF;NR;NS=1025;PP;RA=3949;RL=29;RPP=16.148;RR=51;RUN=1;ReadPosRankSum=-2.397;SAB=0.525;SAF=42;SAP=3.4446;SAR=38;SC=TCATTTTAACGTTTTTTTTTT;SRB=0.54368;SRF=2147;SRP=68.46;SRR=1802;TC;TR=11;TU=T;VQSLOD=3.5989;set=filterInVQSR-2of5;sumGLbyD=3.92 20 2891235 . G GT,GTTT 2869.87 PASS AC=236,246;AF=0.2803,0.2922;AN=842;BaseQRankSum=8.979;DP=1067;FS=3.911;HaplotypeScore=20.3595;InbreedingCoeff=0.6511;IndelType=MULTIALLELIC_INDEL;MQ=44.86;MQ0=114;MQ0Fraction=0.1068;MQRankSum=-2.273;QD=4.00;ReadPosRankSum=-6.601;SB=-991.85;VQSLOD=5.4379;set=VQSR 20 3033550 . TGAG T 2005.90 PASS AA=34;AB=0.51429;ABA=34;ABP=3.1344;ABR=36;AC=22;AF=0.0332;AN=662;BL=1374;BR=1649;BVAR;BaseQRankSum=5.192;DEL;DP=14639;DP4=2271,1492,12,21;Dels=0.02;EL=19;EPP=4.0322;ER=15;FR;FS=16.657;HETAR=17;HOMA=0;HOMR=914;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=-0.0454;IndelType=DEL.NumRepetitions_1.EventLength_3.;LEN=3;LRB=0.090969;LRBP=57.333;MQ=53.99;MQ0Fraction=0.0304;MQM=46.735;MQRankSum=1.938;NF;NR;NS=931;PP;PV4=0.0068,9.4e-05,1,1;RA=2985;RL=11;RPP=12.207;RR=23;RUN=1;ReadPosRankSum=-0.466;SAB=0.41176;SAF=14;SAP=5.3095;SAR=20;SC=CTTGGGAGGCTGAGGTGGGAG;SRB=0.62781;SRF=1874;SRP=426.52;SRR=1111;TC;TR=1;TU=G;VQSLOD=8.9194;set=Intersection;sumGLbyD=24.41 20 3873327 rs61519218 A AAG 683.85 PASS AC=25;AF=0.0313;AN=800;BaseQRankSum=4.839;DB;DP=1718;FS=4.265;HRun=0;HaplotypeScore=20.5789;InbreedingCoeff=0.1055;IndelType=INS.NOVEL_2.;MQ=53.70;MQ0=37;MQ0Fraction=0.0215;MQRankSum=2.468;QD=6.30;ReadPosRankSum=4.254;SB=-403.21;VQSLOD=6.1858;set=VQSR 20 4028835 . GC G 2511.30 PASS AA=66;AB=0.56954;ABA=65;ABP=9.3521;ABR=86;AC=22;AF=0.01836;AN=1198;BL=2303;BR=2463;BVAR;BaseQRankSum=7.621;DEL;DP=22795;DP4=1714,2774,22,37;Dels=0.02;EL=34;EPP=3.1419;ER=32;FQ=999;FR;FS=2.095;HETAR=21;HOMA=0;HOMR=1050;HP=2;HPLen=2;HR=2;HRun=2;HU=C;INDEL;InbreedingCoeff=0.0125;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.033571;LRBP=14.674;MQ=108.09;MQ0=0;MQ0Fraction=0.0000;MQM=53.318;MQRankSum=5.257;NF;NR;NS=1071;PP;PV4=1,5.4e-13,1,0.075;RA=6185;RL=36;RPP=4.1947;RR=30;RUN=1;ReadPosRankSum=-1.059;SAB=0.45455;SAF=30;SAP=4.1947;SAR=36;SC=TGCTGTCACTGCCTTCTCCTA;SRB=0.42118;SRF=2605;SRP=336.76;SRR=3580;TC;TR=2;TU=C;VQSLOD=10.2409;set=Intersection;sumGLbyD=12.71 20 4039609 rs67812039 G GA 43457 PASS AA=909;AB=0.54639;ABA=572;ABP=26.583;ABR=689;AC=302;AF=0.3455;AN=874;BL=37070;BR=38211;BVAR;BaseQRankSum=20.147;DB;DP=25595;DP4=1483,1374,528,542;Dels=0.00;EL=467;EPP=4.5033;ER=442;FQ=999;FR;FS=5.441;HETAR=243;HOMA=127;HOMR=608;HP=4;HPLen=3;HR=3;HRun=3;HU=A;INDEL;INS;InbreedingCoeff=0.1388;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.015157;LRBP=40.563;MQ=119.50;MQ0=0;MQ0Fraction=0.0000;MQM=83.197;MQRankSum=1.080;NF;NR;NS=978;PP;PV4=0.16,1,3.6e-12,1;RA=3033;RL=443;RPP=4.274;RR=466;RUN=1;ReadPosRankSum=-1.000;SAB=0.32233;SAF=293;SAP=252.24;SAR=616;SC=TATGTTGGGAGAAATATCAGT;SRB=0.38378;SRF=1164;SRP=358.85;SRR=1869;TC;TR=4;TU=AG;VQSLOD=9.9146;dbSNP=130;set=Intersection;sumGLbyD=16.79 20 4390056 . TC T 49312 PASS AA=91;AB=0.94353;ABA=86;ABP=2605.4;ABR=1437;AC=39;AF=0.03160;AN=1234;BL=6823;BR=731;BVAR;BaseQRankSum=2.727;DEL;DP=13149;Dels=0.00;EL=41;EPP=4.9431;ER=50;FS=4.002;HETAR=465;HOMA=313;HOMR=292;HRun=3;InbreedingCoeff=0.0326;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.80646;LRBP=10671;MQ0=0;MQ0Fraction=0.0000;MQM=69.824;MQRankSum=-0.903;NS=1073;RA=3078;RL=89;RPP=183.62;RR=2;RUN=1;ReadPosRankSum=-12.526;SAB=0.45055;SAF=41;SAP=4.9431;SAR=50;SRB=0.52567;SRF=1618;SRP=20.622;SRR=1460;VQSLOD=4.3235;set=Intersection;sumGLbyD=3.53 20 4474622 . TA T,TAA,TAAA,TAAAA 94522.28 PASS ABR=114;AC=38,68,16,900;AF=0.03333,0.05965,0.01404,0.78947;AN=1140;BVAR;BaseQRankSum=9.741;DB;DP=16656;Dels=0.00;FR;FS=2.355;HOMA=3;HOMR=936;HP=10;HPLen=10;HR=10;HRun=10;HU=A;INS;InbreedingCoeff=0.4516;IndelType=MULTIALLELIC_INDEL;MQ0=2;MQ0Fraction=0.0008;MQRankSum=-4.096;NF;NR;NS=980;PP;RA=3766;RUN=1;ReadPosRankSum=2.380;SC=AGAAAAAAATTAAAAAAAAAA;SRB=0.49734;SRF=1873;SRP=3.2409;SRR=1893;TC;TR=10;TU=A;VQSLOD=8.8186;set=Intersection;sumGLbyD=38.79 20 4824911 . AC A 41998.70 PASS AC=1172;AF=0.97342;AN=1204;BaseQRankSum=8.604;DP=3615;FS=9.934;HRun=1;HaplotypeScore=39.6843;InbreedingCoeff=0.0980;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=129.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=3.378;QD=11.62;ReadPosRankSum=6.967;SB=-16955.28;VQSLOD=4.2689;set=VQSR 20 4839897 rs35881880 TAA T,TA,TAAA,TAAAAA 3906.80 PASS AC=12,95,137,189;AF=0.01024,0.08106,0.11689,0.16126;AN=1172;BVAR;BaseQRankSum=15.271;DB;DEL;DP=15105;Dels=0.04;FR;FS=43.567;HP=19;HR=13;HRun=13;HU=A;INS;InbreedingCoeff=0.5716;IndelType=MULTIALLELIC_INDEL;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.569;NF;NR;PP;RUN=1;ReadPosRankSum=-13.794;SC=TGTTAAAAAATAAAAAAAAAA;TC;TR=13;TU=A;VQSLOD=8.1773;set=Intersection;sumGLbyD=3.77 20 5507414 . G GCC 439.08 PASS AC=23;AF=0.01876;AN=1226;BaseQRankSum=3.051;DP=3023;FS=3.636;HRun=1;HaplotypeScore=30.3104;InbreedingCoeff=0.0204;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=112.09;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.065;QD=2.85;ReadPosRankSum=-2.709;SB=-302.22;VQSLOD=4.4311;set=VQSR 20 5609676 . GA G,GAA 799.89 PASS AA=42;AB=0.79096;ABA=37;ABP=133.16;ABR=140;AC=43,65;AF=0.03607,0.05453;AF1=0.02826;AN=1192;BL=1360;BR=2334;BVAR;BaseQRankSum=5.069;CI95=0.01242,0.04037;DP=15610;DP4=1548,2441,21,30;Dels=0.02;EL=18;EPP=4.8716;ER=24;FQ=12.1;FR;FS=0.000;HETAR=36;HOMA=1;HOMR=991;HP=13;HPLen=10;HR=10;HRun=10;HU=A;INDEL;INS;InbreedingCoeff=0.2001;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.26367;LRBP=560.68;MQ=63.29;MQ0Fraction=0.0003;MQM=44.143;MQRankSum=1.755;NF;NR;NS=1028;PP;PV4=0.77,1,0.0087,0.0053;RA=4114;RL=15;RPP=10.455;RR=27;RUN=1;ReadPosRankSum=-2.978;SAB=0.5;SAF=21;SAP=3.0103;SAR=21;SC=AAAAAAGAAAGAAAAAAAAAA;SRB=0.39742;SRF=1635;SRP=379;SRR=2479;TC;TR=11;TU=AAAG;VQSLOD=4.1229;set=filterInVQSR-2of5;sumGLbyD=7.95 20 5736211 rs35303106 CT C,CTT 4384.40 PASS AA=117;AB=0.71499;ABA=116;ABP=166.4;ABR=291;AC=32,145;AF=0.02712,0.12288;AN=1180;BL=5556;BR=4901;BVAR;BaseQRankSum=2.708;DB;DP=9157;Dels=0.01;EL=54;EPP=4.5136;ER=63;FR;FS=2.802;HETAR=79;HOMA=1;HOMR=837;HP=16;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.1903;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.062637;LRBP=92.1;MQ0Fraction=0.0273;MQM=48.932;MQRankSum=3.654;NF;NR;NS=917;PP;RA=2785;RL=79;RPP=34.209;RR=38;RUN=1;ReadPosRankSum=0.795;SAB=0.5641;SAF=66;SAP=7.1862;SAR=51;SC=TTTTCTTTTTCTTTTTTTTTT;SRB=0.41795;SRF=1164;SRP=165.85;SRR=1621;TC;TR=11;TU=T;VQSLOD=5.0895;set=Intersection;sumGLbyD=4.66 20 5898626 rs34483659 CAAA C,CA,CAA,CAAAAA 1140.16 PASS ABR=34;AC=19,98,56,199;AF=0.0227,0.1172,0.0670,0.2380;AF1=0.08519;BVAR;BaseQRankSum=5.049;CI95=0.03727,0.1273;DB;DEL;DP=5091;DP4=539,408,121,123;FQ=4.43;FR;FS=5.701;HOMA=64;HOMR=156;HP=19;HR=18;HU=A;HaplotypeScore=11.5333;INDEL;InbreedingCoeff=0.7405;IndelType=MULTIALLELIC_INDEL;MQ0=117;MQ0Fraction=0.0986;MQRankSum=6.290;NF;NR;NS=240;PP;PV4=0.043,1,1,0.0087;QD=1.22;RA=204;RUN=1;ReadPosRankSum=-2.684;SB=-1015.09;SC=ACTAAAAATACAAAAAAAAAA;SRB=0.35294;SRF=72;SRP=41.33;SRR=132;TC;TR=18;TU=A;VQSLOD=4.1696;set=filterInVQSR-2of5 20 5975126 rs10541892 C CAG 504.78 PASS AC=79;AF=0.07004;AN=1128;BaseQRankSum=10.498;DB;DP=2050;FS=38.228;HRun=0;HaplotypeScore=14.1426;InbreedingCoeff=-0.0053;IndelType=INS.NOVEL_2.;MQ=60.40;MQ0=80;MQ0Fraction=0.0390;MQRankSum=5.098;QD=1.63;ReadPosRankSum=-4.851;SB=-590.69;VQSLOD=4.8517;set=VQSR 20 6040983 rs11087710 A AAAAAAGAG,AAAAAGAG,AAAAGAG,AAAAGAGAG,AAAGAG,AAAGAGAG,AAGAG,AAGAGAG,AG,AGAG,AGAGAG 66894.55 PASS ABR=468;AC=80,9,20,136,31,91,33,29,9,3,5;AF=0.0980,0.0110,0.0245,0.1667,0.0380,0.1115,0.0404,0.0355,0.0110,0.0037,0.0061;AN=816;BVAR;BaseQRankSum=-12.470;DB;DP=38726;DP4=426,611,310,472;Dels=0.00;FQ=999;FR;FS=6.635;HOMA=110;HOMR=506;HP=14;HR=15;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.8291;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=54.22;MQ0Fraction=0.0168;MQRankSum=-5.329;NF;NR;NS=861;PP;PV4=0.56,1,6.9e-09,0.31;RA=1828;RUN=1;ReadPosRankSum=-7.857;SC=AAAAAAAAAAAAGAGAGAGAG;SRB=0.62418;SRF=1141;SRP=247.85;SRR=687;TC;TR=15;TU=A;VQSLOD=9.0574;dbSNP=131;set=Intersection;sumGLbyD=36.72 20 7024548 . G GAT 5041.27 PASS AC=123;AF=0.10336;AN=1190;BaseQRankSum=23.097;DP=3045;FS=7.979;HRun=0;HaplotypeScore=15.6967;InbreedingCoeff=0.1062;IndelType=INS.NumRepetitions_5.EventLength_2.RepeatExpansion_AT.;MQ=119.29;MQ0=2;MQ0Fraction=0.0007;MQRankSum=-3.725;QD=8.97;ReadPosRankSum=-1.636;SB=-2257.45;VQSLOD=5.9332;set=VQSR 20 7484554 . A AT 5.09 PASS AC=0;AF=0.0000;AN=710;BaseQRankSum=-0.696;DP=1862;FS=2.835;HRun=9;HaplotypeScore=13.5425;InbreedingCoeff=0.0567;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;MQ=76.92;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.932;ReadPosRankSum=-1.701;VQSLOD=4.3156;set=VQSR 20 7632194 rs77286341 GAA AAA,G 5324 PASS AC=0;AF=0.0000;AN=700;BaseQRankSum=-1.741;DB;DP=1772;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=60.1795;InbreedingCoeff=0.0017;IndelType=MIXED;MQ=70.69;MQ0=13;MQ0Fraction=0.0073;MQRankSum=-1.315;NF;NR;PP;ReadPosRankSum=-3.650;SC=GAGAGAGAGAGAAAGGTGTAA;TC;TR=13;TU=AG;set=filterInVQSR-2of5 20 7767508 rs71329674 G GA 17914 PASS AA=415;AB=0.61617;ABA=337;ABP=105.94;ABR=541;AC=141;AF=0.11614;AN=1214;BL=15187;BR=20323;BVAR;BaseQRankSum=-13.946;DB;DP=28222;Dels=0.00;EL=184;EPP=14.569;ER=231;FQ=999;FR;FS=13.296;HETAR=178;HOMA=35;HOMR=822;HP=14;HPLen=9;HR=9;HRun=9;HU=A;INDEL;INS;InbreedingCoeff=0.0714;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.14464;LRBP=1616.1;MQ=89.69;MQ0=1;MQ0Fraction=0.0003;MQM=51.667;MQRankSum=0.664;NF;NR;NS=1035;PP;RA=3707;RL=171;RPP=30.894;RR=244;RUN=1;ReadPosRankSum=-1.120;SAB=0.45301;SAF=188;SAP=10.969;SAR=227;SC=ATTCTAAAAAGAAAAAAAAAT;SRB=0.38495;SRF=1427;SRP=429.23;SRR=2280;TC;TR=9;TU=A;VQSLOD=9.0748;set=Intersection;sumGLbyD=11.09 20 7920261 . TA T,TAA 802.15 PASS AA=28;AB=0.8;ABA=28;ABP=112.45;ABR=112;AC=22,39;AF=0.01836,0.03255;AN=1198;BL=943;BR=1487;BVAR;BaseQRankSum=2.233;DP=10645;Dels=0.01;EL=11;EPP=5.8022;ER=17;FR;FS=1.691;HETAR=20;HOMA=0;HOMR=1007;HP=10;HPLen=9;HR=9;HRun=9;HU=A;INS;InbreedingCoeff=0.2256;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.22387;LRBP=267.46;MQ0=0;MQ0Fraction=0.0000;MQM=57.571;MQRankSum=0.940;NF;NR;NS=1027;PP;RA=4776;RL=8;RPP=14.178;RR=20;RUN=1;ReadPosRankSum=-1.567;SAB=0.53571;SAF=15;SAP=3.3205;SAR=13;SC=GTAACTGCTATAAAAAAAAAC;SRB=0.48576;SRF=2320;SRP=11.42;SRR=2456;TC;TR=9;TU=A;VQSLOD=4.0815;set=filterInVQSR-2of5;sumGLbyD=5.37 20 8012465 rs10595338 TATGA T 2104.41 PASS AF=0.03339;BaseQRankSum=10.662;DB;DP=11772;DS;Dels=0.01;FR;FS=7.678;HP=1;HPLen=1;HR=1;HRun=0;HU=A;InbreedingCoeff=0.0266;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0Fraction=0.0731;MQRankSum=0.603;NF;NR;PP;ReadPosRankSum=1.276;SC=TGTATGTATGTATGATGTATG;TC;TR=19;TU=ATGT;VQSLOD=4.1376;set=filterInVQSR-2of5;sumGLbyD=6.53 20 8573999 . CGTGT C,CGT,CGTGTGT,TGTGT 45865.96 PASS AC=458,0,731;AF=0.37727,0.00000,0.60214;AN=1214;BVAR;BaseQRankSum=-6.703;DEL;DP=37714;Dels=0.03;FR;FS=11.079;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.7632;IndelType=MIXED;LEN=2;MQ0Fraction=0.0026;MQRankSum=-1.394;NF;NR;PP;RUN=1;ReadPosRankSum=-2.102;SC=TGTGTGTGCGCGTGTGTGTGT;TC;TR=18;TU=GT;VQSLOD=6.1435;set=Intersection;sumGLbyD=3.53 20 8610455 rs10571111 TTTTC T 11763.51 PASS AC=190;AF=0.17056;AN=1114;BaseQRankSum=-14.397;DB;DP=2323;FS=2.321;HRun=0;HaplotypeScore=39.8020;InbreedingCoeff=0.2502;IndelType=DEL.NumRepetitions_2.EventLength_4.;MQ=53.39;MQ0=104;MQ0Fraction=0.0448;MQRankSum=3.519;QD=19.07;ReadPosRankSum=4.150;SB=-4067.02;VQSLOD=5.0554;set=VQSR 20 9139079 . ATT A,AT,ATTT,ATTTT,ATTTTT 8777.90 PASS AC=23,140,114,69,113;AF=0.01993,0.12132,0.09879,0.05979,0.09792;AN=1154;BVAR;BaseQRankSum=-0.022;DEL;DP=25109;DP4=502,657,278,313;FR;FS=11.929;HP=16;HR=16;HU=T;HaplotypeScore=20.2361;INDEL;INS;InbreedingCoeff=0.5704;IndelType=MULTIALLELIC_INDEL;MQ0=16;MQ0Fraction=0.0067;MQRankSum=2.624;NF;NR;PP;PV4=0.14,1,1,1;QD=1.48;RUN=1;ReadPosRankSum=-0.480;SB=-2354.28;SC=CACCTGGCTAATTTTTTTTTT;TC;TR=16;TU=T;VQSLOD=6.9180;set=Intersection 20 9862448 . CT C 49312 PASS AA=60;AB=0.96003;ABA=53;ABP=2440.4;ABR=1273;AC=18;AF=0.01461;AN=1232;BL=3516;BR=140;BVAR;BaseQRankSum=-2.056;DEL;DP=11893;Dels=0.01;EL=35;EPP=6.6294;ER=25;FS=1.787;HETAR=396;HOMA=344;HOMR=334;HRun=1;InbreedingCoeff=0.0379;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.92341;LRBP=6772.5;MQ0Fraction=0.0006;MQM=54.267;MQRankSum=-0.907;NS=1074;RA=2990;RL=60;RPP=133.3;RR=0;RUN=1;ReadPosRankSum=-10.579;SAB=0.58333;SAF=35;SAP=6.6294;SAR=25;SRB=0.47826;SRF=1430;SRP=15.284;SRR=1560;VQSLOD=3.0237;set=filterInVQSR-2of5;sumGLbyD=2.84 20 9863736 rs73618103 G GT 50570.21 PASS AA=2247;AB=0.48878;ABA=1412;ABP=6.0324;ABR=1350;AC=546;AF=0.44463;AN=1228;BL=86886;BR=95862;BVAR;BaseQRankSum=-23.978;DB;DP=32517;DP4=1125,1133,1017,1048;Dels=0.00;EL=1089;EPP=7.6113;ER=1158;FQ=999;FR;FS=2.529;HETAR=445;HOMA=201;HOMR=393;HP=4;HPLen=4;HR=4;HRun=4;HU=T;INDEL;INS;InbreedingCoeff=0.1393;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;KGPilot123;LEN=1;LRB=0.049117;LRBP=960.35;MQ=68.10;MQ0=2;MQ0Fraction=0.0006;MQM=50.931;MQRankSum=-1.580;NF;NR;NS=1039;PP;PV4=0.71,1,0.11,1;RA=3139;RL=1089;RPP=7.6113;RR=1158;RUN=1;ReadPosRankSum=0.846;SAB=0.54161;SAF=1217;SAP=36.804;SAR=1030;SC=TGATTGTATGGTTTTGTCCTT;SRB=0.53425;SRF=1677;SRP=34.987;SRR=1462;TC;TR=4;TU=T;VLD;VQSLOD=10.1800;dbSNP=131;set=Intersection;sumGLbyD=18.20 20 10926959 . AG A 12239 PASS AA=65;AB=0.92801;ABA=64;ABP=1417.6;ABR=825;AC=24;AF=0.0264;AN=908;BL=616;BR=3782;BVAR;BaseQRankSum=9.990;DEL;DP=10708;Dels=0.01;EL=37;EPP=5.7163;ER=28;FS=1.652;HETAR=275;HOMA=70;HOMR=724;HRun=1;InbreedingCoeff=0.0102;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.71987;LRBP=4952;MQ0=1;MQ0Fraction=0.0004;MQM=118.82;MQRankSum=1.018;NS=1069;RA=4746;RL=5;RPP=104.07;RR=60;RUN=1;ReadPosRankSum=-12.039;SAB=0.41538;SAF=27;SAP=7.0526;SAR=38;SRB=0.4764;SRF=2261;SRP=25.968;SRR=2485;VQSLOD=2.9713;set=filterInVQSR-2of5;sumGLbyD=4.10 20 11299648 . TG T 49315 PASS AA=62;AB=0.95292;ABA=54;ABP=2046.7;ABR=1093;AC=28;AF=0.0373;AN=750;BL=3126;BR=528;BVAR;BaseQRankSum=-4.929;DEL;DP=10764;Dels=0.01;EL=26;EPP=6.5127;ER=36;FS=3.851;HETAR=366;HOMA=383;HOMR=304;HRun=1;InbreedingCoeff=0.0267;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.711;LRBP=4014.1;MQ0=1;MQ0Fraction=0.0005;MQM=76.468;MQRankSum=1.327;NS=1070;RA=2588;RL=54;RPP=77.121;RR=8;RUN=1;ReadPosRankSum=-12.507;SAB=0.48387;SAF=30;SAP=3.1504;SAR=32;SRB=0.47643;SRF=1233;SRP=15.499;SRR=1355;VQSLOD=3.8673;set=filterInVQSR-2of5;sumGLbyD=3.00 20 11561096 . CTA C 999 PASS AC=2;AF=0.0029;AF1=0.005602;BaseQRankSum=3.190;CI95=0.004425,0.01106;DP=7521;DP4=1998,1794,2,4;Dels=0.00;FQ=999;FR;FS=5.422;HP=3;HPLen=2;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0056;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;MQ=113.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.297;NF;NR;PP;PV4=0.43,0.024,1,1;ReadPosRankSum=1.406;SC=CAATAGTATTCTATGTCAGTC;TC;TR=1;TU=T;VQSLOD=8.6243;set=Intersection;sumGLbyD=21.89 20 11723671 . C CA 1096.60 PASS AA=35;AB=0.69565;ABA=35;ABP=41.247;ABR=80;AC=10;AF=0.0141;AN=710;BL=2005;BR=1702;BVAR;BaseQRankSum=-3.427;DP=9819;Dels=0.00;EL=20;EPP=4.5614;ER=15;FR;FS=3.814;HETAR=20;HOMA=0;HOMR=1034;HP=8;HPLen=7;HR=7;HRun=7;HU=A;INS;InbreedingCoeff=0.0323;IndelType=INS.NumRepetitions_7.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.081737;LRBP=56.79;MQ0=0;MQ0Fraction=0.0000;MQM=81.057;MQRankSum=0.050;NF;NR;NS=1054;PP;RA=5562;RL=22;RPP=8.0357;RR=13;RUN=1;ReadPosRankSum=-2.012;SAB=0.71429;SAF=25;SAP=16.97;SAR=10;SC=ATATTGAAGACAAAAAAACAG;SRB=0.49371;SRF=2746;SRP=4.9233;SRR=2816;TC;TR=7;TU=A;VQSLOD=7.4342;set=Intersection;sumGLbyD=8.30 20 12238835 rs113904674 CTCTTCATGGTCT C 1813.44 PASS AA=7;AB=0.73077;ABA=7;ABP=15.037;ABR=19;AC=4;AF=0.0056;AN=712;BL=360;BR=368;BVAR;BaseQRankSum=3.891;DB;DEL;DP=10309;Dels=0.00;EL=4;EPP=3.3205;ER=3;FR;FS=0.000;HETAR=3;HOMA=0;HOMR=1076;HP=1;HPLen=2;HR=2;HRun=0;HU=C;InbreedingCoeff=-0.0381;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;LEN=12;LRB=0.010989;LRBP=3.2012;MQ0=0;MQ0Fraction=0.0000;MQM=37;MQRankSum=-3.793;NF;NR;NS=1079;PP;RA=6085;RL=4;RPP=3.3205;RR=3;RUN=1;ReadPosRankSum=1.319;SAB=0.42857;SAF=3;SAP=3.3205;SAR=4;SC=CTTAATGCTCCTCTTCATGGT;SRB=0.51257;SRF=3119;SRP=11.364;SRR=2966;TC;TR=6;TU=CCT;VQSLOD=5.7551;set=Intersection;sumGLbyD=69.48 20 12602812 . AT A 12344 PASS AA=47;AB=0.94372;ABA=43;ABP=1309.5;ABR=721;AC=14;AF=0.0196;AN=716;BL=2714;BR=217;BVAR;BaseQRankSum=1.424;DEL;DP=10743;Dels=0.00;EL=24;EPP=3.0565;ER=23;FS=0.629;HETAR=228;HOMA=65;HOMR=769;HRun=1;InbreedingCoeff=0.0233;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.85193;LRBP=4622.3;MQ0Fraction=0.0000;MQM=99.574;MQRankSum=1.901;NS=1080;RA=4839;RL=46;RPP=96.568;RR=1;RUN=1;ReadPosRankSum=-9.906;SAB=0.53191;SAF=25;SAP=3.4261;SAR=22;SRB=0.51106;SRF=2473;SRP=8.148;SRR=2366;VQSLOD=2.8161;set=filterInVQSR-2of5;sumGLbyD=3.67 20 13600884 . CTG C,CTGTG 1278.10 PASS AA=85;AB=0.77994;ABA=79;ABP=247.38;ABR=280;AC=71,22;AF=0.05907,0.01830;AN=1202;BL=3279;BR=3205;BVAR;BaseQRankSum=8.852;DEL;DP=24185;DP4=1317,931,52,49;Dels=0.03;EL=45;EPP=3.649;ER=40;FQ=999;FR;FS=31.826;HETAR=75;HOMA=4;HOMR=926;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1566;IndelType=MULTIALLELIC_INDEL;LEN=2;LRB=0.011413;LRBP=4.8442;MQ=65.06;MQ0Fraction=0.0012;MQM=48.671;MQRankSum=-0.511;NF;NR;NS=1005;PP;PV4=0.18,1,0.39,0.27;RA=3342;RL=35;RPP=8.7583;RR=50;RUN=1;ReadPosRankSum=-2.329;SAB=0.43529;SAF=37;SAP=6.1015;SAR=48;SC=TCCCTTTACTCTGTGTGTGTG;SRB=0.59066;SRF=1974;SRP=241.62;SRR=1368;TC;TR=15;TU=GT;VQSLOD=3.8635;set=filterInVQSR-2of5;sumGLbyD=4.23 20 13666265 . T TATAG 556.88 PASS AC=21;AF=0.01959;AN=1072;BaseQRankSum=24.958;DP=2706;FS=2.581;HRun=0;HaplotypeScore=25.9952;InbreedingCoeff=0.1419;IndelType=INS.NOVEL_4.;MQ=72.43;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.888;QD=4.38;ReadPosRankSum=2.552;SB=-417.04;VQSLOD=7.3380;set=VQSR 20 13861245 rs72422273 C CTCA 2685.46 PASS AC=140;AF=0.11589;AN=1208;BaseQRankSum=24.355;DB;DP=2910;FS=6.808;HRun=0;HaplotypeScore=19.3095;InbreedingCoeff=-0.0991;IndelType=INS.NumRepetitions_1.EventLength_3.;MQ=78.25;MQ0=22;MQ0Fraction=0.0076;MQRankSum=3.225;QD=3.64;ReadPosRankSum=2.607;SB=-1861.38;VQSLOD=4.1974;set=VQSR 20 13865746 . T TA,TAA 1416.23 PASS AA=63;AB=0.80417;ABA=47;ABP=195.87;ABR=193;AC=122,21;AF=0.10133,0.01744;AN=1204;BL=3673;BR=1145;BVAR;BaseQRankSum=-3.336;DP=10513;Dels=0.00;EL=62;EPP=131.27;ER=1;FR;FS=716.583;HETAR=45;HOMA=1;HOMR=998;HP=2;HR=1;HRun=1;HU=A;INS;InbreedingCoeff=0.0814;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.5247;LRBP=2883.3;MQ0=0;MQ0Fraction=0.0000;MQM=56.143;MQRankSum=-1.197;NF;NR;NS=1044;PP;RA=4529;RL=62;RPP=131.27;RR=1;RUN=1;ReadPosRankSum=-12.295;SAB=1;SAF=63;SAP=139.81;SAR=0;SC=GGAACATGGATACCCCCCTGC;SRB=0.52462;SRF=2376;SRP=26.853;SRR=2153;TC;TR=1;TU=A;VQSLOD=-4.2308;set=filterInVQSR-2of5;sumGLbyD=4.77 20 13881703 . CTT C 152.85 PASS AC=8;AF=0.0093;AN=862;BaseQRankSum=3.941;DP=2063;FS=0.962;HRun=5;HaplotypeScore=24.0313;InbreedingCoeff=0.0790;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_T.;MQ=55.05;MQ0=49;MQ0Fraction=0.0238;MQRankSum=-1.418;QD=3.47;ReadPosRankSum=-0.605;SB=-93.04;VQSLOD=5.3874;set=VQSR 20 14260090 rs73619828 A AT 27935 PASS AA=596;AB=0.59484;ABA=487;ABP=96.922;ABR=715;AC=204;AF=0.17000;AN=1200;BL=21718;BR=28458;BVAR;BaseQRankSum=0.756;DB;DP=23629;DP4=1385,1492,287,328;Dels=0.00;EL=299;EPP=3.0249;ER=297;FQ=999;FR;FS=6.187;HETAR=218;HOMA=38;HOMR=788;HP=9;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.0797;IndelType=INS.NumRepetitions_9.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13433;LRBP=1969;MQ=100.81;MQ0=0;MQ0Fraction=0.0000;MQM=57.084;MQRankSum=2.224;NF;NR;NS=1044;PP;PV4=0.53,1,1.2e-11,1;RA=4143;RL=238;RPP=55.475;RR=358;RUN=1;ReadPosRankSum=0.198;SAB=0.46812;SAF=279;SAP=8.2714;SAR=317;SC=CCTTAAGTTGATTTTTTTTTC;SRB=0.50374;SRF=2087;SRP=3.514;SRR=2056;TC;TR=9;TU=T;VQSLOD=9.0018;set=Intersection;sumGLbyD=10.82 20 14260558 . AC A 238 PASS AC=1;AF=0.0014;AF1=0.003368;BaseQRankSum=2.868;CI95=0.003106,0.006211;DP=9724;DP4=2075,2329,1,7;Dels=0.00;FQ=106;FR;FS=10.678;HP=1;HPLen=2;HR=2;HRun=1;HU=A;INDEL;InbreedingCoeff=-0.0406;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=114.37;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.862;NF;NR;PP;PV4=0.074,0.0096,0.017,1;ReadPosRankSum=-0.042;SC=ATCAGGAATAACTGTGTGACC;TC;TR=2;TU=A;VQSLOD=8.1618;set=Intersection;sumGLbyD=18.65 20 14425481 . GTA G,GTATA 148.85 PASS AC=43,23;AF=0.03473,0.01858;AN=1238;BaseQRankSum=6.289;DP=25167;DP4=1800,2021,38,49;FR;FS=9.416;HP=2;HPLen=1;HR=1;HU=T;HaplotypeScore=17.7453;INDEL;InbreedingCoeff=0.0995;IndelType=MULTIALLELIC_INDEL;MQ0=21;MQ0Fraction=0.0058;MQRankSum=-0.200;NF;NR;PP;PV4=0.59,1,0.04,0.023;QD=0.35;ReadPosRankSum=-1.689;SB=-367.50;SC=CTGTGTGTGTGTATATATATA;TC;TR=13;TU=AT;VQSLOD=3.5796;set=filterInVQSR-2of5 20 14943522 rs11478299 GA AA,G 1761.24 PASS AA=117;AB=0.68142;ABA=108;ABP=99.919;ABR=231;AC=0;AF=0.0000;AF1=0.04204;AN=712;BL=4931;BR=5802;BVAR;BaseQRankSum=9.118;CI95=0.02876,0.05752;DB;DEL;DP=13717;DP4=1908,1684,59,58;Dels=0.05;EL=60;EPP=3.1773;ER=57;FQ=81.9;FR;HETAR=56;HOMA=1;HOMR=1011;HP=8;HPLen=8;HR=8;HU=A;INDEL;InbreedingCoeff=0.1264;IndelType=MIXED;LEN=1;LRB=0.081152;LRBP=156.5;MQ=106.93;MQ0=0;MQ0Fraction=0.0000;MQM=96.855;MQRankSum=1.619;NF;NR;NS=1068;PP;PV4=0.57,1,0.0003,1;QD=7.40;RA=5080;RL=56;RPP=3.4743;RR=61;RUN=1;ReadPosRankSum=0.814;SAB=0.52137;SAF=61;SAP=3.4743;SAR=56;SB=-1122.51;SC=GTTGTTTGGGGAAAAAAAACT;SRB=0.51083;SRF=2595;SRP=8.1825;SRR=2485;TC;TR=8;TU=A;set=filterInVQSR-2of5;sumGLbyD=9.81 20 14974486 . A AG 4101.40 PASS AA=57;AB=0.57143;ABA=51;ABP=8.2839;ABR=68;AC=22;AF=0.01846;AN=1192;BL=2286;BR=2834;BVAR;BaseQRankSum=8.711;DP=20538;DP4=2172,2100,19,13;Dels=0.00;EL=32;EPP=4.877;ER=25;FS=0.517;HETAR=20;HOMA=4;HOMR=1027;HRun=1;INDEL;INS;InbreedingCoeff=0.0677;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.10703;LRBP=130.37;MQ=126.07;MQ0=0;MQ0Fraction=0.0000;MQM=56.088;MQRankSum=-10.756;NS=1051;PV4=0.38,3.5e-51,7.9e-34,1;RA=5203;RL=26;RPP=3.9627;RR=31;RUN=1;ReadPosRankSum=1.283;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.51816;SRF=2696;SRP=17.918;SRR=2507;VQSLOD=8.0072;set=Intersection;sumGLbyD=25.60 20 15111137 . GA G 13533 PASS AA=98;AB=0.84864;ABA=89;ABP=623.8;ABR=499;AC=47;AF=0.03796;AN=1238;BL=5324;BR=856;BVAR;BaseQRankSum=-11.577;DEL;DP=13384;Dels=0.01;EL=53;EPP=4.4284;ER=45;FS=6.099;HETAR=219;HOMA=845;HOMR=18;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.72298;LRBP=7017.4;MQ0Fraction=0.0003;MQM=90.449;MQRankSum=1.408;NS=1083;RA=590;RL=87;RPP=130.99;RR=11;RUN=1;ReadPosRankSum=-18.074;SAB=0.55102;SAF=54;SAP=5.2261;SAR=44;SRB=0.52373;SRF=309;SRP=5.8958;SRR=281;VQSLOD=4.1054;set=filterInVQSR-2of5;sumGLbyD=3.06 20 15283028 . A AC,ACACACACACACAC 140844.83 PASS AA=180;AB=0.61442;ABA=123;ABP=39.285;ABR=196;AC=13,817;AF=0.01111,0.69829;AN=1170;BL=4453;BR=11407;BVAR;BaseQRankSum=24.686;DP=6365;Dels=0.00;EL=124;EPP=58.793;ER=56;FR;FS=10.912;HETAR=87;HOMA=48;HOMR=683;HP=1;HR=1;HRun=1;HU=T;INS;InbreedingCoeff=0.2074;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.43846;LRBP=6624;MQ0Fraction=0.0558;MQM=38.211;MQRankSum=-21.111;NF;NR;NS=818;PP;RA=1732;RL=0;RPP=393.88;RR=180;RUN=1;ReadPosRankSum=-7.620;SAB=0.31111;SAF=56;SAP=58.793;SAR=124;SC=ACACACACACATACACACATA;SRB=0.54042;SRF=936;SRP=27.584;SRR=796;TC;TR=21;TU=AC;VQSLOD=4.7569;set=Intersection;sumGLbyD=18.36 20 15361056 . ATAACT A 4892.81 PASS AA=59;AB=0.63576;ABA=55;ABP=27.184;ABR=96;AC=34;AF=0.0487;AN=698;BL=3164;BR=1999;BVAR;BaseQRankSum=3.391;DEL;DP=7080;Dels=0.03;EL=27;EPP=3.9304;ER=32;FR;FS=4.816;HETAR=35;HOMA=6;HOMR=966;HP=2;HPLen=3;HR=3;HRun=0;HU=A;InbreedingCoeff=0.0785;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.22564;LRBP=573.84;MQ0=0;MQ0Fraction=0.0000;MQM=70.034;MQRankSum=-8.732;NF;NR;NS=1008;PP;RA=3915;RL=42;RPP=26.013;RR=17;RUN=1;ReadPosRankSum=-0.735;SAB=0.44068;SAF=26;SAP=4.8137;SAR=33;SC=AGATTAGGAAATAACTTAGGG;SRB=0.42682;SRF=1671;SRP=185.12;SRR=2244;TC;TR=3;TU=A;VQSLOD=7.0900;set=Intersection;sumGLbyD=43.38 20 15579507 . AATTAGTC A,TATTAGTC 1936.38 PASS AA=16;AB=0.58974;ABA=16;ABP=5.7386;ABR=23;AC=64;AF=0.05229;AN=1224;BL=699;BR=775;BVAR;BaseQRankSum=-21.390;DEL;DP=21920;DP4=2099,2403,6,6;Dels=0.00;EL=8;EPP=3.0103;ER=8;FR;FS=2.920;HETAR=5;HOMA=0;HOMR=1063;HP=3;HPLen=4;HR=4;HU=A;INDEL;InbreedingCoeff=-0.0143;IndelType=MIXED;LEN=7;LRB=0.05156;LRBP=11.519;MQ=129.49;MQ0=0;MQ0Fraction=0.0000;MQM=51.938;MQRankSum=3.331;NF;NR;NS=1068;PP;PV4=1,0.019,1.3e-07,1;RA=5334;RL=5;RPP=7.8961;RR=11;RUN=1;ReadPosRankSum=-16.901;SAB=0.4375;SAF=7;SAP=3.5532;SAR=9;SC=CATACTACAAAATTAGTCATT;SRB=0.41695;SRF=2224;SRP=322.58;SRR=3110;TC;TR=4;TU=A;VQSLOD=3.2237;set=filterInVQSR-2of5;sumGLbyD=43.57 20 15752535 . CT C,GT 3775.20 PASS AA=92;AB=0.78636;ABA=47;ABP=159.71;ABR=173;AC=0;AF=0.0000;AN=608;BL=4955;BR=2380;BVAR;BaseQRankSum=2.910;DEL;DP=3429;Dels=0.04;EL=13;EPP=105.82;ER=79;FR;HETAR=92;HOMA=95;HOMR=544;HP=2;HPLen=2;HR=2;HU=T;InbreedingCoeff=0.0483;IndelType=MIXED;LEN=1;LRB=0.35106;LRBP=1966;MQ0Fraction=0.0232;MQM=35.293;MQRankSum=-2.199;NF;NR;NS=732;PP;QD=4.91;RA=1272;RL=81;RPP=118.66;RR=11;RUN=1;ReadPosRankSum=-1.077;SAB=0.021739;SAF=2;SAP=185.79;SAR=90;SB=-59.51;SC=CAAGACCATCCTTGGCTAACA;SRB=0.14623;SRF=186;SRP=1385.8;SRR=1086;TC;TR=2;TU=T;set=filterInVQSR-2of5;sumGLbyD=9.70 20 15883060 rs73619850 A AT 1325.60 PASS AA=38;AB=0.59302;ABA=35;ABP=9.4742;ABR=51;AC=14;AF=0.0156;AN=896;BL=1078;BR=1638;BVAR;BaseQRankSum=-4.526;DB;DP=19854;DP4=1632,1800,15,20;Dels=0.00;EL=18;EPP=3.2389;ER=20;FR;FS=0.000;HETAR=14;HOMA=1;HOMR=1014;HP=1;HPLen=1;HR=1;HRun=1;HU=T;INDEL;INS;InbreedingCoeff=-0.0131;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.20619;LRBP=253.74;MQ=118.40;MQ0=0;MQ0Fraction=0.0000;MQM=56.526;MQRankSum=0.892;NF;NR;NS=1029;PP;PV4=0.61,1,0.25,0.14;RA=4439;RL=14;RPP=8.7247;RR=24;RUN=1;ReadPosRankSum=-2.061;SAB=0.42105;SAF=16;SAP=5.0675;SAR=22;SC=GGATTGGCAGATAAAAAATGG;SRB=0.46429;SRF=2061;SRP=52.168;SRR=2378;TC;TR=1;TU=T;VQSLOD=9.7576;set=Intersection;sumGLbyD=15.69 20 16122099 . GA G 12914 PASS AA=85;AB=0.85915;ABA=80;ABP=639.4;ABR=488;AC=19;AF=0.01542;AN=1232;BL=805;BR=5457;BVAR;BaseQRankSum=-6.084;DEL;DP=13592;Dels=0.00;EL=45;EPP=3.649;ER=40;FS=0.935;HETAR=218;HOMA=841;HOMR=14;HRun=2;InbreedingCoeff=0.0250;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.74289;LRBP=7507.5;MQ0=0;MQ0Fraction=0.0000;MQM=103.01;MQRankSum=2.843;NS=1075;RA=541;RL=2;RPP=170.62;RR=83;RUN=1;ReadPosRankSum=-16.222;SAB=0.49412;SAF=42;SAP=3.0358;SAR=43;SRB=0.44917;SRF=243;SRP=15.152;SRR=298;VQSLOD=3.9745;set=filterInVQSR-2of5;sumGLbyD=2.97 20 16828509 . G GT 843.62 PASS AA=30;AB=0.70103;ABA=29;ABP=37.06;ABR=68;AC=10;AF=0.0140;AN=714;BL=1368;BR=1786;BVAR;BaseQRankSum=-4.061;DP=8682;Dels=0.01;EL=14;EPP=3.2998;ER=16;FR;FS=2.681;HETAR=22;HOMA=1;HOMR=1020;HP=8;HPLen=8;HR=8;HRun=8;HU=T;INS;InbreedingCoeff=0.1389;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13253;LRBP=123.3;MQ0=0;MQ0Fraction=0.0000;MQM=62.8;MQRankSum=-1.491;NF;NR;NS=1043;PP;RA=4416;RL=11;RPP=7.6428;RR=19;RUN=1;ReadPosRankSum=-1.718;SAB=0.76667;SAF=23;SAP=21.54;SAR=7;SC=CCTTCAAAAGGTTTTTTTTGG;SRB=0.5745;SRF=2537;SRP=215.91;SRR=1879;TC;TR=8;TU=T;VQSLOD=7.6258;set=Intersection;sumGLbyD=10.77 20 17470034 . GC G 46975 PASS AA=57;AB=0.96043;ABA=52;ABP=2422.5;ABR=1262;AC=34;AF=0.02773;AN=1226;BL=418;BR=3446;BVAR;BaseQRankSum=-6.250;DEL;DP=12035;Dels=0.00;EL=22;EPP=9.4485;ER=35;FS=1.350;HETAR=416;HOMA=409;HOMR=244;HRun=1;InbreedingCoeff=0.0083;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78364;LRBP=5155.6;MQ0=0;MQ0Fraction=0.0000;MQM=99.509;MQRankSum=2.192;NS=1076;RA=2396;RL=5;RPP=87.164;RR=52;RUN=1;ReadPosRankSum=-15.199;SAB=0.5614;SAF=32;SAP=4.877;SAR=25;SRB=0.52963;SRF=1269;SRP=21.285;SRR=1127;VQSLOD=3.8440;set=filterInVQSR-2of5;sumGLbyD=3.06 20 17471374 . AGCGGC A 850.03 PASS AC=6;AF=0.0085;AF1=0.01301;AN=704;BaseQRankSum=6.259;CI95=0.00885,0.01991;DP=8180;DP4=2215,1878,4,5;Dels=0.01;FQ=131;FS=0.000;HRun=0;INDEL;InbreedingCoeff=0.0009;IndelType=DEL.NumRepetitions_1.EventLength_5.;MQ=104.41;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-5.521;PV4=0.74,0.37,0.0005,1;ReadPosRankSum=2.468;VQSLOD=6.8773;set=Intersection;sumGLbyD=30.85 20 18433202 rs35582929 G GA 2506.90 PASS AA=55;AB=0.5812;ABA=49;ABP=9.7103;ABR=68;AC=20;AF=0.0218;AN=918;BL=2263;BR=2175;BVAR;BaseQRankSum=-6.639;DB;DP=19467;DP4=1845,2365,27,26;Dels=0.00;EL=21;EPP=9.6826;ER=34;FQ=999;FR;FS=5.633;HETAR=16;HOMA=3;HOMR=1045;HP=2;HPLen=3;HR=3;HRun=1;HU=G;INDEL;INS;InbreedingCoeff=0.0700;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.019829;LRBP=6.7994;MQ=114.03;MQ0=0;MQ0Fraction=0.0000;MQM=83.345;MQRankSum=1.610;NF;NR;NS=1064;PP;PV4=0.33,1,1,1;RA=5380;RL=28;RPP=3.0498;RR=27;RUN=1;ReadPosRankSum=0.873;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TATTTCATGGGAGCATTAAAA;SRB=0.42862;SRF=2306;SRP=241.07;SRR=3074;TC;TR=3;TU=G;VQSLOD=10.0372;dbSNP=126;set=Intersection;sumGLbyD=13.10 20 18551314 rs10659122 CA C,CAA,CAAA,CAAAA,CAAAAA 18810.74 PASS ABR=243;AC=19,169,216,164,188;AF=0.01816,0.16157,0.20650,0.15679,0.17973;BVAR;BaseQRankSum=-5.742;DB;DP=17637;DP4=136,77,560,237;FR;FS=2.693;HOMA=177;HOMR=299;HP=17;HR=17;HU=A;HaplotypeScore=15.5048;INDEL;INS;InbreedingCoeff=0.8901;IndelType=MULTIALLELIC_INDEL;MQ0=11;MQ0Fraction=0.0069;MQRankSum=1.845;NF;NR;NS=658;PP;PV4=0.08,1,1,1;QD=12.66;RA=673;RUN=1;ReadPosRankSum=0.283;SB=-3514.45;SC=GATTCCATCTCAAAAAAAAAA;SRB=0.63596;SRF=428;SRP=111.06;SRR=245;TC;TR=17;TU=A;VQSLOD=10.6964;dbSNP=130;set=Intersection 20 18785519 . G GTC 415.55 PASS AC=28;AF=0.0400;AN=700;BaseQRankSum=10.889;DP=1929;FS=8.778;HRun=0;HaplotypeScore=27.6448;InbreedingCoeff=0.0510;IndelType=INS.NOVEL_2.;MQ=61.99;MQ0=36;MQ0Fraction=0.0187;MQRankSum=4.508;QD=3.08;ReadPosRankSum=8.080;SB=-437.03;VQSLOD=4.9313;set=VQSR 20 20301041 rs35451634 ATATG A 200.42 PASS AC=21;AF=0.0449;AN=468;BaseQRankSum=5.251;DB;DP=579;FS=24.013;HRun=0;HaplotypeScore=27.8977;InbreedingCoeff=0.0113;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=78.47;MQ0=26;MQ0Fraction=0.0449;MQRankSum=-5.284;QD=3.06;ReadPosRankSum=1.793;SB=-55.76;VQSLOD=5.0981;set=VQSR 20 20378174 . TC T 245.55 PASS AC=23;AF=0.01879;AN=1224;BaseQRankSum=0.990;DP=3225;FS=10.413;HRun=1;HaplotypeScore=22.6109;InbreedingCoeff=0.0244;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=93.70;MQ0=3;MQ0Fraction=0.0009;MQRankSum=-3.349;QD=1.86;ReadPosRankSum=-7.227;SB=-188.62;VQSLOD=4.2553;set=VQSR 20 20809160 rs10571503 TAA AAA,T 3496 PASS AC=0;AF=0.0000;AN=612;BaseQRankSum=1.968;DB;DP=1092;FR;HP=4;HPLen=3;HR=3;HRun=0;HU=A;HaplotypeScore=26.1253;InbreedingCoeff=0.0603;IndelType=MIXED;MQ=68.98;MQ0=1;MQ0Fraction=0.0009;MQRankSum=1.520;NF;NR;PP;ReadPosRankSum=-4.042;SC=TATATATATATAAATTTAAAT;TC;TR=13;TU=AT;set=filterInVQSR-2of5 20 22508765 . CT C 53877.84 PASS AA=187;AB=0.78077;ABA=171;ABP=537.09;ABR=609;AC=1017;AF=0.91787;AN=1108;BL=12690;BR=1718;BVAR;BaseQRankSum=13.773;DEL;DP=7430;Dels=0.02;EL=73;EPP=22.53;ER=114;FR;FS=16.352;HETAR=152;HOMA=9;HOMR=786;HP=8;HR=4;HRun=4;HU=T;InbreedingCoeff=0.3885;IndelType=DEL.NumRepetitions_4.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.76152;LRBP=18147;MQ0=0;MQ0Fraction=0.0000;MQM=46.086;MQRankSum=0.971;NF;NR;NS=947;PP;RA=2868;RL=177;RPP=326.86;RR=10;RUN=1;ReadPosRankSum=9.951;SAB=0.34759;SAF=65;SAP=40.738;SAR=122;SC=AAAAAATTTTCTTTTGAACTG;SRB=0.46269;SRF=1327;SRP=37.684;SRR=1541;TC;TR=4;TU=T;VQSLOD=5.1182;set=Intersection;sumGLbyD=25.15 20 22555082 rs11477526 AT A 11503 PASS AA=530;AB=0.50816;ABA=422;ABP=3.5063;ABR=436;AF=0.1614;AN=700;BL=21453;BR=23313;BVAR;BaseQRankSum=17.562;DB;DEL;DP=25587;DP4=1869,1600,283,201;Dels=0.14;EL=259;EPP=3.6003;ER=271;FQ=999;FR;FS=14.595;HETAR=159;HOMA=41;HOMR=846;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;InbreedingCoeff=0.0995;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.041549;LRBP=170.83;MQ=95.89;MQ0=0;MQ0Fraction=0.0000;MQM=72.162;MQRankSum=2.564;NF;NR;NS=1046;PP;PV4=0.058,6.6e-129,0.04,1;RA=4303;RL=264;RPP=3.0267;RR=266;RUN=1;ReadPosRankSum=0.176;SAB=0.58679;SAF=311;SAP=37.688;SAR=219;SC=GGGAAAGCTGATTTACTGATT;SRB=0.54892;SRF=2362;SRP=92.453;SRR=1941;TC;TR=3;TU=T;VQSLOD=8.7746;dbSNP=120;set=Intersection;sumGLbyD=15.27 20 22590907 . A AC 4204.88 PASS AA=67;AB=0.592;ABA=51;ABP=12.2;ABR=74;AF=0.0554;AF1=0.0468;AN=560;BL=2277;BR=2389;BVAR;BaseQRankSum=10.968;CI95=0.03759,0.05639;DP=14380;DP4=2514,2018,33,33;Dels=0.00;EL=22;EPP=20.155;ER=45;FQ=999;FR;FS=3.846;HETAR=25;HOMA=4;HOMR=1049;HP=4;HPLen=5;HR=5;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.0719;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.024003;LRBP=8.8481;MQ=110.68;MQ0=0;MQ0Fraction=0.0000;MQM=96.149;MQRankSum=2.668;NF;NR;NS=1078;PP;PV4=0.39,1,0.46,0.36;RA=5468;RL=33;RPP=3.0427;RR=34;RUN=1;ReadPosRankSum=-1.097;SAB=0.50746;SAF=34;SAP=3.0427;SAR=33;SC=TCATATCAAAAACATTACGTT;SRB=0.54389;SRF=2974;SRP=94.508;SRR=2494;TC;TR=5;TU=A;VQSLOD=10.0712;set=Intersection;sumGLbyD=27.69 20 22806326 rs11468890 ATTCCATCAC A 105320.99 PASS AC=567;AF=0.48795;AN=1162;BVAR;BaseQRankSum=32.858;DB;DEL;DP=26278;DP4=727,796,554,587;Dels=0.30;FQ=999;FR;FS=1.923;HP=3;HPLen=3;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.2548;IndelType=DEL.NumRepetitions_2.EventLength_9.;LEN=9;MQ=89.42;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-23.545;NF;NR;PP;PV4=0.7,1,1.3e-167,1;RUN=1;ReadPosRankSum=4.384;SC=GGCTGCTCCCATTCCATCACT;TC;TR=2;TU=T;VQSLOD=8.2594;set=Intersection;sumGLbyD=69.81 20 22999898 rs55966257 CAGGA C 8019.97 PASS AA=23;AB=0.57778;ABA=19;ABP=5.3748;ABR=26;AC=214;AF=0.18838;AN=1136;BL=1143;BR=1040;BVAR;BaseQRankSum=29.294;DB;DEL;DP=8216;Dels=0.02;EL=11;EPP=3.1047;ER=12;FS=14.938;HETAR=14;HOMA=2;HOMR=948;HRun=0;InbreedingCoeff=0.0797;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.047183;LRBP=13.563;MQ0=0;MQ0Fraction=0.0000;MQM=34.783;MQRankSum=-20.301;NS=964;RA=3637;RL=13;RPP=3.86;RR=10;RUN=1;ReadPosRankSum=-24.607;SAB=0.47826;SAF=11;SAP=3.1047;SAR=12;SRB=0.49024;SRF=1783;SRP=6.02;SRR=1854;VQSLOD=7.9163;set=Intersection;sumGLbyD=9.43 20 23385964 rs57723772 GAA G 8170.95 PASS AC=257;AF=0.20928;AN=1228;BaseQRankSum=32.220;DB;DP=3291;FS=1.688;HRun=3;HaplotypeScore=22.6739;InbreedingCoeff=0.0171;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=58.44;MQ0=32;MQ0Fraction=0.0097;MQRankSum=-4.893;QD=6.55;ReadPosRankSum=-35.524;SB=-3631.67;VQSLOD=5.6549;set=VQSR 20 23534530 . TA T 3542.10 PASS AA=45;AB=0.75658;ABA=37;ABP=89.926;ABR=115;AC=35;AF=0.02991;AN=1170;BL=3090;BR=270;BVAR;BaseQRankSum=-6.892;DEL;DP=8108;Dels=0.00;EL=19;EPP=5.3748;ER=26;FS=1.026;HETAR=76;HOMA=896;HOMR=18;HRun=1;InbreedingCoeff=0.0551;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.83929;LRBP=5142.4;MQ0Fraction=0.0017;MQM=41.578;MQRankSum=0.818;NS=991;RA=203;RL=43;RPP=84.127;RR=2;RUN=1;ReadPosRankSum=-12.923;SAB=0.37778;SAF=17;SAP=8.8491;SAR=28;SRB=0.5665;SRF=115;SRP=10.808;SRR=88;VQSLOD=4.2093;set=Intersection;sumGLbyD=3.49 20 23976810 rs5841018 A ATATTAAT 1782.38 PASS AF=0.1387;AF1=0.01507;BaseQRankSum=3.717;CI95=0.00188,0.03947;DB;DP=1712;DP4=357,376,7,2;Dels=0.00;FQ=31.1;FS=14.489;HPLen=2;HRun=0;INDEL;InbreedingCoeff=0.1123;IndelType=INS.NumRepetitions_1.EventLength_7.;MQ=49.53;MQ0=2;MQ0Fraction=0.0055;MQRankSum=-4.928;PV4=0.1,1,0.00085,0.016;ReadPosRankSum=-4.456;VQSLOD=5.3140;dbSNP=116;set=Intersection;sumGLbyD=19.98 20 24222100 . CTTTTA C 4219.36 PASS AA=57;AB=0.59434;ABA=43;ABP=11.205;ABR=63;AF=0.01803;AF1=0.01547;AN=1220;BL=2073;BR=2345;BVAR;BaseQRankSum=7.990;CI95=0.0114,0.02137;DEL;DP=17536;DP4=2140,2346,7,12;Dels=0.01;EL=32;EPP=4.877;ER=25;FQ=104;FS=0.614;HETAR=21;HOMA=4;HOMR=1042;HRun=0;INDEL;InbreedingCoeff=0.1941;IndelType=DEL.NumRepetitions_2.EventLength_5.;LEN=5;LRB=0.061566;LRBP=39.374;MQ=73.32;MQ0Fraction=0.0021;MQM=39.614;MQRankSum=-5.728;NS=1067;PV4=0.37,1.1e-39,3.5e-09,1;RA=5527;RL=28;RPP=3.0484;RR=29;RUN=1;ReadPosRankSum=0.214;SAB=0.54386;SAF=31;SAP=3.9627;SAR=26;SRB=0.49267;SRF=2723;SRP=5.588;SRR=2804;VQSLOD=7.5428;set=Intersection;sumGLbyD=38.08 20 24395018 . AT A 49310 PASS AA=146;AB=0.91198;ABA=130;ABP=2180.5;ABR=1347;AC=50;AF=0.04045;AN=1236;BL=587;BR=9625;BVAR;BaseQRankSum=-4.610;DEL;DP=12793;Dels=0.01;EL=54;EPP=24.487;ER=92;FS=22.108;HETAR=485;HOMA=384;HOMR=210;HRun=2;InbreedingCoeff=0.0374;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.88504;LRBP=17373;MQ0=0;MQ0Fraction=0.0000;MQM=102.26;MQRankSum=2.256;NS=1080;RA=2377;RL=1;RPP=311.42;RR=145;RUN=1;ReadPosRankSum=-16.347;SAB=0.63699;SAF=93;SAP=26.807;SAR=53;SRB=0.52167;SRF=1240;SRP=12.702;SRR=1137;VQSLOD=3.2421;set=filterInVQSR-2of5;sumGLbyD=3.80 20 24411517 . C CA 246.18 PASS AF=0.01546;AF1=0.01095;BaseQRankSum=7.832;CI95=0.005698,0.01709;DP=7981;DP4=983,2037,7,7;Dels=0.00;FQ=27.9;FS=18.815;HPLen=3;HRun=3;INDEL;InbreedingCoeff=0.0175;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=60.28;MQ0Fraction=0.0137;MQRankSum=-7.243;PV4=0.25,1,2.7e-05,1;ReadPosRankSum=-0.143;VQSLOD=4.3701;set=Intersection;sumGLbyD=6.56 20 24421169 . AG A 27480 PASS AA=182;AB=0.8303;ABA=149;ABP=835;ABR=729;AC=89;AF=0.07224;AN=1232;BL=11276;BR=2214;BVAR;BaseQRankSum=-5.447;DEL;DP=11717;Dels=0.01;EL=103;EPP=9.8827;ER=79;FR;FS=15.492;HETAR=343;HOMA=607;HOMR=114;HP=4;HR=1;HRun=1;HU=G;InbreedingCoeff=0.0353;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.67176;LRBP=13222;MQ0=0;MQ0Fraction=0.0000;MQM=88.324;MQRankSum=2.221;NF;NR;NS=1071;PP;RA=1226;RL=169;RPP=293.37;RR=13;RUN=1;ReadPosRankSum=-19.711;SAB=0.54945;SAF=100;SAP=6.876;SAR=82;SC=CCTTAGCCCCAGAAAACATCT;SRB=0.44535;SRF=546;SRP=34.814;SRR=680;TC;TR=1;TU=G;VQSLOD=4.2669;set=Intersection;sumGLbyD=3.91 20 24765537 rs71841337 ATTT A,AT,ATT,ATTTT,ATTTTT 37852 PASS AC=13,120,527,51,92;AF=0.01102,0.10169,0.44661,0.04322,0.07797;AN=1180;BVAR;BaseQRankSum=8.172;DB;DEL;DP=39116;DP4=200,331,851,1169;FR;FS=2.394;HP=15;HR=15;HU=T;HaplotypeScore=20.8091;INDEL;INS;InbreedingCoeff=0.4815;IndelType=MULTIALLELIC_INDEL;MQ0=1;MQ0Fraction=0.0003;MQRankSum=4.344;NF;NR;PP;PV4=0.067,1,1,0.1;QD=7.90;RUN=1;ReadPosRankSum=1.798;SB=-8371.96;SC=CTCTGCAACAATTTTTTTTTT;TC;TR=15;TU=T;VQSLOD=9.9679;dbSNP=120;set=Intersection 20 25500689 . A AATTT 84980.72 PASS AC=1005;AF=0.89096;AN=1128;BaseQRankSum=17.400;DP=2324;FS=6.721;HRun=0;HaplotypeScore=25.3376;InbreedingCoeff=0.2148;IndelType=INS.NumRepetitions_1.EventLength_4.;MQ=75.19;MQ0=1;MQ0Fraction=0.0004;MQRankSum=-8.221;QD=38.28;ReadPosRankSum=4.504;SB=-34833.07;VQSLOD=4.6038;set=VQSR 20 25550373 . GA G 11251.31 PASS AA=246;AB=0.42963;ABA=154;ABP=14.624;ABR=116;AC=566;AF=0.6521;AN=868;BL=5230;BR=11845;BVAR;BaseQRankSum=7.418;DEL;DP=8885;Dels=0.02;EL=99;EPP=23.348;ER=147;FR;FS=50.357;HETAR=150;HOMA=849;HOMR=14;HP=1;HR=2;HRun=1;HU=G;InbreedingCoeff=0.1365;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.38741;LRBP=5567.9;MQ0=0;MQ0Fraction=0.0000;MQM=97.561;MQRankSum=0.050;NF;NR;NS=1013;PP;RA=269;RL=75;RPP=84.361;RR=171;RUN=1;ReadPosRankSum=-7.128;SAB=0.52846;SAF=130;SAP=4.7404;SAR=116;SC=CACGGAGGCGGAGGAAGCAGC;SRB=0.42379;SRF=114;SRP=16.58;SRR=155;TC;TR=6;TU=AGG;VQSLOD=4.0103;set=filterInVQSR-2of5;sumGLbyD=4.58 20 25903865 . TTC T 7459.23 PASS AC=277;AF=0.23316;AN=1188;BaseQRankSum=31.479;DP=2969;FS=137.723;HRun=0;HaplotypeScore=37.3300;InbreedingCoeff=-0.1755;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TC.;MQ=53.49;MQ0=50;MQ0Fraction=0.0168;MQRankSum=-25.506;QD=4.70;ReadPosRankSum=-5.913;SB=-1747.98;VQSLOD=5.4731;set=VQSR 20 25934237 . C CCACTT 771.36 PASS AC=37;AF=0.0426;AN=868;BaseQRankSum=16.331;DP=2253;FS=4.545;HRun=0;HaplotypeScore=29.9764;InbreedingCoeff=-0.0685;IndelType=INS.NOVEL_5.;MQ=48.12;MQ0=87;MQ0Fraction=0.0386;MQRankSum=-12.497;QD=3.37;ReadPosRankSum=-8.428;SB=-297.70;VQSLOD=4.2324;set=VQSR 20 26054751 rs112967123 TATC T 33244 PASS AA=1863;AB=0.79012;ABA=1788;ABP=6231;ABR=6731;AC=227;AF=0.18218;AN=1246;BL=74924;BR=72452;BVAR;BaseQRankSum=32.258;DB;DEL;DP=36404;DS;Dels=0.05;EL=931;EPP=3.0115;ER=932;FR;FS=265.752;HETAR=527;HOMA=2;HOMR=565;HP=1;HR=2;HRun=0;HU=T;InbreedingCoeff=-0.2137;IndelType=DEL.NumRepetitions_2.EventLength_3.;LEN=3;LRB=0.016773;LRBP=93.048;MQ0Fraction=0.0127;MQM=28.797;MQRankSum=-5.329;NF;NR;NS=1094;PP;RA=14604;RL=1014;RPP=34.743;RR=849;RUN=1;ReadPosRankSum=8.394;SAB=0.65486;SAF=1220;SAP=391.07;SAR=643;SC=TCACCATCATTATCATCATTA;SRB=0.56717;SRF=8283;SRP=575.39;SRR=6321;TC;TR=8;TU=ATC;VQSLOD=1.0486;set=filterInVQSR-2of5;sumGLbyD=6.54 20 26120452 . CAG C 7863.19 PASS AA=163;AB=0.70489;ABA=157;ABP=196.99;ABR=375;AC=171;AF=0.1908;AN=896;BL=3455;BR=4877;BVAR;BaseQRankSum=25.536;DEL;DP=7014;Dels=0.10;EL=58;EPP=32.438;ER=105;FS=231.723;HETAR=90;HOMA=5;HOMR=387;HRun=0;InbreedingCoeff=-0.1966;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.17067;LRBP=530;MQ0Fraction=0.0470;MQM=21.951;MQRankSum=-23.449;NS=482;RA=1117;RL=62;RPP=23.273;RR=101;RUN=1;ReadPosRankSum=1.904;SAB=0.37423;SAF=61;SAP=25.404;SAR=102;SRB=0.41719;SRF=466;SRP=69.544;SRR=651;VQSLOD=-0.9395;set=filterInVQSR-2of5;sumGLbyD=5.06 20 26185812 . AG A 322.58 PASS AF=0.0342;BaseQRankSum=3.668;DP=3014;Dels=0.01;FR;FS=10.238;HP=8;HPLen=6;HR=6;HRun=6;HU=G;InbreedingCoeff=0.1504;IndelType=DEL.NumRepetitions_6.EventLength_1.RepeatExpansion_G.;MQ0Fraction=0.0473;MQRankSum=-5.464;NF;NR;PP;ReadPosRankSum=0.536;SC=GGGTGGGTGGAGGGGGGAGGG;TC;TR=6;TU=G;VQSLOD=5.0767;set=Intersection;sumGLbyD=8.46 20 30963468 . AGTTT A 2041.12 PASS AA=38;AB=0.75694;ABA=35;ABP=85.587;ABR=109;AC=34;AF=0.0377;AN=902;BL=1974;BR=668;BVAR;BaseQRankSum=3.060;DEL;DP=22806;DP4=1997,1747,28,36;Dels=0.02;EL=17;EPP=3.9246;ER=21;FR;FS=16.034;HETAR=29;HOMA=1;HOMR=1009;HP=1;HPLen=1;HR=1;HRun=0;HU=G;INDEL;InbreedingCoeff=0.0752;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.49432;LRBP=1404.9;MQ=87.17;MQ0Fraction=0.0013;MQM=98.079;MQRankSum=6.021;NF;NR;NS=1039;PP;PV4=0.13,1.5e-07,1,0.051;RA=4052;RL=36;RPP=69.069;RR=2;RUN=1;ReadPosRankSum=-1.847;SAB=0.5;SAF=19;SAP=3.0103;SAR=19;SC=AGAAGTAAGTAGTTTGTTTTT;SRB=0.53776;SRF=2179;SRP=53.19;SRR=1873;TC;TR=9;TU=AAGT;VQSLOD=7.3578;set=Intersection;sumGLbyD=14.03 20 31963212 . AAAAAAAAAAAAG A 727.15 PASS AC=5;AF=0.0080;AN=622;BaseQRankSum=4.037;DP=1480;FS=0.000;HRun=0;HaplotypeScore=43.3793;InbreedingCoeff=0.0350;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ=51.77;MQ0=59;MQ0Fraction=0.0399;MQRankSum=-1.799;QD=22.72;ReadPosRankSum=3.591;SB=-364.04;VQSLOD=5.3166;set=VQSR 20 31997272 . CT C,CTT,CTTT 1837.10 PASS AA=63;AB=0.77559;ABA=57;ABP=170.57;ABR=197;AC=79,49,30;AF=0.06594,0.04090,0.02504;AN=1198;BL=2372;BR=2640;BVAR;BaseQRankSum=3.277;DP=9050;Dels=0.03;EL=24;EPP=10.766;ER=39;FR;FS=0.303;HETAR=45;HOMA=1;HOMR=981;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2796;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.053472;LRBP=34.128;MQ0Fraction=0.0000;MQM=50.889;MQRankSum=0.610;NF;NR;NS=1027;PP;RA=3776;RL=30;RPP=3.3205;RR=33;RUN=1;ReadPosRankSum=-0.800;SAB=0.39683;SAF=25;SAP=8.8354;SAR=38;SC=ACCCAACTTCCTTTTTTTTTT;SRB=0.46213;SRF=1745;SRP=50.049;SRR=2031;TC;TR=10;TU=T;VQSLOD=4.1189;set=filterInVQSR-2of5;sumGLbyD=3.66 20 33446974 rs113250263 TAA T,TA,TAAA 17130.16 PASS AC=65,417,184;AF=0.05941,0.38117,0.16819;AN=1094;BVAR;BaseQRankSum=3.400;DB;DEL;DP=22362;DP4=221,247,418,524;Dels=0.33;FR;FS=15.409;HP=15;HR=14;HRun=14;HU=A;INDEL;INS;InbreedingCoeff=0.5215;IndelType=MULTIALLELIC_INDEL;MQ=61.32;MQ0Fraction=0.0021;MQRankSum=0.481;NF;NR;PP;PV4=0.33,1,1,1;RUN=1;ReadPosRankSum=-0.056;SC=CTCCGTCTCATAAAAAAAAAA;TC;TR=14;TU=A;VQSLOD=8.0974;dbSNP=132;set=Intersection;sumGLbyD=12.78 20 33877149 . C CT 1784.40 PASS AA=58;AB=0.73096;ABA=53;ABP=94.289;ABR=144;AC=65;AF=0.05682;AN=1144;BL=3298;BR=1935;BVAR;BaseQRankSum=-2.066;DP=8074;Dels=0.02;EL=22;EPP=10.348;ER=36;FR;FS=11.452;HETAR=47;HOMA=3;HOMR=754;HP=16;HR=12;HRun=12;HU=T;INS;InbreedingCoeff=0.1178;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.26046;LRBP=773.91;MQ0Fraction=0.0165;MQM=52.259;MQRankSum=0.734;NF;NR;NS=804;PP;RA=2141;RL=43;RPP=32.363;RR=15;RUN=1;ReadPosRankSum=-1.273;SAB=0.46552;SAF=27;SAP=3.6093;SAR=31;SC=ATTTTCTTTTCTTTTTTTTTT;SRB=0.37553;SRF=804;SRP=291.14;SRR=1337;TC;TR=12;TU=T;VQSLOD=3.1540;set=filterInVQSR-2of5;sumGLbyD=2.84 20 34387589 rs112431805 CT C,CTT 4039.10 PASS AA=121;AB=0.75368;ABA=117;ABP=268.53;ABR=358;AC=84,139;AF=0.07047,0.11661;AN=1192;BL=5557;BR=3901;BVAR;BaseQRankSum=2.693;DB;DP=10157;Dels=0.03;EL=47;EPP=16.093;ER=74;FR;FS=7.639;HETAR=89;HOMA=2;HOMR=913;HP=13;HR=11;HRun=11;HU=T;INS;InbreedingCoeff=0.2097;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.17509;LRBP=632.63;MQ0Fraction=0.0000;MQM=49.802;MQRankSum=-0.801;NF;NR;NS=1004;PP;RA=3789;RL=77;RPP=22.554;RR=44;RUN=1;ReadPosRankSum=-2.691;SAB=0.3719;SAF=45;SAP=20.256;SAR=76;SC=AAGAAGTGTTCTTTTTTTTTT;SRB=0.40987;SRF=1553;SRP=270.35;SRR=2236;TC;TR=11;TU=T;VQSLOD=4.0473;set=filterInVQSR-2of5;sumGLbyD=4.64 20 34493409 rs73621682 C CAG 62288.93 PASS AA=1069;AB=0.54863;ABA=826;ABP=40.606;ABR=1004;AC=257;AF=0.3640;AN=706;BL=41524;BR=47039;BVAR;BaseQRankSum=-24.248;DB;DP=30195;DP4=1743,1636,614,487;Dels=0.00;EL=582;EPP=21.343;ER=487;FQ=999;FR;FS=5.080;HETAR=298;HOMA=63;HOMR=712;HP=1;HPLen=1;HR=1;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.1437;IndelType=INS.NumRepetitions_2.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.062272;LRBP=748.76;MQ=77.99;MQ0=3;MQ0Fraction=0.0015;MQM=54.446;MQRankSum=0.160;NF;NR;NS=1073;PP;PV4=0.016,1,0.01,1;RA=4461;RL=526;RPP=3.5973;RR=543;RUN=1;ReadPosRankSum=-1.716;SAB=0.57343;SAF=613;SAP=53.08;SAR=456;SC=AGGAAGAGATCAGAGCTCCCC;SRB=0.52634;SRF=2348;SRP=29.892;SRR=2113;TC;TR=4;TU=AG;VQSLOD=8.7047;dbSNP=130;set=Intersection;sumGLbyD=49.82 20 35957317 . CTGACT C,CGACT 4370.96 PASS ABR=81;AC=22,1;AF=0.0321,0.0015;AF1=0.04523;AN=686;BVAR;BaseQRankSum=7.969;CI95=0.0354,0.05752;DEL;DP=16632;DP4=1942,1815,17,21;Dels=0.03;FQ=999;FR;FS=0.531;HOMA=1;HOMR=998;HP=2;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0587;IndelType=MULTIALLELIC_INDEL;MQ=83.38;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-7.201;NF;NR;NS=1020;PP;PV4=0.42,0.00017,4.5e-12,1;RA=4620;RUN=1;ReadPosRankSum=-1.007;SC=CCTCTCAGCTCTGACTGAGTC;SRB=0.50043;SRF=2312;SRP=3.0178;SRR=2308;TC;TR=8;TU=ACTG;VQSLOD=9.9778;dbSNP=130;set=Intersection;sumGLbyD=36.45 20 36136198 . GTGTC G 2078.76 PASS AA=35;AB=0.54167;ABA=33;ABP=4.096;ABR=39;AC=17;AF=0.01384;AN=1228;BL=1212;BR=1523;BVAR;BaseQRankSum=6.900;DEL;DP=22483;DP4=1696,2291,9,16;Dels=0.01;EL=9;EPP=20.94;ER=26;FQ=999;FR;FS=3.023;HETAR=13;HOMA=1;HOMR=1061;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1113;IndelType=DEL.NumRepetitions_2.EventLength_4.;LEN=4;LRB=0.11371;LRBP=79.803;MQ=93.98;MQ0=1;MQ0Fraction=0.0003;MQM=83.686;MQRankSum=-1.683;NF;NR;NS=1075;PP;PV4=0.55,1,0.0083,1;RA=5771;RL=19;RPP=3.5687;RR=16;RUN=1;ReadPosRankSum=0.618;SAB=0.37143;SAF=13;SAP=8.0357;SAR=22;SC=TATCATTTTAGTGTCTGTCTG;SRB=0.44966;SRF=2595;SRP=130.03;SRR=3176;TC;TR=11;TU=CTGT;VQSLOD=10.1935;set=Intersection;sumGLbyD=31.66 20 36250522 . CA C 37933 PASS AA=51;AB=0.95582;ABA=44;ABP=1800.5;ABR=952;AC=23;AF=0.01885;AN=1220;BL=691;BR=3464;BVAR;BaseQRankSum=-2.418;DEL;DP=11998;Dels=0.00;EL=18;EPP=12.59;ER=33;FS=2.307;HETAR=348;HOMA=534;HOMR=164;HRun=1;InbreedingCoeff=0.0763;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.66739;LRBP=4021.7;MQ0=2;MQ0Fraction=0.0006;MQM=53.647;MQRankSum=1.083;NS=1047;RA=1663;RL=2;RPP=97.065;RR=49;RUN=1;ReadPosRankSum=-12.726;SAB=0.68627;SAF=35;SAP=18.381;SAR=16;SRB=0.59651;SRF=992;SRP=137.56;SRR=671;VQSLOD=4.1346;set=filterInVQSR-2of5;sumGLbyD=3.29 20 36285033 rs34715186 AT A 39417 PASS AA=530;AB=0.5406;ABA=447;ABP=16.939;ABR=526;AC=88;AF=0.0950;AN=926;BL=20722;BR=20406;BVAR;BaseQRankSum=15.611;DB;DEL;DP=36713;DP4=2551,2475,236,218;Dels=0.09;EL=241;EPP=12.45;ER=289;FQ=999;FR;FS=1.290;HETAR=141;HOMA=16;HOMR=926;HP=2;HPLen=3;HR=3;HRun=1;HU=A;INDEL;InbreedingCoeff=0.0742;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.0076833;LRBP=8.2825;MQ=104.81;MQ0=0;MQ0Fraction=0.0000;MQM=84.285;MQRankSum=-0.702;NF;NR;NS=1083;PP;PV4=0.62,1,1,1;RA=6562;RL=263;RPP=3.0759;RR=267;RUN=1;ReadPosRankSum=0.090;SAB=0.55849;SAF=296;SAP=18.76;SAR=234;SC=AAAAACACAAATCAGATCGTG;SRB=0.51707;SRF=3393;SRP=19.614;SRR=3169;TC;TR=3;TU=A;VQSLOD=10.5533;dbSNP=126;set=Intersection;sumGLbyD=14.15 20 36384872 . CTG C 43532.41 PASS AC=1213;AF=0.99589;AN=1218;BaseQRankSum=0.802;DP=3208;FS=9.727;HRun=0;HaplotypeScore=46.6153;InbreedingCoeff=0.1085;IndelType=DEL.NumRepetitions_7.EventLength_2.RepeatExpansion_TG.;MQ=58.37;MQ0=50;MQ0Fraction=0.0156;MQRankSum=-1.672;QD=13.57;ReadPosRankSum=2.063;SB=-18894.12;VQSLOD=4.7353;set=VQSR 20 36542802 . GTA G 31310.15 PASS AA=1481;AB=0.67546;ABA=1378;ABP=1138.4;ABR=2868;AC=437;AF=0.35938;AN=1216;BL=25719;BR=95500;BVAR;BaseQRankSum=9.478;DEL;DP=18068;DS;Dels=0.10;EL=889;EPP=132.34;ER=592;FS=320.726;HETAR=591;HOMA=44;HOMR=378;HRun=0;InbreedingCoeff=-0.4197;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.57566;LRBP=87231;MQ0Fraction=0.0091;MQM=29.319;MQRankSum=-3.409;NS=1013;RA=4037;RL=3;RPP=3193;RR=1478;RUN=1;ReadPosRankSum=-6.687;SAB=0.40041;SAF=593;SAP=130.61;SAR=888;SRB=0.39014;SRF=1575;SRP=426.21;SRR=2462;VQSLOD=-1.6586;set=filterInVQSR-2of5;sumGLbyD=5.49 20 36985025 . CCA C 4.57 PASS AC=0;AF=0.0000;AN=682;BaseQRankSum=4.199;DP=1504;FS=1.036;HRun=0;HaplotypeScore=18.5241;InbreedingCoeff=0.0460;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_CA.;MQ=57.04;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.774;ReadPosRankSum=-2.105;VQSLOD=6.7455;set=VQSR 20 37139725 . CAG C 250.77 PASS AF=0.0084;AF1=0.0139;BaseQRankSum=4.131;CI95=0.00885,0.01991;DP=7973;DP4=1808,1990,2,7;Dels=0.01;FQ=104;FR;FS=11.160;HP=3;HPLen=2;HR=1;HRun=0;HU=A;INDEL;InbreedingCoeff=-0.0001;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;MQ=103.71;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.378;NF;NR;PP;PV4=0.18,0.0011,0.041,1;ReadPosRankSum=0.605;SC=AGATGGGGAACAGAGAGCAAG;TC;TR=6;TU=AG;VQSLOD=7.0630;set=Intersection;sumGLbyD=12.13 20 37213224 . G GTA 3230.05 PASS AA=32;AB=0.50769;ABA=32;ABP=3.0437;ABR=33;AC=12;AF=0.0168;AF1=0.02635;AN=714;BL=1271;BR=1743;BVAR;BaseQRankSum=-7.288;CI95=0.02212,0.03319;DP=14304;DP4=2180,2256,13,21;Dels=0.00;EL=20;EPP=7.3532;ER=12;FQ=999;FR;FS=7.863;HETAR=9;HOMA=0;HOMR=1043;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0410;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_TA.;LEN=2;LRB=0.1566;LRBP=163.52;MQ=95.56;MQ0=1;MQ0Fraction=0.0005;MQM=51.562;MQRankSum=0.420;NF;NR;NS=1052;PP;PV4=0.23,1,0.03,0.33;RA=5138;RL=11;RPP=9.7962;RR=21;RUN=1;ReadPosRankSum=-1.122;SAB=0.28125;SAF=9;SAP=16.311;SAR=23;SC=TTTGCATCCAGTAGCACCACT;SRB=0.42293;SRF=2173;SRP=268.11;SRR=2965;TC;TR=1;TU=T;VQSLOD=9.7315;set=Intersection;sumGLbyD=36.69 20 37282014 . ATGG A 2518.52 PASS AF=0.03519;BaseQRankSum=11.994;DP=24592;DP4=415,3804,8,49;DS;Dels=0.01;FQ=999;FR;FS=2.049;HP=1;HPLen=1;HR=1;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1028;IndelType=DEL.NumRepetitions_5.EventLength_3.;MQ=51.01;MQ0Fraction=0.0139;MQRankSum=-5.912;NF;NR;PP;PV4=0.27,1,0.22,0.015;ReadPosRankSum=1.781;SC=GGTGGTGATGATGGTGGTGGT;TC;TR=17;TU=GGT;VQSLOD=2.1183;set=filterInVQSR-2of5;sumGLbyD=9.05 20 37532218 . GTCCGTCCA ATCCGTCCA,G 76120.88 PASS AC=998;AF=0.92924;AN=1074;BaseQRankSum=-2.877;DP=3087;FR;FS=9.889;HP=2;HPLen=2;HR=1;HRun=0;HU=T;HaplotypeScore=71.6244;InbreedingCoeff=-0.0027;IndelType=MIXED;MQ=52.68;MQ0=543;MQ0Fraction=0.1759;MQRankSum=-1.750;NF;NR;PP;QD=24.98;ReadPosRankSum=-0.850;SB=-36635.43;SC=CCGTCCGTCCGTCCGTCCATC;TC;TR=19;TU=CCGT;VQSLOD=5.3068;set=Intersection 20 37712193 . AAG A 2670.33 PASS AA=106;AB=0.62821;ABA=87;ABP=36.418;ABR=147;AC=53;AF=0.0759;AN=698;BL=4672;BR=4303;BVAR;BaseQRankSum=13.696;DEL;DP=15155;DP4=1340,1852,32,52;Dels=0.06;EL=57;EPP=4.3214;ER=49;FR;FS=0.824;HETAR=43;HOMA=7;HOMR=982;HP=1;HPLen=2;HR=2;HRun=0;HU=A;INDEL;InbreedingCoeff=0.0861;IndelType=DEL.NumRepetitions_3.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.041114;LRBP=35.954;MQ=86.12;MQ0=0;MQ0Fraction=0.0000;MQM=54.236;MQRankSum=-5.745;NF;NR;NS=1034;PP;PV4=0.5,7.3e-26,1.1e-10,1;RA=4423;RL=58;RPP=5.0589;RR=48;RUN=1;ReadPosRankSum=2.617;SAB=0.38679;SAF=41;SAP=14.81;SAR=65;SC=GAAAATTCTGAAGAGAGTCAG;SRB=0.43093;SRF=1906;SRP=186.29;SRR=2517;TC;TR=6;TU=AG;VQSLOD=9.8131;set=Intersection;sumGLbyD=14.20 20 37739002 . T TCA 1395.38 PASS AA=16;AB=0.48387;ABA=16;ABP=3.0803;ABR=15;AC=11;AF=0.00950;AN=1158;BL=504;BR=630;BVAR;BaseQRankSum=-3.257;DP=13617;DP4=1660,883,7,5;Dels=0.00;EL=7;EPP=3.5532;ER=9;FR;FS=1.114;HETAR=9;HOMA=0;HOMR=991;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0527;IndelType=INS.NumRepetitions_1.EventLength_2.RepeatExpansion_CA.;LEN=2;LRB=0.11111;LRBP=33.411;MQ=88.41;MQ0=0;MQ0Fraction=0.0000;MQM=83.75;MQRankSum=1.713;NF;NR;NS=1000;PP;PV4=0.76,1,1,0.5;RA=3257;RL=6;RPP=5.1818;RR=10;RUN=1;ReadPosRankSum=1.190;SAB=0.6875;SAF=11;SAP=7.8961;SAR=5;SC=CCTTTTTTGTTCATTTCTGCA;SRB=0.68806;SRF=2241;SRP=1003.5;SRR=1016;TC;TR=2;TU=T;VQSLOD=10.2220;set=Intersection;sumGLbyD=41.32 20 38395256 . TTGAG T 633.19 PASS AF=0.0028;BaseQRankSum=5.667;DP=3839;Dels=0.00;FR;FS=10.238;HP=2;HPLen=3;HR=3;HRun=0;HU=T;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.276;NF;NR;PP;ReadPosRankSum=-1.016;SC=ATGTGTTTGTTTGAGTATGTT;TC;TR=10;TU=GTTT;VQSLOD=6.4906;set=Intersection;sumGLbyD=10.83 20 39345038 . CTGAACCATAATGTG C,CCCATAATGTG 60744.52 PASS AA=23;AB=0.67143;ABA=23;ABP=20.878;ABR=47;AC=232,2;AF=0.19366,0.00167;AN=1198;BL=1607;BR=1843;BVAR;BaseQRankSum=30.955;DEL;DP=31490;DP4=1729,2100,265,278;Dels=0.13;EL=6;EPP=14.434;ER=17;FQ=999;FR;FS=1.767;HETAR=18;HOMA=0;HOMR=1015;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.1991;IndelType=MULTIALLELIC_INDEL;LEN=14;LRB=0.068406;LRBP=38.066;MQ=104.60;MQ0=0;MQ0Fraction=0.0000;MQM=189.83;MQRankSum=-16.579;NF;NR;NS=1033;PP;PV4=0.12,1,5.5e-137,1;RA=5286;RL=14;RPP=5.3706;RR=9;RUN=1;ReadPosRankSum=4.323;SAB=0.56522;SAF=13;SAP=3.86;SAR=10;SC=TGGGCTGGACCTGAACCATAA;SRB=0.46311;SRF=2448;SRP=65.493;SRR=2838;TC;TR=2;TU=C;VQSLOD=6.2643;dbSNP=130;set=Intersection;sumGLbyD=65.43 20 39418008 . AG A 46796 PASS AA=113;AB=0.9511;ABA=80;ABP=2894.6;ABR=1556;AC=30;AF=0.02412;AN=1244;BL=638;BR=6936;BVAR;BaseQRankSum=7.280;DEL;DP=14307;Dels=0.00;EL=50;EPP=6.2579;ER=63;FR;FS=5.707;HETAR=473;HOMA=361;HOMR=246;HP=3;HR=3;HRun=3;HU=G;InbreedingCoeff=0.0272;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.83153;LRBP=11375;MQ0=0;MQ0Fraction=0.0000;MQM=62.398;MQRankSum=3.530;NF;NR;NS=1089;PP;RA=3000;RL=3;RPP=223.02;RR=110;RUN=1;ReadPosRankSum=-18.601;SAB=0.58407;SAF=66;SAP=9.9475;SAR=47;SC=ACTGGGGGAAAGGGATTCTAG;SRB=0.494;SRF=1482;SRP=3.9484;SRR=1518;TC;TR=3;TU=G;VQSLOD=4.5834;set=Intersection;sumGLbyD=3.06 20 39876961 . GT G,GTT,GTTT 2302.10 PASS ABR=496;AC=45,51,45;AF=0.03664,0.04153,0.03664;AN=1228;BVAR;BaseQRankSum=4.462;DP=37649;DP4=1457,1975,57,59;Dels=0.02;FR;FS=9.938;HOMA=0;HOMR=978;HP=10;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.2583;IndelType=MULTIALLELIC_INDEL;MQ=97.28;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.246;NF;NR;NS=1063;PP;PV4=0.15,1,1.9e-09,0.016;RA=5185;RUN=1;ReadPosRankSum=-4.954;SC=AGTTTCTCCGGTTTTTTTTTT;SRB=0.47464;SRF=2461;SRP=31.978;SRR=2724;TC;TR=10;TU=T;VQSLOD=4.9752;set=Intersection;sumGLbyD=4.39 20 41013333 . TC T 20681 PASS AA=137;AB=0.89211;ABA=134;ABP=1661.6;ABR=1108;AC=68;AF=0.05601;AN=1214;BL=1091;BR=8981;BVAR;BaseQRankSum=1.354;DEL;DP=12998;Dels=0.01;EL=57;EPP=11.395;ER=80;FS=0.758;HETAR=359;HOMA=100;HOMR=610;HRun=1;InbreedingCoeff=0.0104;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.78336;LRBP=13424;MQ0=1;MQ0Fraction=0.0003;MQM=67.745;MQRankSum=2.563;NS=1072;RA=4447;RL=5;RPP=258.66;RR=132;RUN=1;ReadPosRankSum=-14.092;SAB=0.59124;SAF=81;SAP=12.917;SAR=56;SRB=0.54194;SRF=2410;SRP=70.947;SRR=2037;VQSLOD=3.7531;set=filterInVQSR-2of5;sumGLbyD=4.14 20 41659532 . GC G 40544 PASS AA=42;AB=0.97149;ABA=39;ABP=2644.5;ABR=1329;AC=15;AF=0.0209;AN=716;BL=2531;BR=135;BVAR;BaseQRankSum=-2.537;DEL;DP=12219;Dels=0.00;EL=25;EPP=6.3192;ER=17;FS=2.656;HETAR=374;HOMA=155;HOMR=551;HRun=1;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.89872;LRBP=4678.9;MQ0=0;MQ0Fraction=0.0000;MQM=103.31;MQRankSum=2.828;NS=1088;RA=4736;RL=41;RPP=85.733;RR=1;RUN=1;ReadPosRankSum=-9.702;SAB=0.57143;SAF=24;SAP=4.8716;SAR=18;SRB=0.5625;SRF=2664;SRP=163.7;SRR=2072;VQSLOD=4.3267;set=Intersection;sumGLbyD=3.22 20 41845580 . GA G 49310 PASS AA=83;AB=0.95258;ABA=69;ABP=2591.6;ABR=1386;AC=46;AF=0.03740;AN=1230;BL=1320;BR=5150;BVAR;BaseQRankSum=-1.121;DEL;DP=13336;Dels=0.00;EL=36;EPP=6.1759;ER=47;FR;FS=0.372;HETAR=442;HOMA=341;HOMR=295;HP=2;HR=3;HRun=1;HU=G;InbreedingCoeff=0.0238;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.59196;LRBP=4926.2;MQ0=0;MQ0Fraction=0.0000;MQM=89.048;MQRankSum=0.897;NF;NR;NS=1080;PP;RA=3006;RL=5;RPP=142.43;RR=78;RUN=1;ReadPosRankSum=-15.412;SAB=0.55422;SAF=46;SAP=5.1294;SAR=37;SC=CCAGCTGTGGGAGAGAAACAT;SRB=0.47971;SRF=1442;SRP=13.762;SRR=1564;TC;TR=6;TU=AG;VQSLOD=4.4669;set=Intersection;sumGLbyD=3.65 20 42209428 . GC G 13163 PASS AA=89;AB=0.86677;ABA=83;ABP=730.96;ABR=540;AC=39;AF=0.03218;AN=1212;BL=950;BR=5334;BVAR;BaseQRankSum=-10.119;DEL;DP=10692;Dels=0.01;EL=48;EPP=4.2058;ER=41;FS=0.000;HETAR=259;HOMA=727;HOMR=54;HRun=1;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.69764;LRBP=6644.4;MQ0=0;MQ0Fraction=0.0000;MQM=126.55;MQRankSum=4.223;NS=1040;RA=723;RL=12;RPP=106.09;RR=77;RUN=1;ReadPosRankSum=-17.362;SAB=0.39326;SAF=35;SAP=11.818;SAR=54;SRB=0.37898;SRF=274;SRP=94.99;SRR=449;VQSLOD=3.7157;set=filterInVQSR-2of5;sumGLbyD=3.48 20 42281109 . T TAG 2321.12 PASS AC=181;AF=0.3740;AN=484;BaseQRankSum=8.977;DP=435;FS=17.001;HRun=0;HaplotypeScore=14.6734;InbreedingCoeff=0.2340;IndelType=INS.NOVEL_2.;MQ=53.88;MQ0=47;MQ0Fraction=0.1080;MQRankSum=0.762;QD=12.41;ReadPosRankSum=3.399;SB=-1299.73;VQSLOD=4.8926;set=VQSR 20 42436117 . TC T 38933 PASS AA=18;AB=0.98435;ABA=17;ABP=2215.9;ABR=1069;AC=15;AF=0.01223;AN=1226;BL=498;BR=428;BVAR;BaseQRankSum=-7.224;DEL;DP=12436;Dels=0.00;EL=1;EPP=33.893;ER=17;FS=2.469;HETAR=303;HOMA=614;HOMR=123;HRun=1;InbreedingCoeff=0.0439;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.075594;LRBP=14.501;MQ0=0;MQ0Fraction=0.0000;MQM=98.611;MQRankSum=1.086;NS=1075;RA=1656;RL=10;RPP=3.4928;RR=8;RUN=1;ReadPosRankSum=-17.765;SAB=0.5;SAF=9;SAP=3.0103;SAR=9;SRB=0.49879;SRF=826;SRP=3.0313;SRR=830;VQSLOD=4.0821;set=filterInVQSR-2of5;sumGLbyD=3.04 20 42682214 . C A,CAT 3904.51 PASS AA=24;AB=0.6383;ABA=17;ABP=10.818;ABR=30;AC=0;AF=0.0000;AN=636;BL=1119;BR=949;BVAR;BaseQRankSum=1.426;DP=6509;Dels=0.00;EL=9;EPP=6.2675;ER=15;FR;HETAR=12;HOMA=3;HOMR=876;HP=2;HPLen=1;HR=1;HRun=0;HU=A;INS;InbreedingCoeff=0.0006;IndelType=MIXED;LEN=2;LRB=0.082205;LRBP=33.356;MQ0Fraction=0.0046;MQM=40.792;MQRankSum=-0.296;NF;NR;NS=891;PP;QD=32.81;RA=2679;RL=15;RPP=6.2675;RR=9;RUN=1;ReadPosRankSum=-1.806;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SB=-924.23;SC=TATACACACACATATATATAC;SRB=0.66293;SRF=1776;SRP=620.76;SRR=903;TC;TR=9;TU=AC;set=filterInVQSR-2of5;sumGLbyD=32.75 20 42973456 . CA C,CAA,CAAA 2675 PASS AA=90;AB=0.79177;ABA=86;ABP=308.39;ABR=327;AC=77,61,39;AF=0.06492,0.05143,0.03288;AN=1186;BL=2983;BR=4446;BVAR;BaseQRankSum=2.422;DP=9416;Dels=0.03;EL=39;EPP=6.4847;ER=51;FR;FS=31.555;HETAR=75;HOMA=1;HOMR=888;HP=11;HR=11;HRun=11;HU=A;INS;InbreedingCoeff=0.2696;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.19693;LRBP=628.63;MQ0=0;MQ0Fraction=0.0000;MQM=55.567;MQRankSum=1.777;NF;NR;NS=964;PP;RA=3601;RL=37;RPP=9.1869;RR=53;RUN=1;ReadPosRankSum=-4.991;SAB=0.55556;SAF=50;SAP=5.423;SAR=40;SC=TAGTGACTGTCAAAAAAAAAA;SRB=0.60622;SRF=2183;SRP=355.91;SRR=1418;TC;TR=11;TU=A;VQSLOD=1.0763;set=filterInVQSR-2of5;sumGLbyD=4.05 20 43091870 . TC T 2455.60 PASS AA=120;AB=0.10619;ABA=101;ABP=155.22;ABR=12;AC=42;AF=0.03825;AN=1098;BL=573;BR=8744;BVAR;BaseQRankSum=-13.513;DEL;DP=9139;Dels=0.00;EL=64;EPP=4.1684;ER=56;FS=9.856;HETAR=118;HOMA=820;HOMR=0;HRun=1;InbreedingCoeff=0.0833;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.877;LRBP=15564;MQ0Fraction=0.0017;MQM=45.1;MQRankSum=2.266;NS=938;RA=24;RL=1;RPP=254.97;RR=119;RUN=1;ReadPosRankSum=-15.803;SAB=0.475;SAF=57;SAP=3.6617;SAR=63;SRB=0.54167;SRF=13;SRP=3.3722;SRR=11;VQSLOD=3.9930;set=filterInVQSR-2of5;sumGLbyD=3.09 20 43233648 rs74585029 GA G,GAA 1504.40 PASS AA=113;AB=0.78652;ABA=95;ABP=320.31;ABR=350;AC=41,65;AF=0.03394,0.05381;AF1=0.0115;AN=1208;BL=4677;BR=5548;BVAR;BaseQRankSum=6.744;CI95=0.004274,0.01852;DB;DEL;DP=13996;DP4=1736,1549,15,17;Dels=0.03;EL=69;EPP=15.021;ER=44;FQ=14;FR;FS=12.174;HETAR=119;HOMA=15;HOMR=892;HP=11;HPLen=10;HR=10;HRun=10;HU=A;INDEL;InbreedingCoeff=0.2359;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.085183;LRBP=164.12;MQ=89.12;MQ0Fraction=0.0000;MQM=69.867;MQRankSum=2.513;NF;NR;NS=1027;PP;PV4=0.59,1,0.065,0.33;RA=3845;RL=46;RPP=11.485;RR=67;RUN=1;ReadPosRankSum=-4.957;SAB=0.33628;SAF=38;SAP=29.318;SAR=75;SC=AAAACAGCCAGAAAAAAAAAA;SRB=0.43667;SRF=1679;SRP=136.95;SRR=2166;TC;TR=10;TU=A;VQSLOD=4.5121;set=Intersection;sumGLbyD=8.22 20 43246548 . AC A,CC 41579.13 PASS AA=382;AB=0.72402;ABA=316;ABP=502.11;ABR=829;AC=1197;AF=0.99254;AN=1206;BL=9889;BR=14293;BVAR;BaseQRankSum=1.373;DEL;DP=10477;DS;Dels=0.05;EL=243;EPP=64.494;ER=139;FS=29.162;HETAR=291;HOMA=85;HOMR=624;HPLen=10;InbreedingCoeff=0.1392;IndelType=MIXED;LEN=1;LRB=0.18212;LRBP=1744.6;MQ0Fraction=0.0024;MQM=48.471;MQRankSum=5.726;NS=1001;RA=3138;RL=174;RPP=9.5816;RR=208;RUN=1;ReadPosRankSum=5.755;SAB=0.79843;SAF=305;SAP=298.51;SAR=77;SRB=0.70363;SRF=2208;SRP=1133.2;SRR=930;VQSLOD=5.6318;set=Intersection;sumGLbyD=5.22 20 43258646 . T TT 1107.17 PASS AC=97;AF=0.08420;AN=1152;BaseQRankSum=4.525;DP=2345;FS=19.308;HRun=9;HaplotypeScore=13.6276;InbreedingCoeff=0.1299;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;MQ=76.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.395;QD=2.67;ReadPosRankSum=-4.696;SB=-899.41;VQSLOD=5.4523;set=VQSR 20 43718299 . ATTACT A 5497.06 PASS AA=56;AB=0.51818;ABA=53;ABP=3.3262;ABR=57;AC=18;AF=0.0251;AF1=0.03729;AN=718;BL=2321;BR=2591;BVAR;BaseQRankSum=11.142;CI95=0.03319,0.04425;DEL;DP=17576;DP4=2460,2692,31,22;Dels=0.02;EL=28;EPP=3.0103;ER=28;FQ=999;FR;FS=9.689;HETAR=15;HOMA=1;HOMR=1068;HP=2;HPLen=2;HR=2;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0448;IndelType=DEL.NumRepetitions_1.EventLength_5.;LEN=5;LRB=0.054967;LRBP=35.238;MQ=96.55;MQ0=0;MQ0Fraction=0.0000;MQM=50.286;MQRankSum=-5.149;NF;NR;NS=1084;PP;PV4=0.13,1,1.2e-12,1;RA=6745;RL=28;RPP=3.0103;RR=28;RUN=1;ReadPosRankSum=0.828;SAB=0.5;SAF=28;SAP=3.0103;SAR=28;SC=ATGACAGTGGATTACTTTAGT;SRB=0.46835;SRF=3159;SRP=61.709;SRR=3586;TC;TR=2;TU=T;VQSLOD=7.8832;set=Intersection;sumGLbyD=46.60 20 43981749 . A AAAAAAC,AC 20899.71 PASS ABR=192;AC=91,0;AF=0.1285,0.0000;AN=708;BVAR;BaseQRankSum=7.858;DP=23372;DP4=1554,1457,55,42;Dels=0.00;FR;FS=0.000;HOMA=4;HOMR=995;HP=6;HPLen=7;HR=7;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.2109;IndelType=MULTIALLELIC_INDEL;MQ=95.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-12.081;NF;NR;NS=1051;PP;PV4=0.35,1,8.9e-73,1;RA=5027;RUN=1;ReadPosRankSum=-1.359;SC=TACACTAGCAAAAAAACAAAA;SRB=0.48518;SRF=2439;SRP=12.6;SRR=2588;TC;TR=7;TU=A;VQSLOD=8.0916;set=Intersection;sumGLbyD=54.33 20 43999274 . TCAAA T 2948.85 PASS AA=59;AB=0.59441;ABA=58;ABP=14.08;ABR=85;AC=20;AF=0.0290;AF1=0.04249;AN=690;BL=2277;BR=2436;BVAR;BaseQRankSum=9.320;CI95=0.0354,0.05088;DEL;DP=14599;DP4=2052,2303,21,22;Dels=0.03;EL=32;EPP=3.9304;ER=27;FQ=999;FR;FS=0.000;HETAR=21;HOMA=0;HOMR=1043;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0037;IndelType=DEL.NumRepetitions_1.EventLength_4.;LEN=4;LRB=0.033736;LRBP=14.658;MQ=90.05;MQ0=0;MQ0Fraction=0.0000;MQM=75.339;MQRankSum=-1.294;NF;NR;NS=1064;PP;PV4=0.88,1,0.0026,1;RA=5732;RL=27;RPP=3.9304;RR=32;RUN=1;ReadPosRankSum=-0.915;SAB=0.47458;SAF=28;SAP=3.3415;SAR=31;SC=GGTACACAGCTCAAACAGTCT;SRB=0.4836;SRF=2772;SRP=16.4;SRR=2960;TC;TR=1;TU=C;VQSLOD=9.8086;set=Intersection;sumGLbyD=27.09 20 44098622 . C CG 1092.40 PASS AA=129;AB=0.77301;ABA=74;ABP=214.06;ABR=252;AC=45;AF=0.0455;AN=988;BL=6586;BR=3029;BVAR;BaseQRankSum=2.802;DP=5177;Dels=0.00;EL=122;EPP=225.63;ER=7;FR;FS=355.273;HETAR=66;HOMA=11;HOMR=734;HP=6;HR=4;HRun=4;HU=G;INS;InbreedingCoeff=0.1759;IndelType=INS.NumRepetitions_4.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.36994;LRBP=2860.4;MQ0=0;MQ0Fraction=0.0000;MQM=52.395;MQRankSum=1.946;NF;NR;NS=811;PP;RA=1981;RL=121;RPP=217.95;RR=8;RUN=1;ReadPosRankSum=-6.413;SAB=0.99225;SAF=128;SAP=274.51;SAR=1;SC=GCGGAAGTGGCGGGGACCCTT;SRB=0.41242;SRF=817;SRP=135;SRR=1164;TC;TR=4;TU=G;VQSLOD=-2.2690;set=filterInVQSR-2of5;sumGLbyD=4.04 20 44327637 . A AG,AGGGGGG 14351.23 PASS AC=9,211;AF=0.0103,0.2409;AN=876;BaseQRankSum=15.517;DP=1704;FS=6.768;HaplotypeScore=31.5906;InbreedingCoeff=0.1538;IndelType=MULTIALLELIC_INDEL;MQ=54.64;MQ0=4;MQ0Fraction=0.0023;MQRankSum=-12.691;QD=20.83;ReadPosRankSum=-3.583;SB=-6278.99;VQSLOD=5.1556;set=VQSR 20 45202636 . GA G 13269 PASS AA=25;AB=0.96162;ABA=18;ABP=871.09;ABR=451;AC=24;AF=0.02013;AN=1192;BL=567;BR=1728;BVAR;BaseQRankSum=-5.361;DEL;DP=10873;Dels=0.00;EL=10;EPP=5.1818;ER=15;FS=0.928;HETAR=169;HOMA=831;HOMR=45;HRun=1;InbreedingCoeff=0.0999;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.50588;LRBP=1278.4;MQ0=0;MQ0Fraction=0.0000;MQM=170.56;MQRankSum=0.161;NS=1049;RA=632;RL=2;RPP=41.315;RR=23;RUN=1;ReadPosRankSum=-14.760;SAB=0.68;SAF=17;SAP=10.046;SAR=8;SRB=0.51424;SRF=325;SRP=4.1235;SRR=307;VQSLOD=3.9290;set=filterInVQSR-2of5;sumGLbyD=3.90 20 45417828 . TGAGC T,TGC 4672.90 PASS ABR=317;AC=69,104;AF=0.05712,0.08609;BVAR;BaseQRankSum=18.527;DEL;DP=11835;DS;FS=184.873;HOMA=48;HOMR=575;HaplotypeScore=65.5875;InbreedingCoeff=0.0599;IndelType=MULTIALLELIC_INDEL;MQ=29.78;MQ0=2988;MQ0Fraction=0.3629;MQRankSum=5.052;NS=713;QD=1.11;RA=1581;RUN=1;ReadPosRankSum=6.574;SB=-2116.87;SRB=0.47502;SRF=751;SRP=11.582;SRR=830;VQSLOD=0.0651;set=filterInVQSR-2of5 20 45525657 rs66759083 TA AA,T 49315 PASS AA=2361;AB=0.45241;ABA=1398;ABP=53.235;ABR=1155;AC=20;AF=0.01701;AN=1176;BL=94913;BR=100886;BVAR;BaseQRankSum=0.740;DB;DEL;DP=30636;DP4=1258,881,1206,999;Dels=0.48;EL=1133;EPP=11.311;ER=1228;FQ=999;FR;FS=7.072;HETAR=503;HOMA=310;HOMR=218;HP=6;HPLen=7;HR=7;HU=T;INDEL;InbreedingCoeff=0.2271;IndelType=MIXED;LEN=1;LRB=0.030506;LRBP=398.68;MQ=102.24;MQ0=0;MQ0Fraction=0.0000;MQM=75.359;MQRankSum=0.148;NF;NR;NS=1031;PP;PV4=0.0064,0,4.6e-23,0.47;RA=2042;RL=1183;RPP=3.0333;RR=1178;RUN=1;ReadPosRankSum=-2.999;SAB=0.52139;SAF=1231;SAP=12.392;SAR=1130;SC=AGGATTTTTTTAAAAAGTTTT;SRB=0.55093;SRF=1125;SRP=49.017;SRR=917;TC;TR=7;TU=T;VQSLOD=7.1651;dbSNP=114;set=Intersection;sumGLbyD=18.51 20 45783456 . T TG 2355.68 PASS AA=64;AB=0.78521;ABA=61;ABP=203.67;ABR=223;AC=15;AF=0.0165;AN=910;BL=815;BR=5486;BVAR;BaseQRankSum=8.593;DP=10348;Dels=0.00;EL=48;EPP=37.754;ER=16;FS=77.861;HETAR=56;HOMA=1;HOMR=970;HRun=1;INS;InbreedingCoeff=-0.0549;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.74131;LRBP=7522.1;MQ0Fraction=0.0122;MQM=44.562;MQRankSum=-1.258;NS=1027;RA=4750;RL=0;RPP=141.98;RR=64;RUN=1;ReadPosRankSum=-7.047;SAB=0.25;SAF=16;SAP=37.754;SAR=48;SRB=0.6;SRF=2850;SRP=415.59;SRR=1900;VQSLOD=1.3146;set=filterInVQSR-2of5;sumGLbyD=6.03 20 46517110 . C CT 868.55 PASS AC=15;AF=0.0218;AN=688;BaseQRankSum=8.522;DP=1752;FS=6.570;HRun=0;HaplotypeScore=14.9548;InbreedingCoeff=0.0452;IndelType=INS.NOVEL_1.Novel_T.;MQ=77.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=3.874;QD=10.98;ReadPosRankSum=-0.733;SB=-396.78;VQSLOD=6.7740;set=VQSR 20 46629361 . TTTCTTTC T,TTTTC 13000.91 PASS AC=188,107;AF=0.2212,0.1259;AN=850;BaseQRankSum=7.214;DP=1846;FS=14.502;HaplotypeScore=40.8481;InbreedingCoeff=0.3210;IndelType=MULTIALLELIC_INDEL;MQ=50.74;MQ0=79;MQ0Fraction=0.0428;MQRankSum=-6.348;QD=13.59;ReadPosRankSum=3.943;SB=-3581.20;VQSLOD=5.9412;set=VQSR 20 46951099 . G GT 1662.30 PASS AA=55;AB=0.7713;ABA=51;ABP=145.58;ABR=172;AC=47;AF=0.03923;AN=1198;BL=3288;BR=2434;BVAR;BaseQRankSum=-4.014;DP=27423;DP4=1483,1590,58,42;Dels=0.01;EL=21;EPP=9.6826;ER=34;FR;FS=9.565;HETAR=48;HOMA=0;HOMR=913;HP=16;HPLen=10;HR=10;HRun=10;HU=T;INDEL;INS;InbreedingCoeff=0.0952;IndelType=INS.NumRepetitions_10orMore.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.14925;LRBP=279.78;MQ=70.36;MQ0Fraction=0.0124;MQM=52.545;MQRankSum=0.717;NF;NR;NS=961;PP;PV4=0.067,1,1,0.17;RA=3035;RL=38;RPP=20.422;RR=17;RUN=1;ReadPosRankSum=-3.014;SAB=0.47273;SAF=26;SAP=3.3656;SAR=29;SC=TTTGTTTTTTGTTTTTTTTTT;SRB=0.36013;SRF=1093;SRP=518.73;SRR=1942;TC;TR=10;TU=T;VQSLOD=5.4779;set=Intersection;sumGLbyD=3.49 20 47201076 rs58052846 C CT 982.16 PASS AC=50;AF=0.0551;AN=908;BaseQRankSum=12.598;DB;DP=2449;FS=35.648;HRun=0;HaplotypeScore=29.4602;InbreedingCoeff=-0.0542;IndelType=INS.NOVEL_1.Novel_T.;MQ=63.54;MQ0=0;MQ0Fraction=0.0000;MQRankSum=2.196;QD=3.16;ReadPosRankSum=-13.833;SB=-488.19;VQSLOD=6.0429;set=VQSR 20 47965974 rs60011158 G GA 999 PASS AA=21;AB=0.57143;ABA=21;ABP=5.1818;ABR=28;AC=7;AF=0.0101;AF1=0.02061;AN=690;BL=1043;BR=577;BVAR;BaseQRankSum=-3.087;CI95=0.01549,0.02655;DB;DP=14578;DP4=1554,3055,6,17;Dels=0.00;EL=11;EPP=3.1137;ER=10;FQ=999;FR;FS=5.982;HETAR=7;HOMA=0;HOMR=1041;HP=2;HPLen=1;HR=1;HRun=1;HU=A;INDEL;INS;InbreedingCoeff=0.0356;IndelType=INS.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28765;LRBP=294.09;MQ=80.17;MQ0=0;MQ0Fraction=0.0000;MQM=64.19;MQRankSum=2.137;NF;NR;NS=1048;PP;PV4=0.51,1,1,1;RA=5224;RL=16;RPP=15.522;RR=5;RUN=1;ReadPosRankSum=0.236;SAB=0.38095;SAF=8;SAP=5.5954;SAR=13;SC=TTCATGTACAGAGCTGCTGTG;SRB=0.31183;SRF=1629;SRP=1609.6;SRR=3595;TC;TR=4;TU=AG;VQSLOD=9.5466;dbSNP=129;set=Intersection;sumGLbyD=13.83 20 48402974 rs57331436 GA G 27741 PASS AA=401;AB=0.5372;ABA=311;ABP=11.089;ABR=361;AC=84;AF=0.1186;AN=708;BL=16591;BR=14776;BVAR;BaseQRankSum=14.621;DB;DEL;DP=30607;DP4=1928,2310,195,225;Dels=0.11;EL=189;EPP=5.8749;ER=212;FQ=999;FR;FS=15.568;HETAR=110;HOMA=30;HOMR=923;HP=4;HPLen=3;HR=1;HRun=3;HU=A;INDEL;InbreedingCoeff=0.1263;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;KGPilot123;LEN=1;LRB=0.057863;LRBP=231.06;MQ=106.68;MQ0=0;MQ0Fraction=0.0000;MQM=63.005;MQRankSum=-2.010;NF;NR;NS=1063;PP;PV4=0.72,1,0.001,1;RA=5258;RL=223;RPP=13.976;RR=178;RUN=1;ReadPosRankSum=1.337;SAB=0.37656;SAF=151;SAP=56.084;SAR=250;SC=TGCCCTCAAAGAGAAAAAGGA;SRB=0.38075;SRF=2002;SRP=652.44;SRR=3256;TC;TR=5;TU=AG;VQSLOD=8.7259;dbSNP=132;set=Intersection;sumGLbyD=15.86 20 49101936 . C CT 404.46 PASS AC=40;AF=0.03559;AN=1124;BaseQRankSum=0.750;DP=2162;FS=14.291;HRun=2;HaplotypeScore=30.9513;InbreedingCoeff=-0.0082;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_T.;MQ=49.78;MQ0=113;MQ0Fraction=0.0523;MQRankSum=-1.289;QD=1.94;ReadPosRankSum=-2.041;SB=-385.48;VQSLOD=4.6365;set=VQSR 20 49731218 . ATTTTATTTTTTATT A,ATTTTATT 8398.93 PASS AF=0.0656,0.0156;AF1=0.0996;BaseQRankSum=13.996;CI95=0.07743,0.1239;DP=6308;DP4=951,1311,23,35;Dels=0.05;FQ=999;FR;FS=12.503;HP=7;HPLen=4;HR=4;HRun=0;HU=T;INDEL;InbreedingCoeff=0.1892;IndelType=MULTIALLELIC_INDEL;MQ=57.61;MQ0Fraction=0.0145;MQRankSum=-5.208;NF;NR;PP;PV4=0.79,1,6.3e-06,0.16;ReadPosRankSum=-2.239;SC=TATTTTATTTATTTTATTTTT;TC;TR=11;TU=ATTT;VQSLOD=4.3191;set=Intersection;sumGLbyD=42.27 20 49894989 . TA T 172.25 PASS AF=0.0140;BaseQRankSum=7.220;DP=3882;Dels=0.00;FS=17.217;HPLen=2;HRun=1;InbreedingCoeff=0.0531;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;MQ0Fraction=0.0214;MQRankSum=-0.661;ReadPosRankSum=-0.592;VQSLOD=3.0905;set=filterInVQSR-2of5;sumGLbyD=6.60 20 50010923 rs66516522 C CT,CTGG 35851 PASS ABR=555;AC=310,11;AF=0.26451,0.00939;BVAR;BaseQRankSum=10.662;DB;DP=8188;FR;FS=34.411;HOMA=261;HOMR=399;HP=5;HR=6;HU=C;HaplotypeScore=45.1715;INS;InbreedingCoeff=0.2090;IndelType=MULTIALLELIC_INDEL;MQ=72.80;MQ0=0;MQ0Fraction=0.0000;MQRankSum=9.015;NF;NR;NS=831;PP;QD=9.69;RA=1986;RUN=1;ReadPosRankSum=-24.284;SB=-6038.55;SC=TGTCTGTCCCCCCTCAGCACT;SRB=0.45972;SRF=913;SRP=31.001;SRR=1073;TC;TR=6;TU=C;VQSLOD=6.1824;set=Intersection 20 50228709 rs71192536 TG T 20517 PASS AA=924;AB=0.50203;ABA=735;ABP=3.0633;ABR=741;AC=200;AF=0.16502;AN=1212;BL=35460;BR=34197;BVAR;BaseQRankSum=13.810;DB;DEL;DP=32402;DP4=1760,2065,395,449;Dels=0.16;EL=439;EPP=7.9831;ER=485;FQ=999;FR;FS=0.558;HETAR=242;HOMA=63;HOMR=764;HP=5;HPLen=3;HR=3;HRun=3;HU=G;INDEL;InbreedingCoeff=0.1050;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.018132;LRBP=52.738;MQ=105.83;MQ0=0;MQ0Fraction=0.0000;MQM=75.87;MQRankSum=3.895;NF;NR;NS=1069;PP;PV4=0.7,1.5e-173,1,1;RA=4708;RL=486;RPP=8.4249;RR=438;RUN=1;ReadPosRankSum=1.586;SAB=0.43615;SAF=403;SAP=35.733;SAR=521;SC=GTTTTCCAGGTGGGAAGACCG;SRB=0.44074;SRF=2075;SRP=146.62;SRR=2633;TC;TR=3;TU=G;VQSLOD=10.4820;dbSNP=120;set=Intersection;sumGLbyD=15.35 20 50236115 . AGG A,ACGGG,AG,AGGG 7429.57 PASS AC=192,13,221,183;AF=0.2115,0.0143,0.2434,0.2015;AN=908;BaseQRankSum=1.045;DP=1177;FS=13.479;HaplotypeScore=11.8294;InbreedingCoeff=0.7959;IndelType=MULTIALLELIC_INDEL;MQ=52.98;MQ0=6;MQ0Fraction=0.0051;MQRankSum=-1.482;QD=7.28;ReadPosRankSum=-2.380;SB=-1229.31;VQSLOD=8.3762;set=VQSR 20 51589568 . TAAAC AAAAC,T 12477.52 PASS AF=0.27949;BaseQRankSum=-28.122;DP=3777;Dels=0.00;FR;FS=31.799;HP=7;HPLen=4;HR=3;HRun=0;HU=A;InbreedingCoeff=-0.1429;IndelType=MIXED;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.196;NF;NR;PP;ReadPosRankSum=-16.483;SC=AAATTCAAAATAAACAAACAA;TC;TR=18;TU=AAAC;VQSLOD=3.9201;set=filterInVQSR-2of5;sumGLbyD=52.43 20 51617742 . TGC T,TGCGC 1374.91 PASS AF=0.06000,0.02000;BaseQRankSum=12.051;DP=6231;Dels=0.00;FS=189.609;HPLen=1;HRun=0;InbreedingCoeff=0.0862;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0180;MQRankSum=-2.959;ReadPosRankSum=-5.090;VQSLOD=-2.8715;set=filterInVQSR-2of5;sumGLbyD=3.97 20 51770354 . AG A 1010.90 PASS AA=26;AB=0.52727;ABA=26;ABP=3.3656;ABR=29;AC=7;AF=0.0097;AF1=0.01637;AN=718;BL=1034;BR=964;BVAR;BaseQRankSum=5.588;CI95=0.01327,0.02212;DEL;DP=16259;DP4=2785,2239,15,10;Dels=0.01;EL=11;EPP=4.3466;ER=15;FQ=999;FR;FS=3.367;HETAR=8;HOMA=0;HOMR=1064;HP=2;HPLen=2;HR=2;HRun=2;HU=G;INDEL;InbreedingCoeff=0.0557;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.035035;LRBP=8.3357;MQ=90.48;MQ0=0;MQ0Fraction=0.0000;MQM=61.346;MQRankSum=-0.019;NF;NR;NS=1072;PP;PV4=0.69,2.1e-08,0.078,1;RA=6173;RL=13;RPP=3.0103;RR=13;RUN=1;ReadPosRankSum=-0.460;SAB=0.61538;SAF=16;SAP=6.017;SAR=10;SC=GTGGTCCTGCAGGTCAATAAT;SRB=0.56342;SRF=3478;SRP=218.68;SRR=2695;TC;TR=2;TU=G;VQSLOD=10.1601;set=Intersection;sumGLbyD=14.60 20 51848430 . AT A,ATT 999 PASS AA=39;AB=0.83408;ABA=37;ABP=219.19;ABR=186;AC=14,33;AF=0.0153,0.0359;AF1=0.03062;AN=918;BL=1676;BR=1732;BVAR;BaseQRankSum=3.338;CI95=0.02212,0.03982;DP=14886;DP4=1970,1762,22,31;Dels=0.01;EL=18;EPP=3.5114;ER=21;FQ=999;FR;FS=3.004;HETAR=31;HOMA=0;HOMR=1040;HP=10;HPLen=9;HR=9;HRun=9;HU=T;INDEL;INS;InbreedingCoeff=0.1629;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.016432;LRBP=5.0085;MQ=80.05;MQ0=0;MQ0Fraction=0.0000;MQM=56.667;MQRankSum=0.325;NF;NR;NS=1071;PP;PV4=0.13,1,0.0095,0.064;RA=5318;RL=21;RPP=3.5114;RR=18;RUN=1;ReadPosRankSum=-0.493;SAB=0.46154;SAF=18;SAP=3.5114;SAR=21;SC=ACAAAACAATATTTTTTTTTC;SRB=0.4968;SRF=2642;SRP=3.4823;SRR=2676;TC;TR=9;TU=T;VQSLOD=5.7417;set=Intersection;sumGLbyD=7.57 20 51897203 . T TG 8427.20 PASS AA=237;AB=0.69846;ABA=215;ABP=246.92;ABR=498;AC=117;AF=0.1662;AN=704;BL=14961;BR=5990;BVAR;BaseQRankSum=22.203;DP=9710;Dels=0.00;EL=83;EPP=49.198;ER=154;FR;FS=9.450;HETAR=123;HOMA=9;HOMR=895;HP=5;HPLen=6;HR=6;HRun=0;HU=T;INS;InbreedingCoeff=-0.0513;IndelType=INS.NOVEL_1.Novel_G.;LEN=1;LRB=0.42819;LRBP=8344.3;MQ0Fraction=0.0291;MQM=45.861;MQRankSum=-10.426;NF;NR;NS=1027;PP;RA=4919;RL=210;RPP=309.85;RR=27;RUN=1;ReadPosRankSum=-1.843;SAB=0.29536;SAF=70;SAP=89.219;SAR=167;SC=TTTGTTTGTTTTTTGTTGTTG;SRB=0.47794;SRF=2351;SRP=23.798;SRR=2568;TC;TR=23;TU=GTTT;VQSLOD=6.2670;set=Intersection;sumGLbyD=8.99 20 52274070 . AAG A 1400.37 PASS AA=30;AB=0.74227;ABA=25;ABP=52.462;ABR=72;AC=21;AF=0.01756;AN=1196;BL=412;BR=1966;BVAR;BaseQRankSum=6.660;DEL;DP=9362;Dels=0.01;EL=16;EPP=3.2998;ER=14;FS=1.485;HETAR=18;HOMA=2;HOMR=1004;HRun=0;InbreedingCoeff=0.0317;IndelType=DEL.NumRepetitions_1.EventLength_2.RepeatExpansion_AG.;LEN=2;LRB=0.65349;LRBP=2208.2;MQ0Fraction=0.0022;MQM=46.133;MQRankSum=-4.743;NS=1024;RA=3931;RL=2;RPP=51.941;RR=28;RUN=1;ReadPosRankSum=-4.152;SAB=0.4;SAF=12;SAP=5.6161;SAR=18;SRB=0.49784;SRF=1957;SRP=3.1699;SRR=1974;VQSLOD=5.6452;set=Intersection;sumGLbyD=11.11 20 52351501 . TAC T 199.59 PASS AC=22;AF=0.0238;AN=926;BaseQRankSum=7.874;DP=22911;DP4=2146,1691,26,22;FR;FS=2.898;HP=4;HPLen=3;HR=1;HRun=0;HU=A;HaplotypeScore=18.6111;INDEL;InbreedingCoeff=-0.0326;IndelType=DEL.NumRepetitions_6.EventLength_2.RepeatExpansion_AC.;MQ0=2;MQ0Fraction=0.0007;MQRankSum=1.011;NF;NR;PP;PV4=0.88,0.14,0.16,0.24;QD=1.10;ReadPosRankSum=-1.053;SB=-306.09;SC=GACACACAAATACACACACAC;TC;TR=13;TU=AC;VQSLOD=4.0486;set=filterInVQSR-2of5 20 52447173 . CA C 503.89 PASS AC=23;AF=0.01891;AN=1216;BaseQRankSum=0.801;DP=3266;FS=2.606;HRun=2;HaplotypeScore=22.1543;InbreedingCoeff=-0.0097;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_A.;MQ=118.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-1.309;QD=2.65;ReadPosRankSum=-7.872;SB=-279.27;VQSLOD=4.1900;set=VQSR 20 52498650 . GT G 24069 PASS AA=74;AB=0.90594;ABA=57;ABP=870.4;ABR=549;AC=28;AF=0.02333;AN=1200;BL=505;BR=4514;BVAR;BaseQRankSum=-3.837;DEL;DP=9798;Dels=0.01;EL=41;EPP=4.8883;ER=33;FS=4.085;HETAR=209;HOMA=663;HOMR=121;HRun=1;InbreedingCoeff=0.0334;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.79876;LRBP=6956.6;MQ0=2;MQ0Fraction=0.0007;MQM=57.784;MQRankSum=-2.951;NS=995;RA=957;RL=8;RPP=101.72;RR=66;RUN=1;ReadPosRankSum=-14.806;SAB=0.39189;SAF=29;SAP=10.522;SAR=45;SRB=0.39916;SRF=382;SRP=87.53;SRR=575;VQSLOD=3.8710;set=filterInVQSR-2of5;sumGLbyD=2.90 20 52823602 rs11469056 CAAA C,CA,CAA,CAAAA,CAAAAA,CAAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA 14515.17 PASS AC=24,83,246,109,83,19,10,16,22,59;AF=0.02128,0.07358,0.21809,0.09663,0.07358,0.01684,0.00887,0.01418,0.01950,0.05230;AN=1128;BVAR;BaseQRankSum=4.150;DB;DEL;DP=28279;FR;FS=2.021;HP=17;HR=17;HU=A;HaplotypeScore=27.8032;INS;InbreedingCoeff=0.7740;IndelType=MULTIALLELIC_INDEL;MQ=69.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.418;NF;NR;PP;QD=7.90;RUN=1;ReadPosRankSum=-3.864;SB=-3244.40;SC=GGTCCTAAGGCAAAAAAAAAA;TC;TR=17;TU=A;VQSLOD=14.1033;set=Intersection 20 53308906 . CT C,CTT 2276 PASS AA=92;AB=0.84453;ABA=81;ABP=540.17;ABR=440;AC=53,81;AF=0.04351,0.06650;AN=1218;BL=3561;BR=4796;BVAR;BaseQRankSum=3.000;DP=11804;Dels=0.02;EL=48;EPP=3.3879;ER=44;FR;FS=13.197;HETAR=69;HOMA=3;HOMR=993;HP=11;HR=10;HRun=10;HU=T;INS;InbreedingCoeff=0.2297;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.14778;LRBP=399.32;MQ0=1;MQ0Fraction=0.0003;MQM=56.348;MQRankSum=3.154;NF;NR;NS=1065;PP;RA=5520;RL=39;RPP=7.6365;RR=53;RUN=1;ReadPosRankSum=-2.140;SAB=0.57609;SAF=53;SAP=7.6365;SAR=39;SC=AATCCAAAGTCTTTTTTTTTT;SRB=0.51576;SRF=2847;SRP=14.92;SRR=2673;TC;TR=10;TU=T;VQSLOD=2.4753;set=filterInVQSR-2of5;sumGLbyD=4.42 20 53334602 . T TG,TGG 905.13 PASS ABR=325;AC=44,22;AF=0.03624,0.01812;BVAR;BaseQRankSum=-4.608;DP=15015;FR;FS=494.901;HOMA=0;HOMR=1004;HP=1;HR=1;HU=G;HaplotypeScore=20.5023;INS;InbreedingCoeff=0.0799;IndelType=MULTIALLELIC_INDEL;MQ=116.70;MQ0=0;MQ0Fraction=0.0000;MQRankSum=8.022;NF;NR;NS=1064;PP;QD=0.35;RA=5690;RUN=1;ReadPosRankSum=-14.522;SB=-311.57;SC=AGCCATTGGCTGTTTCACTGA;SRB=0.40738;SRF=2318;SRP=426.97;SRR=3372;TC;TR=1;TU=G;VQSLOD=-2.3042;set=filterInVQSR-2of5 20 53729115 . T TG 15.48 PASS AC=1;AF=0.0015;AN=668;BaseQRankSum=-1.001;DP=1711;FS=9.048;HRun=2;HaplotypeScore=12.4681;InbreedingCoeff=-0.0320;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;MQ=131.36;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.193;QD=4.57;ReadPosRankSum=0.407;SB=-5.35;VQSLOD=4.8071;set=VQSR 20 54033830 . GTATTTTAAAATCA G 2220.86 PASS AF=0.0113;BaseQRankSum=5.506;DP=2577;Dels=0.01;FR;FS=6.533;HP=5;HPLen=4;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0032;IndelType=DEL.NumRepetitions_1.EventLength_10orMore.;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.969;NF;NR;PP;ReadPosRankSum=1.322;SC=TCAATATTTTGTATTTTAAAA;TC;TR=1;TU=T;VQSLOD=5.5145;set=Intersection;sumGLbyD=95.65 20 54375236 . GT G 626.13 PASS AA=40;AB=0.63551;ABA=39;ABP=20.078;ABR=68;AC=18;AF=0.0256;AN=702;BL=1331;BR=1743;BVAR;BaseQRankSum=9.346;DEL;DP=8568;Dels=0.02;EL=26;EPP=10.828;ER=14;FS=0.610;HETAR=21;HOMA=1;HOMR=1035;HRun=1;InbreedingCoeff=-0.0056;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.13403;LRBP=122.92;MQ0=0;MQ0Fraction=0.0000;MQM=67.125;MQRankSum=-2.537;NS=1058;RA=4870;RL=17;RPP=4.9646;RR=23;RUN=1;ReadPosRankSum=-1.229;SAB=0.525;SAF=21;SAP=3.2274;SAR=19;SRB=0.5271;SRF=2567;SRP=34.087;SRR=2303;VQSLOD=7.9228;set=Intersection;sumGLbyD=10.77 20 54457331 . G GA 1793.40 PASS AA=77;AB=0.66667;ABA=74;ABP=56.573;ABR=148;AC=33;AF=0.02687;AN=1228;BL=3834;BR=1154;BVAR;BaseQRankSum=10.572;DP=10230;Dels=0.00;EL=77;EPP=170.21;ER=0;FS=139.433;HETAR=44;HOMA=1;HOMR=1001;HRun=1;INS;InbreedingCoeff=0.0023;IndelType=INS.NOVEL_1.Novel_A.;LEN=1;LRB=0.53729;LRBP=3129.8;MQ0Fraction=0.0095;MQM=4.7013;MQRankSum=-8.116;NS=1046;RA=4009;RL=77;RPP=170.21;RR=0;RUN=1;ReadPosRankSum=-6.026;SAB=1;SAF=77;SAP=170.21;SAR=0;SRB=0.57022;SRF=2286;SRP=174.7;SRR=1723;VQSLOD=1.1887;set=filterInVQSR-2of5;sumGLbyD=5.90 20 54469810 . CA C 1697.62 PASS AA=93;AB=0.63855;ABA=90;ABP=44.53;ABR=159;AC=34;AF=0.0374;AF1=0.01719;AN=908;BL=3242;BR=5839;BVAR;BaseQRankSum=10.425;CI95=0.009317,0.02795;DEL;DP=15197;DP4=2134,1896,56,46;Dels=0.03;EL=34;EPP=17.604;ER=59;FQ=16;FR;FS=9.985;HETAR=41;HOMA=1;HOMR=1011;HP=9;HPLen=8;HR=8;HRun=8;HU=A;INDEL;InbreedingCoeff=-0.0472;IndelType=DEL.NumRepetitions_8.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.28598;LRBP=1615.8;MQ=83.37;MQ0=1;MQ0Fraction=0.0004;MQM=64.075;MQRankSum=3.036;NF;NR;NS=1053;PP;PV4=0.76,1,0.31,0.22;RA=5150;RL=28;RPP=34.975;RR=65;RUN=1;ReadPosRankSum=-0.252;SAB=0.5914;SAF=55;SAP=9.7582;SAR=38;SC=ATTGCTAAGACAAAAAAAAGA;SRB=0.50621;SRF=2607;SRP=4.7374;SRR=2543;TC;TR=8;TU=A;VQSLOD=8.3677;set=Intersection;sumGLbyD=9.90 20 54542453 . GTATA G,GTA 5109.66 PASS ABR=112;AC=66,56;AF=0.0682,0.0579;AN=968;BVAR;BaseQRankSum=17.089;DB;DEL;DP=5519;DS;Dels=0.06;FS=99.502;HOMA=15;HOMR=409;HRun=0;InbreedingCoeff=0.1584;IndelType=MULTIALLELIC_INDEL;MQ0Fraction=0.0178;MQRankSum=-6.854;NS=460;RA=864;RUN=1;ReadPosRankSum=0.855;SRB=0.79282;SRF=685;SRP=646.5;SRR=179;VQSLOD=0.6375;set=filterInVQSR-2of5;sumGLbyD=8.53 20 54629773 . CA C 1799.50 PASS AA=49;AB=0.82707;ABA=46;ABP=250.17;ABR=220;AC=9;AF=0.00746;AN=1206;BL=173;BR=2277;BVAR;BaseQRankSum=5.240;DEL;DP=8557;Dels=0.01;EL=49;EPP=109.41;ER=0;FS=32.359;HETAR=35;HOMA=1;HOMR=325;HRun=1;InbreedingCoeff=0.0892;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_A.;LEN=1;LRB=0.85878;LRBP=3926.6;MQ0Fraction=0.0602;MQM=32.163;MQRankSum=-3.926;NS=361;RA=1091;RL=0;RPP=109.41;RR=49;RUN=1;ReadPosRankSum=-4.512;SAB=0;SAF=0;SAP=109.41;SAR=49;SRB=0.49404;SRF=539;SRP=3.3467;SRR=552;VQSLOD=1.1233;set=filterInVQSR-2of5;sumGLbyD=3.54 20 54710245 . TA T 999 PASS AF=0.0084;AF1=0.0148;BaseQRankSum=3.954;CI95=0.00885,0.02212;DP=8043;DP4=2000,1849,10,7;Dels=0.01;FQ=999;FR;FS=0.000;HP=9;HPLen=6;HR=3;HRun=6;HU=A;INDEL;InbreedingCoeff=0.1181;IndelType=DEL.NumRepetitions_3.EventLength_1.RepeatExpansion_A.;MQ=78.51;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.095;NF;NR;PP;PV4=0.63,0.00056,1,1;ReadPosRankSum=-0.448;SC=CAACAAAAAATAAATAAATAA;TC;TR=15;TU=AAAT;VQSLOD=7.8129;set=Intersection;sumGLbyD=19.02 20 54968173 . A AAT,AATAT,AT,ATAT 89535.82 PASS ABR=994;AC=561,278,2,3;AF=0.50179,0.24866,0.00179,0.00268;AN=1118;BVAR;BaseQRankSum=-2.699;DB;DP=27837;DP4=168,177,1045,866;Dels=0.00;FQ=999;FR;FS=12.472;HOMA=71;HOMR=455;HP=3;HPLen=4;HR=4;HRun=0;HU=A;INDEL;INS;InbreedingCoeff=0.6391;IndelType=MULTIALLELIC_INDEL;KGPilot123;MQ=80.36;MQ0Fraction=0.0055;MQRankSum=-1.512;NF;NR;NS=913;PP;PV4=0.046,1,1,1;RA=2015;RUN=1;ReadPosRankSum=1.015;SC=GGCCACTTAAAATATATATAT;SRB=0.44864;SRF=904;SRP=49.187;SRR=1111;TC;TR=15;TU=AT;VQSLOD=9.0092;dbSNP=132;set=Intersection;sumGLbyD=42.33 20 55176688 . TA T 421.84 PASS AF=0.01322;AF1=0.01845;BaseQRankSum=5.383;CI95=0.01282,0.02564;DP=10531;DP4=1975,2017,16,14;Dels=0.01;FQ=91.2;FR;FS=7.401;HP=6;HPLen=5;HR=5;HRun=5;HU=A;INDEL;InbreedingCoeff=0.0829;IndelType=DEL.NumRepetitions_5.EventLength_1.RepeatExpansion_A.;MQ=75.80;MQ0=1;MQ0Fraction=0.0003;MQRankSum=-0.471;NF;NR;PP;PV4=0.72,1,1,1;ReadPosRankSum=0.223;SC=CTGCAAAATATAAAAATTAGG;TC;TR=5;TU=A;VQSLOD=6.6000;set=Intersection;sumGLbyD=12.15 20 55664086 . GTT ATT,G,GT,GTTT 5622.44 PASS AC=6,71,136;AF=0.00498,0.05887,0.11277;AN=1206;BVAR;BaseQRankSum=3.173;DB;DEL;DP=40384;DP4=1567,1317,54,29;Dels=0.05;FR;FS=1.949;HP=14;HR=11;HRun=11;HU=T;INDEL;INS;InbreedingCoeff=0.3490;IndelType=MIXED;MQ=77.90;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.052;NF;NR;PP;PV4=0.057,1,0.2,1.2e-05;RUN=1;ReadPosRankSum=-13.646;SC=AATTTTATTTGTTTTTTTTTT;TC;TR=11;TU=T;VQSLOD=11.7964;set=Intersection;sumGLbyD=8.09 20 56045006 . TG T 342.15 PASS AC=72;AF=0.0940;AN=766;BaseQRankSum=4.992;DP=1238;FS=1.460;HRun=7;HaplotypeScore=20.2784;InbreedingCoeff=0.1795;IndelType=DEL.NumRepetitions_7.EventLength_1.RepeatExpansion_G.;MQ=66.42;MQ0=1;MQ0Fraction=0.0008;MQRankSum=-0.937;QD=1.84;ReadPosRankSum=-4.385;SB=-320.83;VQSLOD=5.2383;set=VQSR 20 56158711 . AG A 922.47 PASS AA=18;AB=0.575;ABA=17;ABP=4.9646;ABR=23;AC=2;AF=0.0028;AN=714;BL=953;BR=808;BVAR;BaseQRankSum=3.129;DEL;DP=10462;Dels=0.01;EL=9;EPP=3.0103;ER=9;FR;FS=8.724;HETAR=4;HOMA=0;HOMR=1058;HP=1;HPLen=2;HR=2;HRun=1;HU=A;InbreedingCoeff=0.0262;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.08234;LRBP=28.936;MQ0=0;MQ0Fraction=0.0000;MQM=55.889;MQRankSum=2.052;NF;NR;NS=1062;PP;RA=6300;RL=9;RPP=3.0103;RR=9;RUN=1;ReadPosRankSum=-0.317;SAB=0.66667;SAF=12;SAP=7.3532;SAR=6;SC=TGGCCTAGCAAGCATCGTGAC;SRB=0.48143;SRF=3033;SRP=21.883;SRR=3267;TC;TR=8;TU=AAGC;VQSLOD=8.3252;set=Intersection;sumGLbyD=13.22 20 56258618 rs113670927 T C,TGC,TGTGC,TGTGTGC 37834.99 PASS ABR=441;AC=11,100,43;AF=0.0123,0.1119,0.0481;AN=894;BVAR;BaseQRankSum=19.514;DB;DP=23173;DP4=541,920,413,579;Dels=0.00;FQ=999;FR;FS=1.238;HOMA=28;HOMR=808;HP=2;HPLen=1;HR=1;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.2154;IndelType=MIXED;MQ=57.25;MQ0Fraction=0.0275;MQRankSum=-6.684;NF;NR;NS=976;PP;PV4=0.023,1,1,1;RA=3294;RUN=1;ReadPosRankSum=11.873;SC=TGCGTGTGTGTGTGTGTGTGT;SRB=0.42441;SRF=1398;SRP=166.5;SRR=1896;TC;TR=30;TU=GT;VQSLOD=6.7457;dbSNP=114;set=Intersection;sumGLbyD=21.27 20 56395857 . T TAGGCAG 6614.22 PASS AA=30;AB=0.63415;ABA=30;ABP=15.827;ABR=52;AC=14;AF=0.0197;AF1=0.03154;AN=710;BL=991;BR=1813;BVAR;BaseQRankSum=-4.589;CI95=0.02434,0.04204;DP=13879;DP4=1543,1833,12,14;Dels=0.00;EL=14;EPP=3.2998;ER=16;FQ=999;FR;FS=1.482;HETAR=11;HOMA=0;HOMR=1051;HP=1;HPLen=2;HR=2;HRun=0;HU=T;INDEL;INS;InbreedingCoeff=0.0774;IndelType=INS.NumRepetitions_2.EventLength_6.;LEN=6;LRB=0.29315;LRBP=526.27;MQ=90.42;MQ0=0;MQ0Fraction=0.0000;MQM=39.433;MQRankSum=-7.011;NF;NR;NS=1062;PP;PV4=1,1,3.7e-09,1;RA=5322;RL=9;RPP=13.433;RR=21;RUN=1;ReadPosRankSum=0.679;SAB=0.43333;SAF=13;SAP=4.1684;SAR=17;SC=AAGAGCATCTTAGGCAGAGGC;SRB=0.47294;SRF=2517;SRP=36.853;SRR=2805;TC;TR=2;TU=T;VQSLOD=8.3045;set=Intersection;sumGLbyD=68.22 20 56969289 . GTTTGT G 600.69 PASS AF=0.0056;AF1=0.007726;BaseQRankSum=2.907;CI95=0.004425,0.01327;DP=9643;DP4=1892,1749,6,3;Dels=0.00;FQ=117;FR;FS=16.601;HP=5;HPLen=3;HR=3;HRun=0;HU=T;INDEL;InbreedingCoeff=0.0236;IndelType=DEL.NumRepetitions_3.EventLength_5.;MQ=92.59;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-2.134;NF;NR;PP;PV4=0.51,1,0.07,0.3;ReadPosRankSum=0.236;SC=TAAGGACGTTGTTTGTTTTGT;TC;TR=10;TU=GTTT;VQSLOD=5.8458;set=Intersection;sumGLbyD=39.51 20 57187557 . AG A,AGG 1486.69 PASS AA=130;AB=0.55446;ABA=90;ABP=8.2132;ABR=112;AC=56,26;AF=0.0574,0.0266;AN=976;BL=3817;BR=5968;BVAR;BaseQRankSum=5.517;DEL;DP=14174;DP4=925,721,59,48;Dels=0.05;EL=52;EPP=14.302;ER=78;FR;FS=0.917;HETAR=44;HOMA=17;HOMR=864;HP=4;HPLen=4;HR=4;HRun=4;HU=G;INDEL;InbreedingCoeff=0.2856;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.21983;LRBP=1029.8;MQ=91.56;MQ0=0;MQ0Fraction=0.0000;MQM=63.631;MQRankSum=1.900;NF;NR;NS=925;PP;PV4=0.84,1,1,0.39;RA=2746;RL=44;RPP=32.476;RR=86;RUN=1;ReadPosRankSum=-0.639;SAB=0.44615;SAF=58;SAP=6.2842;SAR=72;SC=TCAGGCCCGCAGGGGTCAGGG;SRB=0.5772;SRF=1585;SRP=145.17;SRR=1161;TC;TR=4;TU=G;VQSLOD=7.7167;set=Intersection;sumGLbyD=14.85 20 57282771 . T TG 506.43 PASS AA=34;AB=0.70312;ABA=19;ABP=25.946;ABR=45;AC=34;AF=0.0373;AN=912;BL=886;BR=1938;BVAR;BaseQRankSum=3.744;DP=4276;Dels=0.00;EL=18;EPP=3.2658;ER=16;FR;FS=0.639;HETAR=17;HOMA=9;HOMR=737;HP=9;HR=8;HRun=8;HU=G;INS;InbreedingCoeff=0.2149;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.37252;LRBP=853.99;MQ0=0;MQ0Fraction=0.0000;MQM=49.706;MQRankSum=-0.051;NF;NR;NS=763;PP;RA=1822;RL=9;RPP=19.36;RR=25;RUN=1;ReadPosRankSum=-2.111;SAB=0.55882;SAF=19;SAP=4.0322;SAR=15;SC=TCGGGGGGCGTGGGGGGGGTG;SRB=0.51098;SRF=931;SRP=4.9172;SRR=891;TC;TR=8;TU=G;VQSLOD=5.7772;set=Intersection;sumGLbyD=7.95 20 57419740 rs11481507 A AT 82613.57 PASS AA=3850;AB=0.41404;ABA=1786;ABP=198.63;ABR=1262;AC=919;AF=0.75328;AN=1220;BL=140665;BR=151383;BVAR;BaseQRankSum=-27.490;DB;DP=31794;DP4=588,585,1571,1721;Dels=0.00;EL=1924;EPP=3.0126;ER=1926;FQ=999;FR;FS=2.191;HETAR=482;HOMA=454;HOMR=135;HP=3;HPLen=3;HR=3;HRun=3;HU=T;INDEL;INS;InbreedingCoeff=0.0861;IndelType=INS.NumRepetitions_3.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.036699;LRBP=857.15;MQ=123.92;MQ0=0;MQ0Fraction=0.0000;MQM=91.654;MQRankSum=3.016;NF;NR;NS=1071;PP;PV4=0.16,1,0.12,1;RA=1850;RL=1874;RPP=8.8784;RR=1976;RUN=1;ReadPosRankSum=-0.685;SAB=0.47636;SAF=1834;SAP=21.693;SAR=2016;SC=TACACTAGTGATTTAACCCTA;SRB=0.49027;SRF=907;SRP=4.5315;SRR=943;TC;TR=3;TU=T;VQSLOD=9.2768;dbSNP=126;set=Intersection;sumGLbyD=22.78 20 57558194 . CT C,CTT,CTTT 6470.30 PASS ABR=451;AC=104,161,177;AF=0.08919,0.13808,0.15180;BVAR;BaseQRankSum=1.172;DP=7985;FR;FS=2.202;HOMA=19;HOMR=778;HP=22;HR=15;HU=T;HaplotypeScore=16.1921;INS;InbreedingCoeff=0.6440;IndelType=MULTIALLELIC_INDEL;MQ=69.24;MQ0=27;MQ0Fraction=0.0109;MQRankSum=-0.003;NF;NR;NS=943;PP;QD=2.22;RA=2531;RUN=1;ReadPosRankSum=-0.104;SB=-2096.85;SC=GCCTTTTTTTCTTTTTTTTTT;SRB=0.34848;SRF=882;SRP=507.73;SRR=1649;TC;TR=15;TU=T;VQSLOD=6.5151;set=Intersection 20 57693627 . AG A 1991.90 PASS AA=52;AB=0.49462;ABA=47;ABP=3.0336;ABR=46;AC=15;AF=0.01227;AN=1222;BL=1902;BR=1478;BVAR;BaseQRankSum=-6.121;DEL;DP=26459;DP4=2647,2873,16,20;Dels=0.01;EL=25;EPP=3.1773;ER=27;FR;FS=3.135;HETAR=15;HOMA=1;HOMR=1064;HP=2;HPLen=3;HR=3;HRun=2;HU=A;INDEL;InbreedingCoeff=0.0866;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.12544;LRBP=118.51;MQ=116.26;MQ0=0;MQ0Fraction=0.0000;MQM=114.65;MQRankSum=1.942;NF;NR;NS=1080;PP;PV4=0.74,6.9e-08,1,0.38;RA=6781;RL=33;RPP=11.195;RR=19;RUN=1;ReadPosRankSum=-1.795;SAB=0.5;SAF=26;SAP=3.0103;SAR=26;SC=ATTGGAGGAAAGGCTTTTTCA;SRB=0.46247;SRF=3136;SRP=85.976;SRR=3645;TC;TR=3;TU=A;VQSLOD=8.6672;set=Intersection;sumGLbyD=13.55 20 57716287 . A AT 66.47 PASS AC=6;AF=0.00506;AN=1186;BaseQRankSum=1.369;DP=2744;FS=3.834;HRun=8;HaplotypeScore=11.2046;InbreedingCoeff=0.1196;IndelType=INS.NumRepetitions_8.EventLength_1.RepeatExpansion_T.;MQ=73.00;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-0.086;QD=2.14;ReadPosRankSum=-2.588;SB=-53.80;VQSLOD=4.2080;set=VQSR 20 58121928 rs73625057 T TGG 6649.17 PASS AA=132;AB=0.57854;ABA=110;ABP=16.996;ABR=151;AC=57;AF=0.0617;AN=924;BL=4530;BR=4790;BVAR;BaseQRankSum=-13.456;DB;DP=30353;DP4=2107,2168,61,66;Dels=0.00;EL=67;EPP=3.0761;ER=65;FR;FS=0.708;HETAR=46;HOMA=8;HOMR=1023;HP=3;HPLen=2;HR=2;HRun=2;HU=G;INDEL;INS;InbreedingCoeff=0.1241;IndelType=INS.NumRepetitions_2.EventLength_1.RepeatExpansion_G.;LEN=2;LRB=0.027897;LRBP=18.76;MQ=109.61;MQ0=1;MQ0Fraction=0.0004;MQM=79.833;MQRankSum=-0.699;NF;NR;NS=1077;PP;PV4=0.79,1,0.49,0.036;RA=5754;RL=61;RPP=4.6554;RR=71;RUN=1;ReadPosRankSum=-3.309;SAB=0.45455;SAF=60;SAP=5.3792;SAR=72;SC=GATTAGAATGTGGATATCTTT;SRB=0.48836;SRF=2810;SRP=9.7866;SRR=2944;TC;TR=4;TU=GT;VQSLOD=8.5770;set=Intersection;sumGLbyD=27.19 20 58468826 . ACAAG A 999 PASS AF=0.0014;AF1=0.003429;BaseQRankSum=4.082;CI95=0.003106,0.006211;DP=8461;DP4=2500,1817,8,2;Dels=0.01;FQ=999;FR;FS=5.034;HP=2;HPLen=1;HR=1;HRun=0;HU=C;INDEL;InbreedingCoeff=-0.0183;IndelType=DEL.NumRepetitions_1.EventLength_4.;MQ=120.69;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.141;NF;NR;PP;PV4=0.21,1,0.054,1;ReadPosRankSum=2.096;SC=ATCCTGAAACACAAGAAGAAA;TC;TR=5;TU=AC;VQSLOD=7.4928;set=Intersection;sumGLbyD=29.17 20 58731262 . TC T 999 PASS AA=21;AB=0.48649;ABA=19;ABP=3.069;ABR=18;AC=7;AF=0.0101;AF1=0.01493;AN=694;BL=939;BR=848;BVAR;BaseQRankSum=4.205;CI95=0.01106,0.02212;DEL;DP=12598;DP4=1766,1428,11,15;Dels=0.01;EL=13;EPP=5.5954;ER=8;FQ=999;FR;FS=1.796;HETAR=8;HOMA=1;HOMR=1031;HP=7;HPLen=8;HR=8;HRun=2;HU=T;INDEL;InbreedingCoeff=-0.0030;IndelType=DEL.NumRepetitions_2.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.050923;LRBP=13.073;MQ=124.57;MQ0=0;MQ0Fraction=0.0000;MQM=67.905;MQRankSum=1.103;NF;NR;NS=1040;PP;PV4=0.23,1,1,1;RA=4884;RL=10;RPP=3.1137;RR=11;RUN=1;ReadPosRankSum=-0.091;SAB=0.47619;SAF=10;SAP=3.1137;SAR=11;SC=TCATTTTTTTTCCTTGAAACT;SRB=0.58006;SRF=2833;SRP=274.9;SRR=2051;TC;TR=8;TU=T;VQSLOD=10.8783;set=Intersection;sumGLbyD=15.11 20 59181229 rs11476579 CTT C,CT,CTTT,CTTTT 7787.17 PASS AC=19,195,104,91;AF=0.01599,0.16414,0.08754,0.07660;AF1=0.2124;AN=1188;BVAR;BaseQRankSum=6.347;CI95=0.146,0.2743;DB;DEL;DP=26140;DP4=932,880,352,375;Dels=0.13;FQ=85.6;FR;FS=11.914;HP=14;HR=14;HRun=14;HU=T;INDEL;INS;InbreedingCoeff=0.4183;IndelType=MULTIALLELIC_INDEL;MQ=86.88;MQ0=0;MQ0Fraction=0.0000;MQRankSum=1.469;NF;NR;PP;PV4=0.17,1,1,1;RUN=1;ReadPosRankSum=-1.055;SC=GGTGAGAAAGCTTTTTTTTTT;TC;TR=14;TU=T;VQSLOD=7.4340;dbSNP=120;set=Intersection;sumGLbyD=7.02 20 59213979 rs112141381 G GC 9068 PASS AA=131;AB=0.47115;ABA=110;ABP=4.5136;ABR=98;AF=0.0586;AN=700;BL=5395;BR=5816;BVAR;BaseQRankSum=15.453;DB;DP=23381;DP4=2191,2184,71,49;Dels=0.00;EL=66;EPP=3.0269;ER=65;FR;FS=7.907;HETAR=35;HOMA=5;HOMR=1019;HP=2;HPLen=3;HR=3;HRun=0;HU=G;INDEL;INS;InbreedingCoeff=0.0283;IndelType=INS.NOVEL_1.Novel_C.;LEN=1;LRB=0.037552;LRBP=37.34;MQ=72.13;MQ0=0;MQ0Fraction=0.0000;MQM=54.496;MQRankSum=0.897;NF;NR;NS=1059;PP;PV4=0.052,1,0.066,1;RA=4976;RL=59;RPP=5.8117;RR=72;RUN=1;ReadPosRankSum=-0.811;SAB=0.58015;SAF=76;SAP=10.32;SAR=55;SC=GATGGACTGGGACAGTGACTC;SRB=0.49457;SRF=2461;SRP=4.2828;SRR=2515;TC;TR=3;TU=G;VQSLOD=9.3917;set=Intersection;sumGLbyD=28.58 20 59252945 . CT C,CTT 557.18 PASS AA=24;AB=0.84868;ABA=23;ABP=163.53;ABR=129;AC=21,29;AF=0.01759,0.02429;BL=1217;BR=1336;BVAR;BaseQRankSum=5.135;DP=9970;Dels=0.01;EL=13;EPP=3.3722;ER=11;FS=2.302;HETAR=21;HOMA=1;HOMR=1012;HRun=9;INS;InbreedingCoeff=0.1549;IndelType=MULTIALLELIC_INDEL;LEN=1;LRB=0.046612;LRBP=15.055;MQ0=0;MQ0Fraction=0.0000;MQM=67.208;MQRankSum=0.086;NS=1034;RA=4421;RL=11;RPP=3.3722;RR=13;RUN=1;ReadPosRankSum=-1.826;SAB=0.41667;SAF=10;SAP=4.4579;SAR=14;SRB=0.49649;SRF=2195;SRP=3.4823;SRR=2226;VQSLOD=2.8923;set=filterInVQSR-2of5;sumGLbyD=5.47 20 60016966 . CT C 42650 PASS AA=37;AB=0.97834;ABA=31;ABP=2847;ABR=1400;AC=15;AF=0.0163;AN=920;BL=2596;BR=778;BVAR;BaseQRankSum=-0.632;DEL;DP=10967;Dels=0.00;EL=14;EPP=7.7641;ER=23;FS=4.094;HETAR=421;HOMA=256;HOMR=385;HRun=1;InbreedingCoeff=-0.0051;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_T.;LEN=1;LRB=0.53883;LRBP=2130.2;MQ0=0;MQ0Fraction=0.0000;MQM=120.3;MQRankSum=-0.911;NS=1072;RA=3413;RL=31;RPP=39.691;RR=6;RUN=1;ReadPosRankSum=-12.062;SAB=0.48649;SAF=18;SAP=3.069;SAR=19;SRB=0.47407;SRF=1618;SRP=22.943;SRR=1795;VQSLOD=3.3758;set=filterInVQSR-2of5;sumGLbyD=3.27 20 60188651 . AG A 17624.52 PASS AA=462;AB=0.76548;ABA=409;ABP=1070.7;ABR=1335;AC=403;AF=0.34444;AN=1170;BL=13877;BR=25909;BVAR;BaseQRankSum=6.180;DEL;DP=9900;Dels=0.08;EL=353;EPP=282.84;ER=109;FR;FS=2699.057;HETAR=346;HOMA=26;HOMR=633;HP=3;HR=4;HRun=1;HU=A;InbreedingCoeff=-0.2900;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;LEN=1;LRB=0.30242;LRBP=7904.3;MQ0Fraction=0.0004;MQM=56.119;MQRankSum=1.644;NF;NR;NS=1005;PP;RA=3521;RL=112;RPP=269.25;RR=350;RUN=1;ReadPosRankSum=2.490;SAB=0.0064935;SAF=3;SAP=980.34;SAR=459;SC=AGGCTTCAAAAGAAAAAAAAA;SRB=0.55978;SRF=1971;SRP=112.32;SRR=1550;TC;TR=4;TU=A;VQSLOD=-34.0667;set=filterInVQSR-2of5;sumGLbyD=7.81 20 60195570 . GTACATACATACA ATACATACATACA,G,GTACATACA 20140 PASS ABR=102;AC=105,2;AF=0.08794,0.00168;AN=1194;BVAR;BaseQRankSum=-28.899;DB;DEL;DP=14347;Dels=0.02;FR;FS=52.125;HOMA=1;HOMR=1006;HP=1;HPLen=1;HR=1;HRun=0;HU=T;InbreedingCoeff=0.0695;IndelType=MIXED;MQ0Fraction=0.0007;MQRankSum=1.957;NF;NR;NS=1035;PP;RA=4759;RUN=1;ReadPosRankSum=-22.252;SAB=0.5;SAP=3.0103;SC=TGATAGATTCGTACATACATA;SRB=0.47615;SRF=2266;SRP=26.522;SRR=2493;TC;TR=21;TU=ACAT;VQSLOD=2.7673;set=filterInVQSR-2of5;sumGLbyD=19.14 20 60670601 rs72127450 AT A,ATT 6401.59 PASS AC=177,79;AF=0.16239,0.07248;AF1=0.1602;AN=1090;BVAR;BaseQRankSum=8.618;CI95=0.1106,0.2058;DB;DEL;DP=17508;DP4=1285,1094,313,259;Dels=0.10;FQ=94.1;FR;FS=0.000;HP=12;HR=12;HRun=12;HU=T;INDEL;INS;InbreedingCoeff=0.1076;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=64.73;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.620;NF;NR;PP;PV4=0.78,1,0.012,1;RUN=1;ReadPosRankSum=-1.294;SC=AGCCAGGCACATTTTTTTTTT;TC;TR=12;TU=T;VQSLOD=6.1650;dbSNP=130;set=Intersection;sumGLbyD=5.80 20 60685780 . TC T 1123.58 PASS AC=79;AF=0.07655;AN=1032;BaseQRankSum=14.949;DP=2084;FS=23.521;HRun=1;HaplotypeScore=19.7117;InbreedingCoeff=0.1356;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;MQ=53.57;MQ0=61;MQ0Fraction=0.0293;MQRankSum=-7.958;QD=4.35;ReadPosRankSum=-13.757;SB=-791.28;VQSLOD=6.3549;set=VQSR 20 60744906 rs113528167 CG C 422.53 PASS AC=48;AF=0.0732;AN=656;BaseQRankSum=17.669;DB;DP=1189;FS=0.356;HRun=1;HaplotypeScore=15.1808;InbreedingCoeff=0.2111;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_G.;MQ=82.83;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-10.455;QD=2.71;ReadPosRankSum=-16.887;SB=-326.46;VQSLOD=7.1707;set=VQSR 20 60848742 . CGT C,CGTGT 999 PASS AF=0.00980,0.01225;BaseQRankSum=5.597;DP=17065;DP4=1928,2188,17,13;Dels=0.01;FR;HP=1;HPLen=2;HR=2;HRun=0;HU=C;INDEL;InbreedingCoeff=0.2094;IndelType=MULTIALLELIC_INDEL;MQ=115.78;MQ0=0;MQ0Fraction=0.0000;MQRankSum=0.281;NF;NR;PP;PV4=0.36,0.4,0.12,0.12;ReadPosRankSum=-1.465;SB=-157.35;SC=TAGACGCTTCCGTGTGTGTGT;TC;TR=11;TU=GT;VQSLOD=1.7100;set=filterInVQSR-2of5;sumGLbyD=16.39 20 61023668 rs57452309 G GAGC 6896.67 PASS AC=115;AF=0.1445;AN=796;BaseQRankSum=12.146;DB;DP=1423;FS=5.070;HRun=0;HaplotypeScore=29.8897;InbreedingCoeff=0.0740;IndelType=INS.NOVEL_3.;MQ=77.02;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-9.005;QD=19.16;ReadPosRankSum=-17.440;SB=-3045.82;VQSLOD=4.5788;set=VQSR 20 61180519 . C CA,CT 1774.30 PASS ABR=135;AC=27,15;AF=0.02538,0.01410;BVAR;BaseQRankSum=-2.189;DP=8393;FR;FS=27.692;HOMA=2;HOMR=825;HP=6;HPLen=3;HR=3;HU=T;HaplotypeScore=19.5313;INS;InbreedingCoeff=0.0868;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=56.11;MQ0=172;MQ0Fraction=0.0667;MQRankSum=2.605;NF;NR;NS=854;PP;QD=1.99;RA=2868;RUN=1;ReadPosRankSum=-7.324;SB=-385.54;SC=TTCTTTCTTTCTTTCTTTCTT;SRB=0.32741;SRF=939;SRP=745.08;SRR=1929;TC;TR=69;TU=CTTT;VQSLOD=3.4398;set=filterInVQSR-2of5 20 61184281 . AC A 9798.10 PASS AA=24;AB=0.96507;ABA=16;ABP=863.43;ABR=442;AC=4;AF=0.00341;AN=1174;BL=349;BR=1039;BVAR;BaseQRankSum=2.048;DEL;DP=10073;Dels=0.00;EL=11;EPP=3.3722;ER=13;FS=2.097;HETAR=141;HOMA=69;HOMR=829;HRun=1;InbreedingCoeff=0.0697;IndelType=DEL.NumRepetitions_1.EventLength_1.RepeatExpansion_C.;LEN=1;LRB=0.49712;LRBP=747.85;MQ0=0;MQ0Fraction=0.0000;MQM=98.042;MQRankSum=1.881;NS=1042;RA=3625;RL=5;RPP=20.744;RR=19;RUN=1;ReadPosRankSum=-8.009;SAB=0.75;SAF=18;SAP=16.039;SAR=6;SRB=0.52662;SRF=1909;SRP=25.323;SRR=1716;VQSLOD=1.8117;set=filterInVQSR-2of5;sumGLbyD=5.55 20 62074219 . C CTAT,CTGT 2328 PASS ABR=99;AC=20,6;AF=0.01754,0.00526;BVAR;BaseQRankSum=11.221;DP=9498;DS;FS=4.510;HOMA=15;HOMR=645;HaplotypeScore=82.8868;INS;InbreedingCoeff=0.0880;IndelType=MULTIALLELIC_INDEL;LEN=3;MQ=29.88;MQ0=1378;MQ0Fraction=0.2286;MQRankSum=-5.309;NS=689;QD=0.77;RA=1679;RUN=1;ReadPosRankSum=-3.510;SAR=1;SB=-93.21;SRB=0.70697;SRF=1187;SRP=627.71;SRR=492;VQSLOD=1.8325;set=filterInVQSR-2of5 20 62304449 . CA C,CAA 6680.17 PASS AC=141,69;AF=0.12567,0.06150;AF1=0.08178;AN=1122;BVAR;BaseQRankSum=9.754;CI95=0.05088,0.1128;DEL;DP=15867;DP4=1252,1289,232,208;Dels=0.10;FQ=52.6;FR;FS=6.576;HP=11;HR=11;HRun=11;HU=A;INDEL;INS;InbreedingCoeff=0.1950;IndelType=MULTIALLELIC_INDEL;LEN=1;MQ=60.48;MQ0Fraction=0.0004;MQRankSum=-0.049;NF;NR;PP;PV4=0.2,1,1,1;RUN=1;ReadPosRankSum=-2.137;SC=GATTCTGTGTCAAAAAAAAAA;TC;TR=11;TU=A;VQSLOD=7.4714;set=Intersection;sumGLbyD=8.36 20 62804895 rs57769591 CCTT C 1148 PASS AC=8;AF=0.0085;AF1=0.002839;AN=938;BaseQRankSum=4.952;CI95=0.002212,0.006637;DB;DP=8889;DP4=2574,1668,4,8;FQ=12.3;FS=2.289;HPLen=3;HRun=0;HaplotypeScore=29.4184;INDEL;InbreedingCoeff=-0.0270;IndelType=DEL.NumRepetitions_1.EventLength_3.;MQ0=876;MQ0Fraction=0.2674;MQRankSum=-0.641;PV4=0.074,1,1,1;QD=1.03;ReadPosRankSum=0.118;SB=-65.30;VQSLOD=6.4881;dbSNP=126;set=Intersection 20 62907688 . AAT A 6629.57 PASS AC=164;AF=0.13735;AN=1194;BaseQRankSum=27.368;DP=2746;FS=5.985;HRun=0;HaplotypeScore=14.7748;InbreedingCoeff=0.1433;IndelType=DEL.NumRepetitions_2.EventLength_2.RepeatExpansion_AT.;MQ=96.65;MQ0=0;MQ0Fraction=0.0000;MQRankSum=-3.318;QD=10.81;ReadPosRankSum=0.789;SB=-2662.16;VQSLOD=6.1473;set=VQSR pysam-0.7.7/tests/vcf-examples/8.vcf0000664000076400007650000032364111754437212017127 0ustar andreasandreas##fileformat=VCFv4.0 ##FILTER= ##FILTER= ##FILTER= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##ValidationMetrics_HardyWeinbergViolations="25 (8%)" ##ValidationMetrics_HomVarViolations="0 (0%)" ##ValidationMetrics_NoCallViolations="13 (4%)" ##ValidationMetrics_PolymorphicPassingRecords="195 (75%)" ##ValidationMetrics_RecordsPassingFilters="258 (87%)" ##ValidationMetrics_RecordsProcessed=296 ##ValidationMetrics_SamplesAssayed=383 ##VariantValidationAssessor="analysis_type=VariantValidationAssessor input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[rawData/plink.renamed.sorted.fixed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub maxHardy=20.0 maxNoCall=0.05 maxHomVar=1.1" ##source=PLINK #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 20 676148 . A AC . PASS AC=0;AN=758;HW=0.00;HetPct=0.0;HomRefPct=99.0;HomVarPct=0.0;NoCallPct=1.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1342549 . A AAGAT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1366475 . CT C . PASS AC=0;AN=764;HW=0.00;HetPct=0.0;HomRefPct=99.7;HomVarPct=0.0;NoCallPct=0.3 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1550416 . C CT . PASS AC=0;AN=760;HW=0.00;HetPct=0.0;HomRefPct=99.2;HomVarPct=0.0;NoCallPct=0.8 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 3700705 . CTTTGGG C . 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T TC . 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C CCACAAGAAG . 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A AC . 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T TG . 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CG C . 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GT G . 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GTC G . 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A AT . 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ATC A . 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A AGT . 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A AC . 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T TG . 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A AC . 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GT G . 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TATTA T . PASS AC=0;AN=762;HW=0.00;HetPct=0.0;HomRefPct=99.5;HomVarPct=0.0;NoCallPct=0.5 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 61531765 . AG A . PASS AC=0;AN=766;HW=0.00;HetPct=0.0;HomRefPct=100.0;HomVarPct=0.0;NoCallPct=0.0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/vcf-examples/18.vcf0000664000076400007650000027233611754437212017214 0ustar andreasandreas##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DNA_pool_A chr1 1281168 . A G 14 . DP=37;AF1=0.6243;CI95=0.5,1;DP4=4,0,6,0;MQ=15;PV4=1,0.027,1,1 PL:GT:GQ 43,0,4:0/1:6 chr1 1281205 . T C 26 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 58,9,0:1/1:63 chr1 1281206 . G C 25 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 57,9,0:1/1:63 chr1 1922737 . G C 13.2 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=22 PL:GT:GQ 46,63,0:1/1:99 chr1 21197513 . A G 55.1 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=41 PL:GT:GQ 88,21,0:1/1:84 chr1 21343209 . T C 5.45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=14 PL:GT:GQ 37,51,0:1/1:99 chr1 22097362 . T C 4.75 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 35,9,0:1/1:63 chr1 22254012 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 22650927 . G A 48.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=24 PL:GT:GQ 81,21,0:1/1:84 chr1 23535401 . C T 40.4 . DP=25;AF1=1;CI95=0.5,1;DP4=0,16,0,5;MQ=19;PV4=1,0.2,1,1 PL:GT:GQ 73,13,0:1/1:65 chr1 23543855 . T C 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 82,18,0:1/1:90 chr1 24245107 . C G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,1,1 PL:GT:GQ 62,0,35:0/1:38 chr1 24274412 . G C 39.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=32 PL:GT:GQ 72,12,0:1/1:72 chr1 36529832 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr1 37788090 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 43120440 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=49;PV4=1,1,1,1 PL:GT:GQ 64,0,31:0/1:34 chr1 43980466 . C T 43 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=19 PL:GT:GQ 76,45,0:1/1:99 chr1 46047795 . T C 29.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=31 PL:GT:GQ 62,18,0:1/1:90 chr1 48860309 . C T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=46 PL:GT:GQ 141,18,0:1/1:90 chr1 49415599 . T C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 34,6,0:1/1:49 chr1 51601816 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 51955459 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr1 68479569 . T G 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 43,6,0:1/1:49 chr1 69032455 . A G 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 47,9,0:1/1:63 chr1 71888225 . G T 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr1 72381528 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr1 82004013 . A G 37.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 70,12,0:1/1:72 chr1 86289622 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 50,9,0:1/1:63 chr1 90267663 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr1 92699542 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr1 94867317 . G A 26.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 58,6,0:1/1:49 chr1 96428713 . C G 3.98 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=27 PL:GT:GQ 33,6,0:1/1:49 chr1 100466329 . G C 4.85 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 36,18,0:1/1:90 chr1 101909281 . G A 70 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=46;PV4=1,1,0.096,1 PL:GT:GQ 100,0,88:0/1:91 chr1 106216572 . T A 22 . DP=18;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=21 PL:GT:GQ 55,48,0:1/1:99 chr1 107901770 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 40,6,0:1/1:49 chr1 108431179 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=41 PL:GT:GQ 155,24,0:1/1:96 chr1 112005344 . C T 99 . DP=52;AF1=1;CI95=1,1;DP4=7,0,27,0;MQ=44;PV4=1,1,1,1 PL:GT:GQ 196,25,0:1/1:99 chr1 116625452 . C T 36 . DP=44;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,20;MQ=49;PV4=1,2.3e-69,0.42,1 PL:GT:GQ 66,0,179:0/1:69 chr1 118060710 . G T 6.98 . DP=8;AF1=0.4999;CI95=0.5,0.5;DP4=4,0,3,0;MQ=47;PV4=1,0.0071,1,1 PL:GT:GQ 36,0,73:0/1:39 chr1 118198177 . A G 15.9 . DP=23;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr1 118586346 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr1 120809555 . G A 20 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=6,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 50,0,106:0/1:53 chr1 130723110 . C A 20.7 . DP=8;AF1=0.5939;CI95=0.5,1;DP4=0,6,0,2;MQ=26;PV4=1,1,1,1 PL:GT:GQ 50,0,5:0/1:7 chr1 133979895 . T C 14.9 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 46,6,0:1/1:49 chr1 134977940 . C T 30 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,1,0.26,1 PL:GT:GQ 60,0,31:0/1:34 chr1 141768589 . G A 18.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=4,0,4,0;MQ=51;PV4=1,2.7e-05,1,1 PL:GT:GQ 48,0,100:0/1:51 chr1 141768590 . G A 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=2,0,4,0;MQ=50;PV4=1,0.0033,1,1 PL:GT:GQ 52,0,40:0/1:43 chr1 146506051 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 76,9,0:1/1:63 chr1 150997009 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr1 162915612 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 168455400 . A G 4.12 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,27;MQ=10 PL:GT:GQ 35,81,0:1/1:99 chr1 172784744 . T C 17.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 49,6,0:1/1:49 chr1 183627307 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 185789457 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr1 187081827 . T C 4.77 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=17 PL:GT:GQ 36,30,0:1/1:99 chr1 188468339 . C T 33 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=24 PL:GT:GQ 66,39,0:1/1:99 chr1 188595435 . C T 41.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr1 188670561 . G C 3.55 . DP=22;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=18 PL:GT:GQ 34,27,0:1/1:99 chr1 188924877 . G A 6.2 . DP=10;AF1=0.9999;CI95=0.5,1;DP4=2,0,3,0;MQ=21;PV4=1,1,1,0.3 PL:GT:GQ 35,3,0:1/1:41 chr1 190536295 . G A 68 . DP=38;AF1=1;CI95=1,1;DP4=0,0,36,0;MQ=18 PL:GT:GQ 101,108,0:1/1:99 chr1 191129408 . T A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr1 195937816 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr1 198857619 . T C 89 . DP=61;AF1=0.5;CI95=0.5,0.5;DP4=0,38,0,17;MQ=30;PV4=1,0.032,1,1 PL:GT:GQ 119,0,139:0/1:99 chr1 199057483 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 44,6,0:1/1:49 chr1 200133619 . G C 5.83 . DP=49;AF1=1;CI95=0.5,1;DP4=2,0,8,0;MQ=17;PV4=1,0.059,1,0.2 PL:GT:GQ 37,12,0:1/1:72 chr1 200729661 . A T 36 . DP=15;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=27 PL:GT:GQ 69,42,0:1/1:99 chr1 201374519 . T C 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 102,12,0:1/1:72 chr1 202811668 . G A 20.2 . DP=4;AF1=0.5163;CI95=0.5,1;DP4=0,1,0,3;MQ=24;PV4=1,1,1,1 PL:GT:GQ 50,0,12:0/1:15 chr1 202960650 . C T 16.6 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 49,12,0:1/1:72 chr1 205686638 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr1 205949857 . A G 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=21 PL:GT:GQ 33,15,0:1/1:75 chr1 209806643 . A G 13.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=21 PL:GT:GQ 46,24,0:1/1:96 chr1 209871501 . C T 25 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=5,0,4,0;MQ=41;PV4=1,7.7e-06,1,1 PL:GT:GQ 55,0,84:0/1:58 chr1 211051323 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=49 PL:GT:GQ 176,24,0:1/1:96 chr1 211389716 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr1 211868415 . G A 3.54 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=14 PL:GT:GQ 34,33,0:1/1:99 chr1 211914531 . C T 84.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 116,7,0:1/1:57 chr1 214691313 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr1 215184650 . C T 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 72,6,0:1/1:49 chr1 215995258 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr1 217031394 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr1 217986960 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr1 218086681 . A G 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 142,27,0:1/1:99 chr1 218546019 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr1 218632417 . G T 17.1 . DP=19;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=26 PL:GT:GQ 50,21,0:1/1:84 chr1 218833355 . C G 23 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=5,0,2,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 53,0,63:0/1:56 chr1 219303186 . T C 7.79 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=12 PL:GT:GQ 40,75,0:1/1:99 chr1 219517634 . G A 26.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 59,12,0:1/1:72 chr1 219590158 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 33,12,0:1/1:72 chr1 219709853 . A T 99 . DP=124;AF1=0.5;CI95=0.5,0.5;DP4=80,0,41,0;MQ=44;PV4=1,0.26,1,1 PL:GT:GQ 143,0,156:0/1:99 chr1 222457988 . A G 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 42,6,0:1/1:49 chr1 222477914 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr1 223010233 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr1 223796360 . G A 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=21 PL:GT:GQ 37,6,0:1/1:49 chr1 224273784 . A T 14.2 . DP=18;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=15 PL:GT:GQ 47,30,0:1/1:99 chr1 224454685 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 79,15,0:1/1:75 chr1 224514706 . G C 21 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=19 PL:GT:GQ 54,114,0:1/1:99 chr1 224515793 . C T 99 . DP=26;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=45 PL:GT:GQ 211,78,0:1/1:99 chr1 224692969 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr1 225607249 . A G 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr1 226923918 . C A 29.1 . DP=52;AF1=1;CI95=0.5,1;DP4=0,2,0,10;MQ=27;PV4=1,1,1,1 PL:GT:GQ 62,18,0:1/1:90 chr1 227125189 . T C 56.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=41 PL:GT:GQ 89,12,0:1/1:72 chr1 227133712 . A T 20.1 . DP=26;AF1=0.5;CI95=0.5,0.5;DP4=11,0,10,0;MQ=23;PV4=1,1,0.48,1 PL:GT:GQ 50,0,39:0/1:42 chr1 227943954 . G C 47 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 79,9,0:1/1:63 chr1 227943974 . G A 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 66,12,0:1/1:72 chr1 228067480 . A G 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr1 228067510 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr1 228088778 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=23 PL:GT:GQ 37,6,0:1/1:49 chr1 228117888 . A C 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 45,6,0:1/1:49 chr1 228139641 . T C 44.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 77,12,0:1/1:72 chr1 228577146 . T C 26 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,14;MQ=22;PV4=1,1,1,0.027 PL:GT:GQ 56,0,77:0/1:59 chr1 229001369 . C A 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 77,9,0:1/1:63 chr1 229001386 . C T 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 39,6,0:1/1:49 chr1 229348080 . T C 18.1 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=40;PV4=1,0.33,0.17,0.33 PL:GT:GQ 48,0,31:0/1:34 chr1 229439710 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=32 PL:GT:GQ 66,12,0:1/1:72 chr1 229655149 . T C 30 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=30 PL:GT:GQ 63,24,0:1/1:96 chr1 229660873 . C G 81 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=0,20,0,7;MQ=36;PV4=1,1,1,1 PL:GT:GQ 111,0,120:0/1:99 chr2a 3661005 . C G 24 . DP=13;AF1=0.5001;CI95=0.5,0.5;DP4=7,0,4,0;MQ=27;PV4=1,1.1e-05,1,1 PL:GT:GQ 54,0,34:0/1:37 chr2a 4140063 . G A 81 . DP=26;AF1=0.6671;CI95=0.5,1;DP4=18,0,8,0;MQ=24;PV4=1,8.3e-09,1,1 PL:GT:GQ 110,0,3:0/1:5 chr2a 4248440 . T C 20 . DP=28;AF1=0.5;CI95=0.5,0.5;DP4=11,0,7,0;MQ=25;PV4=1,1,0.47,1 PL:GT:GQ 50,0,92:0/1:53 chr2a 4707656 . A G 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 95,9,0:1/1:63 chr2a 5194801 . G A 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=24 PL:GT:GQ 38,6,0:1/1:49 chr2a 14111103 . A G 7.84 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=20 PL:GT:GQ 40,21,0:1/1:84 chr2a 17799746 . A G 11.3 . DP=5;AF1=0.5001;CI95=0.5,0.5;DP4=0,3,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 41,0,35:0/1:37 chr2a 24728910 . G A 45.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 78,15,0:1/1:75 chr2a 29627939 . G T 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=27 PL:GT:GQ 36,9,0:1/1:63 chr2a 31373164 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr2a 33935228 . T C 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr2a 36311856 . G A 99 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=44 PL:GT:GQ 213,87,0:1/1:99 chr2a 39281204 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr2a 41087565 . C T 74.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=38 PL:GT:GQ 107,12,0:1/1:72 chr2a 45574768 . C A 11.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=18 PL:GT:GQ 43,9,0:1/1:63 chr2a 55464464 . T C 26.1 . DP=7;AF1=0.9966;CI95=0.5,1;DP4=5,0,2,0;MQ=26;PV4=1,1,1,1 PL:GT:GQ 55,1,0:1/1:23 chr2a 63107673 . T A 70.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=34 PL:GT:GQ 103,12,0:1/1:72 chr2a 63141732 . A T 22.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 54,6,0:1/1:49 chr2a 63141910 . G A 3.41 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr2a 63141911 . C T 9.55 . DP=16;AF1=0.5031;CI95=0.5,0.5;DP4=0,2,0,3;MQ=33;PV4=1,0.43,1,1 PL:GT:GQ 39,0,19:0/1:22 chr2a 63143543 . C T 28 . DP=18;AF1=1;CI95=1,1;DP4=0,1,0,17;MQ=16;PV4=1,1,1,1 PL:GT:GQ 61,42,0:1/1:99 chr2a 66419805 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 34,15,0:1/1:75 chr2a 66563922 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr2a 67719136 . C T 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 71,6,0:1/1:49 chr2a 72781453 . A C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr2a 76733211 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 78190502 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr2a 85021209 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr2a 88554861 . A T 39 . DP=74;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=46;PV4=1,1,1,1 PL:GT:GQ 69,0,92:0/1:72 chr2a 88554877 . A G 92 . DP=90;AF1=0.5;CI95=0.5,0.5;DP4=0,23,0,13;MQ=41;PV4=1,0.3,1,1 PL:GT:GQ 122,0,128:0/1:99 chr2a 88824857 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr2a 93546675 . C T 26 . DP=6;AF1=0.5;CI95=0.5,0.5;DP4=4,0,2,0;MQ=46;PV4=1,1,1,1 PL:GT:GQ 56,0,87:0/1:59 chr2a 94788853 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr2a 96738146 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr2a 102737384 . A G 12.3 . DP=18;AF1=1;CI95=1,1;DP4=0,0,18,0;MQ=11 PL:GT:GQ 45,54,0:1/1:99 chr2a 103407172 . A G 35 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=19 PL:GT:GQ 68,24,0:1/1:96 chr2a 105774580 . T G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=30 PL:GT:GQ 135,39,0:1/1:99 chr2a 106376301 . C G 24.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 57,18,0:1/1:90 chr2a 106376315 . C T 8.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=19 PL:GT:GQ 41,18,0:1/1:90 chr2a 112422267 . C T 30 . DP=20;AF1=0.5;CI95=0.5,0.5;DP4=14,0,5,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 60,0,131:0/1:63 chr2b 3049384 . A C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049385 . G C 14.9 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 3049406 . C G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=36 PL:GT:GQ 135,18,0:1/1:90 chr2b 4213802 . T C 89.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr2b 5022895 . G A 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr2b 6037666 . G T 56 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=17 PL:GT:GQ 89,39,0:1/1:99 chr2b 13656952 . G A 19.2 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr2b 15026944 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 37,6,0:1/1:49 chr2b 23362613 . A G 5.64 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 37,15,0:1/1:75 chr2b 45947861 . C G 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=50 PL:GT:GQ 101,33,0:1/1:99 chr2b 46597824 . T C 65.6 . DP=39;AF1=0.5939;CI95=0.5,1;DP4=23,0,10,0;MQ=22;PV4=1,0.014,1,1 PL:GT:GQ 95,0,5:0/1:7 chr2b 49665191 . G T 34.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 67,21,0:1/1:84 chr2b 61001546 . A G 48 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=26 PL:GT:GQ 81,24,0:1/1:96 chr2b 88502851 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=37;PV4=1,1,0.46,1 PL:GT:GQ 33,0,34:0/1:33 chr2b 91675431 . C T 30 . DP=14;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=27 PL:GT:GQ 63,24,0:1/1:96 chr2b 91870148 . T G 67 . DP=14;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=47;PV4=1,1,1,1 PL:GT:GQ 100,31,0:1/1:99 chr2b 97066826 . G A 20.1 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=0,6,0,2;MQ=31;PV4=1,1,1,1 PL:GT:GQ 50,0,35:0/1:38 chr2b 97670822 . G A 4.85 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=18 PL:GT:GQ 36,18,0:1/1:90 chr2b 102773175 . A G 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 49,9,0:1/1:63 chr2b 109805532 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=45 PL:GT:GQ 176,24,0:1/1:96 chr2b 110841448 . A G 11.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 42,6,0:1/1:49 chr2b 123217025 . T C 31.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=37 PL:GT:GQ 64,12,0:1/1:72 chr2b 123263214 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr2b 127747292 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=52 PL:GT:GQ 100,9,0:1/1:63 chr2b 130121958 . A G 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 122,15,0:1/1:75 chr2b 130253633 . A G 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr2b 130692761 . C T 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=51 PL:GT:GQ 82,18,0:1/1:90 chr2b 130743365 . A G 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 140,15,0:1/1:75 chr2b 131553874 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=37 PL:GT:GQ 43,9,0:1/1:63 chr2b 131716894 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 137,24,0:1/1:96 chr2b 131716936 . G A 99 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=36 PL:GT:GQ 173,36,0:1/1:99 chr2b 131716952 . A G 99 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,14;MQ=36;PV4=1,1,1,1 PL:GT:GQ 152,0,43:0/1:46 chr2b 133360184 . C T 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,20;MQ=32 PL:GT:GQ 163,60,0:1/1:99 chr2b 133644741 . T A 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=27 PL:GT:GQ 49,15,0:1/1:75 chr2b 133720595 . T C 41 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=29 PL:GT:GQ 74,36,0:1/1:99 chr2b 133727192 . C T 19.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr2b 133727260 . G A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr2b 133800294 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=23 PL:GT:GQ 40,6,0:1/1:49 chr2b 134582754 . A C 56.1 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=36 PL:GT:GQ 89,21,0:1/1:84 chr2b 134582763 . G C 78 . DP=37;AF1=1;CI95=1,1;DP4=0,0,0,36;MQ=34 PL:GT:GQ 111,108,0:1/1:99 chr2b 134809668 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 527814 . C G 46 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=6,0,3,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 76,0,106:0/1:79 chr3 559510 . G A 38 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=10,0,17,0;MQ=28;PV4=1,1,0.014,1 PL:GT:GQ 68,0,111:0/1:71 chr3 879433 . T G 32 . DP=4;AF1=0.5001;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 62,0,34:0/1:37 chr3 1809645 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr3 3235812 . C T 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 38,6,0:1/1:49 chr3 3250176 . A G 83 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=32 PL:GT:GQ 116,24,0:1/1:96 chr3 5049073 . T A 99 . DP=25;AF1=0.5;CI95=0.5,0.5;DP4=16,0,9,0;MQ=39;PV4=1,1,1,1 PL:GT:GQ 136,0,129:0/1:99 chr3 5142874 . G A 99 . DP=38;AF1=1;CI95=1,1;DP4=0,0,38,0;MQ=28 PL:GT:GQ 179,114,0:1/1:99 chr3 5554864 . T C 3.54 . DP=7;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,3;MQ=27;PV4=1,1,1,1 PL:GT:GQ 31,0,35:0/1:33 chr3 5749648 . G A 21.2 . DP=26;AF1=0.7303;CI95=0.5,1;DP4=0,7,0,7;MQ=26;PV4=1,0.16,1,0.17 PL:GT:GQ 50,0,2:0/1:3 chr3 16451708 . A T 71.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 104,15,0:1/1:75 chr3 23410276 . G A 99 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 140,15,0:1/1:75 chr3 51368824 . A G 28 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 60,9,0:1/1:63 chr3 53000453 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 53000463 . A G 54 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=19 PL:GT:GQ 87,30,0:1/1:99 chr3 59077423 . C T 77.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=33 PL:GT:GQ 110,15,0:1/1:75 chr3 60040501 . T C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 43,9,0:1/1:63 chr3 64203481 . A G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 66,12,0:1/1:72 chr3 67947441 . C T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr3 76372631 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 76,9,0:1/1:63 chr3 80611316 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr3 81554381 . G T 17.6 . DP=24;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 50,12,0:1/1:72 chr3 87614647 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr3 93900455 . A T 11.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=13 PL:GT:GQ 44,15,0:1/1:75 chr3 96174457 . A G 4.11 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=24 PL:GT:GQ 34,9,0:1/1:63 chr3 96215569 . A C 3.41 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr3 96587998 . A C 7.08 . DP=9;AF1=1;CI95=1,1;DP4=0,0,6,0;MQ=17 PL:GT:GQ 39,18,0:1/1:90 chr3 99711220 . A C 12.8 . DP=11;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 42,2,0:1/1:37 chr3 99789741 . C G 99 . DP=18;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=47 PL:GT:GQ 210,51,0:1/1:99 chr3 103667651 . A C 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 33,6,0:1/1:49 chr3 104604896 . G C 55 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 87,9,0:1/1:63 chr3 104997217 . G A 33.1 . DP=18;AF1=1;CI95=1,1;DP4=1,0,16,0;MQ=34;PV4=1,3e-10,0.17,0.36 PL:GT:GQ 66,19,0:1/1:76 chr3 106097816 . A G 28 . DP=15;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=26 PL:GT:GQ 61,45,0:1/1:99 chr3 106822259 . G C 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=50 PL:GT:GQ 140,15,0:1/1:75 chr3 109946413 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 44,6,0:1/1:49 chr3 121238963 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 126248567 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 45,6,0:1/1:49 chr3 129733836 . A G 6.2 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.02,0.31,1 PL:GT:GQ 35,0,28:0/1:30 chr3 131372785 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=34 PL:GT:GQ 76,9,0:1/1:63 chr3 132290987 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=45 PL:GT:GQ 54,9,0:1/1:63 chr3 136054421 . C T 73 . DP=82;AF1=1;CI95=1,1;DP4=0,0,78,0;MQ=28 PL:GT:GQ 106,235,0:1/1:99 chr3 141075246 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 62,6,0:1/1:49 chr3 141075262 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr3 141430649 . G T 81.8 . DP=6;AF1=1;CI95=0.5,1;DP4=0,1,0,4;MQ=41;PV4=1,0.34,1,0.25 PL:GT:GQ 113,6,0:1/1:49 chr3 143617747 . G T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 54,9,0:1/1:63 chr3 163576128 . C T 5.6 . DP=4;AF1=0.7302;CI95=0.5,1;DP4=2,0,2,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 33,0,2:0/1:3 chr3 163839828 . A G 4.45 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=26 PL:GT:GQ 35,12,0:1/1:72 chr3 175839340 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr3 190193258 . G T 3.98 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr3 190777007 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr3 190970350 . A G 61 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=37 PL:GT:GQ 94,30,0:1/1:99 chr3 198686408 . G A 36.6 . DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,16;MQ=25;PV4=1,1,0.026,1 PL:GT:GQ 69,11,0:1/1:66 chr3 199277478 . T C 3.61 . DP=6;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 34,18,0:1/1:90 chr3 199780181 . G T 77 . DP=45;AF1=0.5;CI95=0.5,0.5;DP4=0,35,0,10;MQ=33;PV4=1,1,1,1 PL:GT:GQ 107,0,114:0/1:99 chr3 199889335 . A C 9.54 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=18 PL:GT:GQ 42,24,0:1/1:96 chr3 200018161 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 195475 . A G 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr4 639141 . C A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 46,6,0:1/1:49 chr4 639152 . C T 15.2 . DP=17;AF1=0.5016;CI95=0.5,0.5;DP4=0,2,0,2;MQ=33;PV4=1,1,1,1 PL:GT:GQ 45,0,22:0/1:25 chr4 986497 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=33 PL:GT:GQ 163,30,0:1/1:99 chr4 986516 . C T 55.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=37 PL:GT:GQ 88,21,0:1/1:84 chr4 1207485 . A C 14.9 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 46,6,0:1/1:49 chr4 1323502 . G A 13.2 . DP=13;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=22 PL:GT:GQ 46,33,0:1/1:99 chr4 1613521 . G A 89 . DP=16;AF1=1;CI95=1,1;DP4=0,0,16,0;MQ=32 PL:GT:GQ 122,48,0:1/1:99 chr4 1748790 . C T 38 . DP=21;AF1=0.5005;CI95=0.5,0.5;DP4=6,0,8,0;MQ=40;PV4=1,0.09,1,1 PL:GT:GQ 68,0,27:0/1:30 chr4 2255732 . T C 99 . DP=29;AF1=1;CI95=1,1;DP4=0,0,28,0;MQ=31 PL:GT:GQ 186,84,0:1/1:99 chr4 3010159 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr4 3545023 . A G 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=38 PL:GT:GQ 145,27,0:1/1:99 chr4 3586344 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 3879337 . A G 16.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr4 3940733 . A G 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr4 4410338 . T C 13.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 46,15,0:1/1:75 chr4 4796408 . T C 41 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=17 PL:GT:GQ 74,48,0:1/1:99 chr4 4796414 . A G 11.3 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,15;MQ=17 PL:GT:GQ 44,45,0:1/1:99 chr4 6436959 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr4 9494256 . T C 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=37 PL:GT:GQ 32,6,0:1/1:49 chr4 24881479 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 46,9,0:1/1:63 chr4 26128644 . A G 23 . DP=18;AF1=0.5006;CI95=0.5,0.5;DP4=8,0,10,0;MQ=22;PV4=1,1,1,1 PL:GT:GQ 53,0,26:0/1:29 chr4 42109100 . G A 17.1 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 49,9,0:1/1:63 chr4 42309652 . C T 68 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr4 46913966 . C T 9.08 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=16 PL:GT:GQ 41,12,0:1/1:72 chr4 50335142 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr4 51658550 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr4 58258023 . T C 26 . DP=5;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,2;MQ=34;PV4=1,1,1,0.05 PL:GT:GQ 56,0,32:0/1:35 chr4 59219112 . C A 42.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 75,12,0:1/1:72 chr4 62746067 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr4 67404338 . G T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=39 PL:GT:GQ 66,12,0:1/1:72 chr4 73353380 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr4 73946294 . G C 4.77 . DP=51;AF1=0.4999;CI95=0.5,0.5;DP4=0,5,0,3;MQ=40;PV4=1,0.19,0.37,0.11 PL:GT:GQ 33,0,64:0/1:36 chr4 79607484 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 82337365 . G C 90 . DP=54;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=28 PL:GT:GQ 123,48,0:1/1:99 chr4 82653801 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 34,9,0:1/1:63 chr4 87130164 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 87130176 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 43,9,0:1/1:63 chr4 91459729 . C A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr4 96130778 . G C 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,19;MQ=45 PL:GT:GQ 211,57,0:1/1:99 chr4 100709417 . A G 45.1 . DP=16;AF1=0.505;CI95=0.5,0.5;DP4=12,0,4,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 75,0,17:0/1:20 chr4 107276770 . C T 70 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=31;PV4=1,1,1,1 PL:GT:GQ 100,0,97:0/1:98 chr4 115327550 . G C 42 . DP=67;AF1=1;CI95=1,1;DP4=0,1,0,66;MQ=35;PV4=1,3.2e-24,0.13,1 PL:GT:GQ 75,162,0:1/1:99 chr4 136558502 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr4 159572459 . G A 15.1 . DP=126;AF1=0.5;CI95=0.5,0.5;DP4=0,69,0,57;MQ=39;PV4=1,4.1e-96,0.077,1 PL:GT:GQ 45,0,175:0/1:48 chr4 174968484 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr4 175030633 . T C 14.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=29 PL:GT:GQ 47,18,0:1/1:90 chr4 183410027 . G T 6.2 . DP=31;AF1=0.5003;CI95=0.5,0.5;DP4=2,0,2,0;MQ=45;PV4=1,0.035,1,0.21 PL:GT:GQ 35,0,28:0/1:30 chr4 190907368 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr4 192175690 . A G 76.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=0,3,0,4;MQ=35;PV4=1,1,1,1 PL:GT:GQ 105,0,0:1/1:10 chr4 192673268 . G A 14.2 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=22 PL:GT:GQ 47,27,0:1/1:99 chr4 192943966 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr4 195460104 . C G 23.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=19 PL:GT:GQ 56,24,0:1/1:96 chr4 198277830 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 170098 . A G 13 . DP=12;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 44,6,0:1/1:49 chr5 395814 . T C 4.77 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,2;MQ=36;PV4=1,1,0.48,1 PL:GT:GQ 33,0,33:0/1:33 chr5 414024 . T A 10.4 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20 PL:GT:GQ 42,9,0:1/1:63 chr5 496767 . T C 13.9 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr5 805676 . C G 45 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=32 PL:GT:GQ 78,51,0:1/1:99 chr5 1252896 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr5 1418370 . G A 3.65 . DP=8;AF1=0.7301;CI95=0.5,1;DP4=4,0,4,0;MQ=13;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr5 1494911 . G C 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr5 1494932 . C T 6.98 . DP=8;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=46;PV4=1,0.1,0.077,1 PL:GT:GQ 36,0,31:0/1:33 chr5 1506037 . T C 24.1 . DP=24;AF1=1;CI95=0.5,1;DP4=11,0,13,0;MQ=16;PV4=1,1,1,1 PL:GT:GQ 55,5,0:1/1:46 chr5 1509406 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr5 1733649 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,25;MQ=47 PL:GT:GQ 212,75,0:1/1:99 chr5 1747304 . A G 12.3 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 45,36,0:1/1:99 chr5 1747308 . C A 44 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=19 PL:GT:GQ 77,36,0:1/1:99 chr5 3519783 . C T 21.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 54,24,0:1/1:96 chr5 4101593 . A G 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr5 7204332 . T A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=24 PL:GT:GQ 34,6,0:1/1:49 chr5 11510398 . A C 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=51;PV4=1,1,0,1 PL:GT:GQ 64,0,31:0/1:34 chr5 15406720 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 36,6,0:1/1:49 chr5 25152417 . C A 10.9 . DP=28;AF1=0.5718;CI95=0.5,1;DP4=0,2,0,6;MQ=25;PV4=1,1,0.21,1 PL:GT:GQ 40,0,6:0/1:8 chr5 39072637 . A G 35.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=50 PL:GT:GQ 68,15,0:1/1:75 chr5 46022699 . G A 44 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=35 PL:GT:GQ 76,9,0:1/1:63 chr5 55664181 . C G 10.4 . DP=8;AF1=0.9999;CI95=0.5,1;DP4=3,0,5,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 40,3,0:1/1:41 chr5 56253386 . T C 50.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=36 PL:GT:GQ 83,21,0:1/1:84 chr5 56253447 . C T 42.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=45 PL:GT:GQ 75,12,0:1/1:72 chr5 71950166 . G T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr5 72703090 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr5 73570280 . G T 5.45 . DP=41;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=15 PL:GT:GQ 37,123,0:1/1:99 chr5 73701762 . G T 40.8 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 72,6,0:1/1:49 chr5 76956867 . T C 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 41,6,0:1/1:49 chr5 79097961 . C G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 54,9,0:1/1:63 chr5 87026167 . T C 22 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 97680525 . T C 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 33,12,0:1/1:72 chr5 100674737 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr5 105389966 . T C 3.52 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=15 PL:GT:GQ 33,9,0:1/1:63 chr5 109998341 . A C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr5 120629105 . C T 6.79 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 37,6,0:1/1:49 chr5 128383954 . C T 23 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,3.3e-07,1,1 PL:GT:GQ 53,0,98:0/1:56 chr5 133925142 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr5 135375404 . T C 11.8 . DP=6;AF1=1;CI95=0.5,1;DP4=1,0,3,0;MQ=31;PV4=1,0.03,1,1 PL:GT:GQ 42,4,0:1/1:45 chr5 136498281 . T G 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr5 136717285 . A G 82.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 115,12,0:1/1:72 chr5 136910734 . G A 62 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,13;MQ=23;PV4=1,1,1,1 PL:GT:GQ 95,31,0:1/1:99 chr5 141208149 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr5 148056348 . C A 37.1 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=38;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr5 151941534 . G T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 79,12,0:1/1:72 chr5 159967229 . G C 22.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 55,12,0:1/1:72 chr5 174024541 . T G 29.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,2,0:1/1:37 chr5 175525290 . A G 3.27 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=20 PL:GT:GQ 33,12,0:1/1:72 chr5 175988954 . A C 14.2 . DP=23;AF1=0.5;CI95=0.5,0.5;DP4=0,6,0,4;MQ=47;PV4=1,1,0.2,1 PL:GT:GQ 44,0,76:0/1:47 chr5 176782226 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr5 179132834 . C G 99 . DP=28;AF1=1;CI95=1,1;DP4=0,0,0,28;MQ=41 PL:GT:GQ 207,84,0:1/1:99 chr5 180155809 . G C 3.01 . DP=36;AF1=0.4997;CI95=0.5,0.5;DP4=25,0,9,0;MQ=35;PV4=1,1e-15,1,1 PL:GT:GQ 30,0,121:0/1:33 chr5 181282819 . T G 38.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,2,0,9;MQ=23;PV4=1,1,1,1 PL:GT:GQ 71,14,0:1/1:70 chr5 182426125 . G C 29 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 61,9,0:1/1:63 chr5 182443682 . G A 3.69 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=21 PL:GT:GQ 34,15,0:1/1:75 chr5 183008993 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr5 183312016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr6_cox_hap1 519146 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 49,9,0:1/1:63 chr6_cox_hap1 687497 . A G 33 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,0.0016,1,1 PL:GT:GQ 63,3,0:1/1:41 chr6_qbl_hap2 120066 . T C 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 139,27,0:1/1:99 chr6 277954 . C T 53 . DP=41;AF1=1;CI95=1,1;DP4=4,0,37,0;MQ=19;PV4=1,1,0.3,1 PL:GT:GQ 86,49,0:1/1:99 chr6 593158 . A G 4.61 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 34,6,0:1/1:49 chr6 2865562 . T G 25 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=23 PL:GT:GQ 58,27,0:1/1:99 chr6 3751403 . G A 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=32 PL:GT:GQ 75,15,0:1/1:75 chr6 3884989 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 4127278 . A T 13.9 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr6 5887783 . C G 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 142,21,0:1/1:84 chr6 5887811 . C T 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=34 PL:GT:GQ 88,21,0:1/1:84 chr6 6937170 . G C 99 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,47;MQ=28 PL:GT:GQ 157,141,0:1/1:99 chr6 7262317 . C T 13.2 . DP=50;AF1=0.5;CI95=0.5,0.5;DP4=21,0,9,0;MQ=36;PV4=1,4e-05,0.17,0.26 PL:GT:GQ 43,0,158:0/1:46 chr6 7533214 . A G 10.4 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=26 PL:GT:GQ 42,9,0:1/1:63 chr6 20979907 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr6 22321632 . A G 41 . DP=5;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=46;PV4=1,0.24,0.19,0.33 PL:GT:GQ 71,0,28:0/1:31 chr6 25352296 . G A 7.8 . DP=4;AF1=0.5003;CI95=0.5,0.5;DP4=0,1,0,3;MQ=38;PV4=1,1,0.16,1 PL:GT:GQ 37,0,28:0/1:30 chr6 26298040 . T A 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=48;PV4=1,1,0.21,0.33 PL:GT:GQ 64,0,31:0/1:34 chr6 33428755 . G A 70 . DP=14;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=32 PL:GT:GQ 103,27,0:1/1:99 chr6 39512099 . G A 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=50 PL:GT:GQ 88,21,0:1/1:84 chr6 39961094 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 40452120 . A G 40.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr6 43204766 . A G 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=51 PL:GT:GQ 176,24,0:1/1:96 chr6 52696512 . C T 70 . DP=76;AF1=0.5;CI95=0.5,0.5;DP4=0,34,0,42;MQ=18;PV4=1,0.11,1,1 PL:GT:GQ 100,0,51:0/1:54 chr6 53785550 . A G 99 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=46 PL:GT:GQ 190,30,0:1/1:99 chr6 53897484 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr6 57038290 . C T 10.2 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 41,6,0:1/1:49 chr6 62925087 . G C 35 . DP=5;AF1=0.5008;CI95=0.5,0.5;DP4=1,0,4,0;MQ=36;PV4=1,1,0.2,1 PL:GT:GQ 65,0,25:0/1:28 chr6 62925094 . T C 25.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 58,15,0:1/1:75 chr6 70834405 . G A 72.1 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=29 PL:GT:GQ 105,21,0:1/1:84 chr6 71026058 . C T 48.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=42 PL:GT:GQ 81,18,0:1/1:90 chr6 74420752 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 76,9,0:1/1:63 chr6 77498624 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 48,6,0:1/1:49 chr6 80416836 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 113611590 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr6 119308431 . T C 38.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 71,12,0:1/1:72 chr6 151758592 . T C 3.07 . DP=17;AF1=0.9966;CI95=0.5,1;DP4=0,8,0,9;MQ=13;PV4=1,1,1,1 PL:GT:GQ 29,1,0:1/1:23 chr6 151759358 . A G 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=12,0,15,0;MQ=44;PV4=1,1,1,0.19 PL:GT:GQ 171,0,128:0/1:99 chr6 154741755 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr6 161061053 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 40,6,0:1/1:49 chr6 161474189 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 36,6,0:1/1:49 chr6 164304657 . C T 10.4 . DP=63;AF1=0.5;CI95=0.5,0.5;DP4=0,29,0,19;MQ=22;PV4=1,7.7e-11,1,0.049 PL:GT:GQ 40,0,37:0/1:38 chr6 164703105 . T C 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=40 PL:GT:GQ 165,30,0:1/1:99 chr6 167518328 . A G 78 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=27,0,14,0;MQ=33;PV4=1,0.026,0.43,0.056 PL:GT:GQ 108,0,149:0/1:99 chr6 169906323 . G A 41.8 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr6 171893912 . G A 69.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=33 PL:GT:GQ 102,15,0:1/1:75 chr6 173631604 . A G 6.98 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=4,0,3,0;MQ=37;PV4=1,0.069,1,1 PL:GT:GQ 36,0,34:0/1:35 chr7 835856 . C T 27.5 . DP=13;AF1=0.9998;CI95=0.5,1;DP4=4,0,6,0;MQ=23;PV4=1,0.46,1,1 PL:GT:GQ 57,2,0:1/1:37 chr7 1046005 . C T 11.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=36 PL:GT:GQ 43,9,0:1/1:63 chr7 1564339 . C T 71 . DP=66;AF1=0.5;CI95=0.5,0.5;DP4=36,0,24,0;MQ=29;PV4=1,1,0.35,1 PL:GT:GQ 101,0,134:0/1:99 chr7 1806266 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr7 1936013 . G T 7.77 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=17 PL:GT:GQ 39,9,0:1/1:63 chr7 2319532 . C A 4.11 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=14 PL:GT:GQ 34,9,0:1/1:63 chr7 2682121 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr7 3248116 . T C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=37;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr7 3624766 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr7 5291140 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=37 PL:GT:GQ 45,6,0:1/1:49 chr7 5314457 . C A 3.56 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=18 PL:GT:GQ 34,24,0:1/1:95 chr7 5595072 . T A 79 . DP=13;AF1=0.5;CI95=0.5,0.5;DP4=8,0,5,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 109,0,57:0/1:60 chr7 5646060 . G C 7.79 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=10 PL:GT:GQ 40,30,0:1/1:99 chr7 6056816 . C G 7.08 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=23;PV4=1,1,1,1 PL:GT:GQ 35,1,0:1/1:23 chr7 6412641 . C T 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr7 6766874 . A G 34.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=43 PL:GT:GQ 67,15,0:1/1:75 chr7 8482729 . C T 5.08 . DP=16;AF1=0.8276;CI95=0.5,1;DP4=3,0,3,0;MQ=22;PV4=1,1,1,0.19 PL:GT:GQ 32,0,1:1/1:5 chr7 9238362 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr7 9687781 . G A 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,12;MQ=48;PV4=1,6.5e-38,1,1 PL:GT:GQ 63,0,170:0/1:66 chr7 9752803 . A T 14.2 . DP=17;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 47,27,0:1/1:99 chr7 10240910 . T C 45.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 78,12,0:1/1:72 chr7 11046187 . C T 86.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=47 PL:GT:GQ 119,12,0:1/1:72 chr7 11548207 . C G 14.6 . DP=13;AF1=1;CI95=0.5,1;DP4=6,1,0,5;MQ=18;PV4=0.015,1,1,1 PL:GT:GQ 46,7,0:1/1:57 chr7 11580317 . C T 42 . DP=12;AF1=1;CI95=1,1;DP4=0,1,0,10;MQ=22;PV4=1,1,1,1 PL:GT:GQ 75,23,0:1/1:92 chr7 11585384 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr7 13498356 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 73,6,0:1/1:49 chr7 13500887 . G A 15.1 . DP=11;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=22 PL:GT:GQ 48,30,0:1/1:99 chr7 13827079 . C T 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr7 14403976 . T G 59 . DP=30;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 92,24,0:1/1:96 chr7 14756588 . A G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,5.3e-18,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 14756619 . T G 44 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=5,0,10,0;MQ=44;PV4=1,6.4e-10,1,1 PL:GT:GQ 74,0,70:0/1:72 chr7 36734598 . A C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734599 . A T 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 42,6,0:1/1:49 chr7 36734603 . G C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=40 PL:GT:GQ 40,6,0:1/1:49 chr7 40634921 . A C 55 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=39 PL:GT:GQ 88,39,0:1/1:99 chr7 48271285 . A T 73 . DP=15;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=25 PL:GT:GQ 106,30,0:1/1:99 chr7 56264700 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr7 62326003 . C A 26.1 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 59,18,0:1/1:90 chr7 109468934 . T G 5.13 . DP=10;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=39;PV4=1,0.031,1,1 PL:GT:GQ 33,2,0:1/1:37 chr7 110208327 . C G 16.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 48,6,0:1/1:49 chr7 125654934 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=27 PL:GT:GQ 34,9,0:1/1:63 chr7 125770209 . A C 32 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=11,0,13,0;MQ=34;PV4=1,0.00017,0.16,0.22 PL:GT:GQ 62,0,105:0/1:65 chr7 125770265 . G C 36 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,5,0,5;MQ=48;PV4=1,0.0047,0.016,0.035 PL:GT:GQ 66,0,110:0/1:69 chr7 126687042 . A G 21.1 . DP=36;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=22 PL:GT:GQ 54,21,0:1/1:84 chr7 132292897 . G T 99 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=43 PL:GT:GQ 167,21,0:1/1:84 chr7 132334562 . A C 23 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=23 PL:GT:GQ 56,30,0:1/1:99 chr7 132431838 . C T 13.3 . DP=5;AF1=1;CI95=0.5,1;DP4=1,0,4,0;MQ=23;PV4=1,1,1,1 PL:GT:GQ 44,5,0:1/1:46 chr7 136324945 . T C 13.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 46,12,0:1/1:72 chr7 136957634 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr7 141746871 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 40,6,0:1/1:49 chr7 146831870 . C T 4.77 . DP=14;AF1=0.5003;CI95=0.5,0.5;DP4=1,0,3,0;MQ=37;PV4=1,0.0029,0.28,1 PL:GT:GQ 33,0,28:0/1:30 chr7 147142770 . T C 45 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=31 PL:GT:GQ 77,9,0:1/1:63 chr7 147713906 . C T 4.77 . DP=8;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,4,0;MQ=35;PV4=1,8.9e-06,0.48,0.27 PL:GT:GQ 33,0,29:0/1:31 chr7 148742642 . G A 68 . DP=14;AF1=0.5032;CI95=0.5,0.5;DP4=4,0,10,0;MQ=28;PV4=1,1,1,1 PL:GT:GQ 98,0,19:0/1:22 chr7 148879148 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr7 149484407 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr7 152444478 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 44,6,0:1/1:49 chr7 154106613 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr7 154776891 . G T 14.4 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr7 155882061 . A C 29 . DP=24;AF1=0.502;CI95=0.5,0.5;DP4=0,1,0,4;MQ=46;PV4=1,0.018,0.15,0.29 PL:GT:GQ 59,0,21:0/1:24 chr7 155956844 . G C 23 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,4;MQ=38;PV4=1,1,0.38,1 PL:GT:GQ 53,0,103:0/1:56 chr7 156277694 . G A 62 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=46 PL:GT:GQ 95,24,0:1/1:96 chr7 156720588 . T C 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr7 156807649 . T C 3.01 . DP=30;AF1=0.4997;CI95=0.5,0.5;DP4=0,4,0,3;MQ=43;PV4=1,0.16,0.15,1 PL:GT:GQ 30,0,72:0/1:33 chr7 157331292 . G T 43.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=34 PL:GT:GQ 76,21,0:1/1:84 chr7 157382957 . T C 33.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr8 556382 . A G 37.1 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=31;PV4=1,1,1,1 PL:GT:GQ 66,1,0:1/1:23 chr8 1661673 . T C 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 7379751 . C A 6.24 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 38,21,0:1/1:84 chr8 8160505 . A T 68.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 101,12,0:1/1:72 chr8 8160508 . C T 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 57,12,0:1/1:72 chr8 16781011 . A G 55.5 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=34 PL:GT:GQ 88,12,0:1/1:72 chr8 18716499 . A T 20 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=0,4,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 50,0,52:0/1:51 chr8 23326483 . A G 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 92,9,0:1/1:63 chr8 25842819 . T A 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 43,6,0:1/1:49 chr8 26300279 . T C 34 . DP=44;AF1=1;CI95=1,1;DP4=0,0,41,0;MQ=21 PL:GT:GQ 67,123,0:1/1:99 chr8 29673470 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 73,6,0:1/1:49 chr8 29673473 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=41 PL:GT:GQ 40,6,0:1/1:49 chr8 31685466 . C T 34 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=10,0,5,0;MQ=28;PV4=1,0.072,1,0.36 PL:GT:GQ 64,0,50:0/1:53 chr8 37378739 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr8 51325952 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr8 59221963 . G A 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr8 62764995 . T G 20 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=32 PL:GT:GQ 52,9,0:1/1:63 chr8 63157426 . C G 41.6 . DP=22;AF1=1;CI95=0.5,1;DP4=0,7,0,15;MQ=19;PV4=1,1,1,0.25 PL:GT:GQ 74,11,0:1/1:66 chr8 68710444 . G A 30 . DP=5;AF1=0.6671;CI95=0.5,1;DP4=3,0,2,0;MQ=32;PV4=1,1,1,1 PL:GT:GQ 59,0,3:0/1:5 chr8 76416560 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=46 PL:GT:GQ 122,12,0:1/1:72 chr8 81425275 . T G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=50 PL:GT:GQ 100,9,0:1/1:63 chr8 89842286 . G C 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 34,6,0:1/1:49 chr8 100926281 . G A 38 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 70,9,0:1/1:63 chr8 102746002 . G C 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr8 107850176 . C T 43.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=45 PL:GT:GQ 76,18,0:1/1:90 chr8 109966441 . T C 27.3 . DP=9;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=38 PL:GT:GQ 60,15,0:1/1:75 chr8 118811716 . G T 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=50 PL:GT:GQ 155,18,0:1/1:90 chr8 119440254 . A T 58.5 . DP=5;AF1=0.8277;CI95=0.5,1;DP4=2,0,3,0;MQ=34;PV4=1,1,1,0.14 PL:GT:GQ 87,0,1:1/1:5 chr8 121236024 . G A 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 71,6,0:1/1:49 chr8 125489079 . C T 13 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 128502549 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 128502551 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr8 130951113 . G A 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=19 PL:GT:GQ 34,6,0:1/1:49 chr8 135307123 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 36,6,0:1/1:49 chr8 138814155 . C T 57.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 90,18,0:1/1:90 chr8 140566111 . A G 18.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=15 PL:GT:GQ 51,36,0:1/1:99 chr8 141586480 . T G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr8 143376712 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr8 150662729 . T C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr8 150741294 . A G 25.1 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=34 PL:GT:GQ 58,18,0:1/1:90 chr8 150975618 . A G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr8 151580103 . T C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20 PL:GT:GQ 36,6,0:1/1:49 chr8 151634410 . G T 48 . DP=17;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,5;MQ=39;PV4=1,0.072,1,1 PL:GT:GQ 78,0,125:0/1:81 chr8 151709267 . G A 91.1 . DP=8;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=40;PV4=1,1,0.28,0.37 PL:GT:GQ 121,0,16:0/1:19 chr8 152636420 . G A 8.75 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=0,1,0,2;MQ=30;PV4=1,1,1,1 PL:GT:GQ 37,1,0:1/1:23 chr8 152706967 . G A 3.01 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=16 PL:GT:GQ 33,30,0:1/1:99 chr8 152786522 . T C 80.1 . DP=16;AF1=0.5102;CI95=0.5,0.5;DP4=0,4,0,12;MQ=31;PV4=1,0.25,1,1 PL:GT:GQ 110,0,14:0/1:17 chr8 152863132 . T G 5.44 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=30 PL:GT:GQ 36,9,0:1/1:63 chr9 23235268 . C T 12 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 43,6,0:1/1:49 chr9 26391176 . T C 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 47,6,0:1/1:49 chr9 26868232 . C G 63 . DP=20;AF1=0.5025;CI95=0.5,0.5;DP4=7,0,13,0;MQ=22;PV4=1,0.2,1,0.44 PL:GT:GQ 93,0,20:0/1:23 chr9 34223668 . C T 22 . DP=16;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,7;MQ=27;PV4=1,0.14,0.34,1 PL:GT:GQ 52,0,79:0/1:55 chr9 39696645 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 40654130 . T G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr9 41145321 . T G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 79,12,0:1/1:72 chr9 42273483 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr9 55633192 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 58705807 . T C 70 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=24 PL:GT:GQ 103,30,0:1/1:99 chr9 61697149 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 63152790 . A C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr9 63703913 . C G 90.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=38 PL:GT:GQ 123,21,0:1/1:84 chr9 65116068 . T C 70 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=49 PL:GT:GQ 103,39,0:1/1:99 chr9 71266598 . C A 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 33,6,0:1/1:49 chr9 73188677 . G T 52 . DP=294;AF1=1;CI95=1,1;DP4=44,0,245,0;MQ=33;PV4=1,0.28,0.0092,1 PL:GT:GQ 85,147,0:1/1:99 chr9 78854179 . G T 22 . DP=97;AF1=0.5;CI95=0.5,0.5;DP4=21,0,12,0;MQ=44;PV4=1,0.02,0.032,0.0033 PL:GT:GQ 52,0,158:0/1:55 chr9 82964679 . A C 13.2 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=36 PL:GT:GQ 45,9,0:1/1:63 chr9 84124545 . G T 57 . DP=11;AF1=0.5;CI95=0.5,0.5;DP4=2,0,3,0;MQ=49;PV4=1,1,0.024,1 PL:GT:GQ 87,0,59:0/1:62 chr9 86552862 . C T 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=26 PL:GT:GQ 47,15,0:1/1:75 chr9 87548941 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr9 89021101 . G A 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr9 90447825 . G A 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 40,6,0:1/1:49 chr9 92462035 . C A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 40,6,0:1/1:49 chr9 93077294 . T G 5.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 36,9,0:1/1:63 chr9 93998137 . G A 68 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=46 PL:GT:GQ 100,9,0:1/1:63 chr9 93998148 . C T 21.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=36 PL:GT:GQ 54,15,0:1/1:75 chr9 95028964 . C A 99 . DP=83;AF1=0.5;CI95=0.5,0.5;DP4=0,57,0,26;MQ=32;PV4=1,9.3e-08,1,0.092 PL:GT:GQ 134,0,120:0/1:99 chr9 103829155 . A G 33 . DP=96;AF1=1;CI95=1,1;DP4=0,0,96,0;MQ=16 PL:GT:GQ 66,255,0:1/1:99 chr9 104981331 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 73,6,0:1/1:49 chr9 111070656 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr9 117395657 . T C 16.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 49,15,0:1/1:75 chr9 117718907 . A G 46.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=29 PL:GT:GQ 79,18,0:1/1:90 chr9 119149161 . T C 3.14 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr9 124528802 . G A 78 . DP=23;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=25 PL:GT:GQ 111,39,0:1/1:99 chr9 126707903 . G A 26 . DP=37;AF1=0.5;CI95=0.5,0.5;DP4=0,21,0,8;MQ=46;PV4=1,2.6e-07,0.21,0.42 PL:GT:GQ 56,0,175:0/1:59 chr9 128700686 . C G 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 66,12,0:1/1:72 chr9 129084077 . G A 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr9 129116900 . A T 20 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 52,9,0:1/1:63 chr9 130290720 . C G 21.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=42 PL:GT:GQ 53,6,0:1/1:49 chr9 130306057 . C G 71 . DP=14;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=28 PL:GT:GQ 104,42,0:1/1:99 chr9 130528990 . G A 99 . DP=31;AF1=1;CI95=1,1;DP4=0,0,31,0;MQ=27 PL:GT:GQ 174,93,0:1/1:99 chr9 130529002 . A T 7.79 . DP=30;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=15 PL:GT:GQ 40,33,0:1/1:99 chr9 130639996 . A G 8.44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 39,6,0:1/1:49 chr9 130704890 . A G 3.27 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=26 PL:GT:GQ 33,12,0:1/1:72 chr9 130708345 . G A 13.3 . DP=11;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=38;PV4=1,0.096,1,1 PL:GT:GQ 42,1,0:1/1:23 chr9 131001601 . T A 3.98 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 33,6,0:1/1:49 chr9 131058539 . T A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 44,6,0:1/1:49 chr9 131808965 . C T 42 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 75,27,0:1/1:99 chr9 132551867 . C T 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 49,9,0:1/1:63 chr9 132685120 . A G 4.75 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 35,9,0:1/1:63 chr9 133175050 . A G 18.1 . DP=30;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=20 PL:GT:GQ 51,51,0:1/1:99 chr9 133584978 . A G 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=45 PL:GT:GQ 212,75,0:1/1:99 chr9 133661895 . A G 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 138,42,0:1/1:99 chr9 133670376 . T C 68 . DP=19;AF1=1;CI95=1,1;DP4=0,1,0,16;MQ=39;PV4=1,1.4e-20,1,1 PL:GT:GQ 101,39,0:1/1:99 chr9 133843777 . T C 99 . DP=9;AF1=0.5129;CI95=0.5,0.5;DP4=1,0,8,0;MQ=43;PV4=1,1,1,1 PL:GT:GQ 154,0,13:0/1:16 chr9 134017265 . G C 3.27 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=13 PL:GT:GQ 33,12,0:1/1:72 chr9 134105563 . T C 34.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=39 PL:GT:GQ 67,18,0:1/1:90 chr9 134608906 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr9 134861929 . T A 9.49 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 41,9,0:1/1:63 chr10 796662 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 54,9,0:1/1:63 chr10 1216716 . T A 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr10 1220781 . G A 21 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=18 PL:GT:GQ 54,27,0:1/1:99 chr10 1225208 . T C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=47 PL:GT:GQ 100,9,0:1/1:63 chr10 1727946 . T C 14.2 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 47,21,0:1/1:84 chr10 5986542 . T C 83 . DP=93;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 116,30,0:1/1:99 chr10 6436277 . G A 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 36,6,0:1/1:49 chr10 7704114 . C A 35 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=0,2,0,4;MQ=29;PV4=1,0.27,1,0.27 PL:GT:GQ 65,3,0:1/1:41 chr10 10881734 . A G 9.52 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=4,0,5,0;MQ=42;PV4=1,0.0026,0.14,1 PL:GT:GQ 39,0,91:0/1:42 chr10 13099383 . G A 27.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 60,12,0:1/1:72 chr10 15764077 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 43,9,0:1/1:63 chr10 18091502 . T C 47 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 79,9,0:1/1:63 chr10 19645913 . A T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 47,6,0:1/1:49 chr10 22845062 . C T 18.1 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=18 PL:GT:GQ 51,21,0:1/1:84 chr10 28282802 . T C 69 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=42 PL:GT:GQ 102,36,0:1/1:99 chr10 28496872 . T G 8.44 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 39,6,0:1/1:49 chr10 32746793 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 73,6,0:1/1:49 chr10 41437604 . T G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr10 43051239 . C T 6.98 . DP=3;AF1=0.5001;CI95=0.5,0.5;DP4=1,0,2,0;MQ=40;PV4=1,0.33,0.33,1 PL:GT:GQ 36,0,31:0/1:33 chr10 44455192 . C T 4.41 . DP=6;AF1=0.8276;CI95=0.5,1;DP4=0,3,0,3;MQ=21;PV4=1,1,1,1 PL:GT:GQ 31,0,1:1/1:5 chr10 48387336 . A G 13 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr10 51561705 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr10 51561712 . C G 39.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 71,6,0:1/1:49 chr10 55617954 . G A 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 39,6,0:1/1:49 chr10 55718281 . T A 3.41 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=32 PL:GT:GQ 32,6,0:1/1:49 chr10 55888771 . T C 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr10 56025569 . C G 34.1 . DP=3;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,2;MQ=39;PV4=1,1,1,1 PL:GT:GQ 64,0,16:0/1:19 chr10 57384943 . G T 84 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=16,0,13,0;MQ=26;PV4=1,0.015,1,1 PL:GT:GQ 114,0,110:0/1:99 chr10 59873077 . T G 49 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=42 PL:GT:GQ 82,24,0:1/1:96 chr10 61329572 . C T 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 47,6,0:1/1:49 chr10 63790636 . T G 32.1 . DP=19;AF1=1;CI95=1,1;DP4=1,0,10,0;MQ=28;PV4=1,0.14,1,1 PL:GT:GQ 65,22,0:1/1:88 chr10 64466048 . C G 18.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=28 PL:GT:GQ 51,18,0:1/1:90 chr10 65053440 . G T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=39 PL:GT:GQ 153,30,0:1/1:99 chr10 65407358 . C G 84.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 117,15,0:1/1:75 chr10 65605291 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr10 66104447 . T C 99 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,21;MQ=34;PV4=1,1,0.15,1 PL:GT:GQ 136,0,162:0/1:99 chr10 82160859 . G C 99 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,13;MQ=36 PL:GT:GQ 153,39,0:1/1:99 chr10 82198579 . C T 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr10 87086290 . A G 4.13 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=17 PL:GT:GQ 35,27,0:1/1:99 chr10 89550621 . T G 74 . DP=47;AF1=1;CI95=1,1;DP4=0,0,0,45;MQ=45 PL:GT:GQ 107,135,0:1/1:99 chr10 92325046 . G A 42.3 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=45 PL:GT:GQ 75,15,0:1/1:75 chr10 94488050 . A G 5.46 . DP=4;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=43;PV4=1,0.16,1,1 PL:GT:GQ 34,0,34:0/1:34 chr10 95024815 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr10 95466306 . G A 53 . DP=7;AF1=0.6671;CI95=0.5,1;DP4=0,4,0,3;MQ=33;PV4=1,1,1,1 PL:GT:GQ 82,0,3:0/1:5 chr10 100256777 . T G 3.83 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=23 PL:GT:GQ 34,12,0:1/1:72 chr10 101510485 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 101530760 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr10 101879744 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=44 PL:GT:GQ 54,9,0:1/1:63 chr10 102147276 . G C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=33 PL:GT:GQ 43,9,0:1/1:63 chr10 102642248 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr10 107666616 . T C 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=43 PL:GT:GQ 40,6,0:1/1:49 chr10 108319945 . C G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 43,9,0:1/1:63 chr10 109734371 . G A 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr10 112870604 . C T 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=36 PL:GT:GQ 79,12,0:1/1:72 chr10 115304673 . T C 11.3 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr10 119380588 . G A 14.2 . DP=4;AF1=0.502;CI95=0.5,0.5;DP4=1,0,3,0;MQ=43;PV4=1,0.18,0.32,1 PL:GT:GQ 44,0,21:0/1:24 chr10 123063756 . C T 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=23 PL:GT:GQ 46,9,0:1/1:63 chr10 128424770 . T G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 45,6,0:1/1:49 chr10 131229204 . T C 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr10 132420570 . G C 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr10 132528066 . C T 99 . DP=19;AF1=1;CI95=1,1;DP4=0,0,19,0;MQ=42 PL:GT:GQ 213,57,0:1/1:99 chr10 132644619 . G A 19.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 52,15,0:1/1:75 chr10 132707581 . G C 9.11 . DP=51;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=25;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr10 133026892 . T C 55.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=44 PL:GT:GQ 88,18,0:1/1:90 chr11 768033 . T C 33.5 . DP=4;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 768042 . T C 33.5 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=0,2,0,2;MQ=32;PV4=1,1,1,1 PL:GT:GQ 62,0,1:1/1:5 chr11 874568 . G C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 66,12,0:1/1:72 chr11 1009210 . T C 4 . DP=70;AF1=0.6241;CI95=0.5,1;DP4=0,3,0,8;MQ=24;PV4=1,1,0.5,1 PL:GT:GQ 31,0,4:0/1:6 chr11 1016692 . C T 27 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=22 PL:GT:GQ 60,114,0:1/1:99 chr11 1034477 . A G 66 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 98,9,0:1/1:63 chr11 1074037 . G A 4.13 . DP=9;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,5,0;MQ=24;PV4=1,1,0.43,1 PL:GT:GQ 32,0,30:0/1:31 chr11 1556298 . G A 11.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=33 PL:GT:GQ 44,12,0:1/1:72 chr11 1824777 . T C 27 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=28 PL:GT:GQ 60,30,0:1/1:99 chr11 3395801 . C T 22 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 54,9,0:1/1:63 chr11 3411901 . G A 4.75 . DP=17;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=29 PL:GT:GQ 35,9,0:1/1:63 chr11 3731606 . A C 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr11 3783855 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr11 3967636 . A G 4.29 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 35,15,0:1/1:75 chr11 4385618 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr11 4424365 . T A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 5295586 . C T 3.01 . DP=52;AF1=0.4997;CI95=0.5,0.5;DP4=33,0,10,0;MQ=29;PV4=1,0.0045,0.3,0.17 PL:GT:GQ 30,0,131:0/1:33 chr11 6157144 . C G 45.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=35 PL:GT:GQ 78,21,0:1/1:84 chr11 6352044 . C T 18 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=31 PL:GT:GQ 50,9,0:1/1:63 chr11 6767356 . T C 9.63 . DP=3;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,1,0:1/1:23 chr11 6999404 . G C 21 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=37 PL:GT:GQ 53,9,0:1/1:63 chr11 9120930 . C G 17.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 9373125 . T C 19.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 51,6,0:1/1:49 chr11 9585101 . C T 67 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=45 PL:GT:GQ 100,42,0:1/1:99 chr11 10266192 . A C 14.3 . DP=22;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=27 PL:GT:GQ 47,18,0:1/1:90 chr11 10303263 . T C 8.64 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=18 PL:GT:GQ 41,51,0:1/1:99 chr11 10420170 . T C 35 . DP=17;AF1=1;CI95=1,1;DP4=0,1,0,15;MQ=28;PV4=1,0.12,1,0.4 PL:GT:GQ 68,36,0:1/1:99 chr11 10912169 . G A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=49 PL:GT:GQ 155,18,0:1/1:90 chr11 11315826 . T G 6.29 . DP=27;AF1=1;CI95=1,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 38,18,0:1/1:90 chr11 11603859 . A C 22 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,9,0,6;MQ=34;PV4=1,9.5e-13,0.22,1 PL:GT:GQ 52,0,115:0/1:55 chr11 11700034 . C T 33 . DP=11;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=30 PL:GT:GQ 66,27,0:1/1:99 chr11 11822758 . G A 15.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,3;MQ=38;PV4=1,0.18,1,1 PL:GT:GQ 45,0,88:0/1:48 chr11 11976636 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=24 PL:GT:GQ 54,9,0:1/1:63 chr11 14380517 . C G 16.1 . DP=10;AF1=0.5;CI95=0.5,0.5;DP4=5,0,5,0;MQ=48;PV4=1,2.1e-05,0.13,1 PL:GT:GQ 46,0,113:0/1:49 chr11 14419212 . A G 91.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 124,18,0:1/1:90 chr11 14846792 . A G 55 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=19 PL:GT:GQ 88,33,0:1/1:99 chr11 15494556 . C T 99 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=22,0,14,0;MQ=34;PV4=1,0.0071,1,1 PL:GT:GQ 146,0,159:0/1:99 chr11 16262879 . A C 16.1 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=43;PV4=1,0.061,0.24,0.33 PL:GT:GQ 46,0,28:0/1:31 chr11 21514947 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=41 PL:GT:GQ 57,12,0:1/1:72 chr11 22532576 . C G 28 . DP=17;AF1=1;CI95=1,1;DP4=0,0,0,17;MQ=17 PL:GT:GQ 61,51,0:1/1:99 chr11 23529238 . G T 4.29 . DP=13;AF1=0.5334;CI95=0.5,1;DP4=1,0,3,0;MQ=37;PV4=1,1,0.34,0.21 PL:GT:GQ 32,0,9:0/1:12 chr11 24249554 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr11 24853167 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=51 PL:GT:GQ 73,6,0:1/1:49 chr11 33353903 . T C 24.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=36 PL:GT:GQ 57,15,0:1/1:75 chr11 35126569 . T C 24.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 57,12,0:1/1:72 chr11 35132248 . C T 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr11 35155482 . T C 68 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=46 PL:GT:GQ 101,66,0:1/1:99 chr11 52494088 . T C 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=37 PL:GT:GQ 140,27,0:1/1:99 chr11 57899943 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 62261460 . G T 19.1 . DP=15;AF1=0.5;CI95=0.5,0.5;DP4=0,7,0,5;MQ=27;PV4=1,1.1e-06,1,1 PL:GT:GQ 49,0,58:0/1:51 chr11 67456049 . C T 39.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=19 PL:GT:GQ 72,18,0:1/1:90 chr11 68509708 . C G 3.65 . DP=9;AF1=0.7301;CI95=0.5,1;DP4=0,5,0,4;MQ=17;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr11 70115115 . T A 99 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=49 PL:GT:GQ 140,15,0:1/1:75 chr11 72643951 . T C 70 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=39 PL:GT:GQ 103,66,0:1/1:99 chr11 72647930 . G A 36 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=0,1,0,3;MQ=41;PV4=1,1,0.3,1 PL:GT:GQ 66,0,28:0/1:31 chr11 73330148 . C T 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr11 81720893 . A G 5.83 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=19 PL:GT:GQ 37,12,0:1/1:72 chr11 83813797 . A G 23.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 56,12,0:1/1:72 chr11 85949488 . C A 54 . DP=17;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=37 PL:GT:GQ 87,42,0:1/1:99 chr11 87634829 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=51 PL:GT:GQ 40,6,0:1/1:49 chr11 90913093 . A T 35.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 67,6,0:1/1:49 chr11 93793348 . G A 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=31 PL:GT:GQ 139,24,0:1/1:96 chr11 100802294 . T C 16.6 . DP=21;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=35 PL:GT:GQ 49,12,0:1/1:72 chr11 107455449 . C T 8.44 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=26 PL:GT:GQ 39,6,0:1/1:49 chr11 111344355 . A G 69.5 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=43 PL:GT:GQ 102,12,0:1/1:72 chr11 111611115 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr11 113050466 . G C 6.02 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=30 PL:GT:GQ 36,6,0:1/1:49 chr11 114332544 . T C 3.54 . DP=17;AF1=0.4999;CI95=0.5,0.5;DP4=0,4,0,5;MQ=37;PV4=1,0.32,0.13,1 PL:GT:GQ 31,0,37:0/1:33 chr11 114332549 . G A 3.54 . DP=17;AF1=0.4998;CI95=0.5,0.5;DP4=0,9,0,8;MQ=36;PV4=1,3.1e-10,0.088,1 PL:GT:GQ 31,0,127:0/1:34 chr11 114843578 . G C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr11 115580279 . A G 99 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=48 PL:GT:GQ 190,45,0:1/1:99 chr11 116434328 . G A 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 50,12,0:1/1:72 chr11 125914161 . A G 20.8 . DP=7;AF1=0.95;CI95=0.5,1;DP4=3,0,4,0;MQ=38;PV4=1,0.074,1,1 PL:GT:GQ 49,0,0:1/1:10 chr11 125917089 . C T 12.3 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,28,0,12;MQ=44;PV4=1,4.7e-25,1,1 PL:GT:GQ 42,0,167:0/1:45 chr11 127194100 . A G 60 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=49 PL:GT:GQ 93,24,0:1/1:96 chr12 70856 . G A 27.5 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 60,12,0:1/1:72 chr12 153693 . T C 52.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=38 PL:GT:GQ 85,15,0:1/1:75 chr12 924547 . C G 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 69,6,0:1/1:49 chr12 1555916 . G A 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 39,15,0:1/1:75 chr12 1919860 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 2283756 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=34 PL:GT:GQ 45,6,0:1/1:49 chr12 2805983 . G C 12.7 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=35 PL:GT:GQ 45,12,0:1/1:72 chr12 6088203 . T C 72.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=37 PL:GT:GQ 105,15,0:1/1:75 chr12 7099460 . G C 10.8 . DP=6;AF1=0.8277;CI95=0.5,1;DP4=3,0,3,0;MQ=26;PV4=1,0.027,1,1 PL:GT:GQ 39,0,1:1/1:5 chr12 7099464 . G A 13.3 . DP=6;AF1=0.9966;CI95=0.5,1;DP4=2,0,3,0;MQ=28;PV4=1,0.16,1,1 PL:GT:GQ 42,1,0:1/1:23 chr12 7198516 . T G 4.61 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 34,6,0:1/1:49 chr12 23331895 . C T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr12 28209020 . T G 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 47,15,0:1/1:75 chr12 30074073 . C T 32.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 64,6,0:1/1:49 chr12 30563452 . T C 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563453 . A G 25 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=46 PL:GT:GQ 57,9,0:1/1:63 chr12 30563464 . C A 78.8 . DP=8;AF1=1;CI95=0.5,1;DP4=0,2,0,5;MQ=34;PV4=1,0.29,1,1 PL:GT:GQ 110,6,0:1/1:49 chr12 31505085 . G A 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr12 34041336 . G A 5.46 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=2,0,2,0;MQ=36;PV4=1,1,0.48,0.21 PL:GT:GQ 34,0,34:0/1:34 chr12 49003648 . C G 42 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=39 PL:GT:GQ 75,24,0:1/1:96 chr12 51280690 . G A 69 . DP=98;AF1=0.5;CI95=0.5,0.5;DP4=13,0,18,0;MQ=45;PV4=1,1,0.051,1 PL:GT:GQ 99,0,84:0/1:87 chr12 69206633 . T C 17.1 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=17 PL:GT:GQ 50,33,0:1/1:99 chr12 80417253 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr12 86633033 . C T 34 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=0,1,0,2;MQ=43;PV4=1,1,0.33,1 PL:GT:GQ 64,0,31:0/1:34 chr12 98097274 . C T 47.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=31 PL:GT:GQ 80,15,0:1/1:75 chr12 105269319 . C T 19 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=26 PL:GT:GQ 51,9,0:1/1:63 chr12 109053425 . G A 9.53 . DP=8;AF1=0.5012;CI95=0.5,0.5;DP4=2,0,6,0;MQ=25;PV4=1,1,0.19,1 PL:GT:GQ 39,0,23:0/1:26 chr12 111904540 . A G 3.41 . DP=65;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 32,6,0:1/1:49 chr12 115038686 . T C 15.2 . DP=7;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=27 PL:GT:GQ 48,21,0:1/1:84 chr12 115039419 . A G 4.11 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=30 PL:GT:GQ 34,9,0:1/1:63 chr12 115103890 . G A 66 . DP=39;AF1=1;CI95=1,1;DP4=0,0,0,38;MQ=49 PL:GT:GQ 99,114,0:1/1:99 chr12 115833830 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr12 116361873 . T G 6.34 . DP=5;AF1=0.7302;CI95=0.5,1;DP4=0,2,0,2;MQ=23;PV4=1,1,1,1 PL:GT:GQ 34,0,2:0/1:3 chr12 123583527 . G A 14.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 46,9,0:1/1:63 chr12 124115330 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=38 PL:GT:GQ 76,9,0:1/1:63 chr12 125062296 . G A 41.8 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr12 126718106 . A G 8.76 . DP=50;AF1=0.5163;CI95=0.5,1;DP4=2,0,6,0;MQ=26;PV4=1,0.33,0.37,1 PL:GT:GQ 38,0,12:0/1:15 chr12 133348311 . G A 24 . DP=18;AF1=0.5;CI95=0.5,0.5;DP4=14,0,3,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 54,0,118:0/1:57 chr12 134494475 . C T 28 . DP=18;AF1=0.6671;CI95=0.5,1;DP4=8,0,10,0;MQ=18;PV4=1,1,1,1 PL:GT:GQ 57,0,3:0/1:5 chr12 134831761 . C T 41.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=27 PL:GT:GQ 74,15,0:1/1:75 chr12 134992770 . A C,T 84 . DP=47;AF1=1;CI95=1,1;DP4=0,0,26,0;MQ=29 PL:GT:GQ 117,72,114,0,44,114:1/1:99 chr12 135261117 . G A 49.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 82,18,0:1/1:90 chr12 135261144 . A G 99 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=46 PL:GT:GQ 155,18,0:1/1:90 chr12 135460302 . G A 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=40 PL:GT:GQ 198,69,0:1/1:99 chr12 135463758 . A G 83 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,16;MQ=26 PL:GT:GQ 116,48,0:1/1:99 chr12 135523325 . G A 99 . DP=23;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=26 PL:GT:GQ 136,66,0:1/1:99 chr12 135782401 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr12 135795472 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr13 18040027 . G C 42 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=33 PL:GT:GQ 74,9,0:1/1:63 chr13 19494625 . G T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 73,6,0:1/1:49 chr13 20121126 . A G 15.1 . DP=36;AF1=0.5;CI95=0.5,0.5;DP4=25,0,9,0;MQ=36;PV4=1,1,0.13,1 PL:GT:GQ 45,0,153:0/1:48 chr13 21536703 . A G 9.31 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr13 23160035 . G T 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 33,6,0:1/1:49 chr13 23476554 . C A 6.79 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=52 PL:GT:GQ 37,6,0:1/1:49 chr13 26632967 . C G 32 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=34 PL:GT:GQ 65,27,0:1/1:99 chr13 26790010 . T C 89.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 122,15,0:1/1:75 chr13 36083571 . T C 43 . DP=84;AF1=1;CI95=1,1;DP4=1,0,37,0;MQ=16;PV4=1,1,1,0.3 PL:GT:GQ 76,99,0:1/1:99 chr13 44432419 . C T 3.58 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=19 PL:GT:GQ 34,21,0:1/1:84 chr13 46592359 . T C 16.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 48,6,0:1/1:49 chr13 52764657 . A T 3.14 . DP=32;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=22 PL:GT:GQ 33,15,0:1/1:75 chr13 53084193 . C T 9.11 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=0,1,0,2;MQ=29;PV4=1,1,1,1 PL:GT:GQ 38,2,0:1/1:37 chr13 57763228 . C T 45 . DP=555;AF1=1;CI95=1,1;DP4=2,0,21,0;MQ=23;PV4=1,0.00021,1,0.3 PL:GT:GQ 78,45,0:1/1:99 chr13 73857921 . G C 31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 63,9,0:1/1:63 chr13 76718001 . G A 59 . DP=4;AF1=0.5004;CI95=0.5,0.5;DP4=1,0,3,0;MQ=45;PV4=1,1,0.12,1 PL:GT:GQ 89,0,28:0/1:31 chr13 100912695 . A T 23 . DP=22;AF1=0.5;CI95=0.5,0.5;DP4=0,16,0,6;MQ=31;PV4=1,0.029,1,0.35 PL:GT:GQ 53,0,103:0/1:56 chr13 101332001 . G C 21 . DP=23;AF1=1;CI95=1,1;DP4=0,0,23,0;MQ=21 PL:GT:GQ 54,69,0:1/1:99 chr13 102637334 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr13 102895627 . C T 63 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=48 PL:GT:GQ 96,27,0:1/1:99 chr13 103830322 . T C 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr13 112842448 . G A 39 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=27 PL:GT:GQ 72,27,0:1/1:99 chr13 113310291 . C T 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=43 PL:GT:GQ 66,12,0:1/1:72 chr13 114775162 . A G 80 . DP=17;AF1=1;CI95=1,1;DP4=0,0,17,0;MQ=21 PL:GT:GQ 113,51,0:1/1:99 chr13 115267482 . A G 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr13 116068676 . C T 3.83 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=27 PL:GT:GQ 34,12,0:1/1:72 chr13 116455918 . A G 33 . DP=29;AF1=0.5;CI95=0.5,0.5;DP4=13,0,15,0;MQ=42;PV4=1,1.8e-20,0.3,1 PL:GT:GQ 63,0,146:0/1:66 chr13 116765012 . G A 30.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 62,6,0:1/1:49 chr13 116779773 . C T 17.1 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=27,0,11,0;MQ=24;PV4=1,4.5e-35,1,1 PL:GT:GQ 47,0,106:0/1:50 chr13 116779791 . C T 57 . DP=38;AF1=0.5;CI95=0.5,0.5;DP4=24,0,14,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 87,0,103:0/1:90 chr14 20159250 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=39 PL:GT:GQ 43,9,0:1/1:63 chr14 23510676 . T C 52 . DP=22;AF1=1;CI95=1,1;DP4=0,0,22,0;MQ=32 PL:GT:GQ 85,66,0:1/1:99 chr14 24735256 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 29525577 . G A 21 . DP=10;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=16 PL:GT:GQ 54,27,0:1/1:99 chr14 36186389 . C T 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 36186394 . A G 6.79 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20 PL:GT:GQ 37,6,0:1/1:49 chr14 37440609 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 40432807 . A G 18.6 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=23 PL:GT:GQ 51,12,0:1/1:72 chr14 59466268 . T C 15.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 47,9,0:1/1:63 chr14 61368162 . G T 7.18 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=17 PL:GT:GQ 39,15,0:1/1:75 chr14 65152922 . G A 92 . DP=33;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,15;MQ=36;PV4=1,0.059,0.35,1 PL:GT:GQ 122,0,144:0/1:99 chr14 69749148 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=25 PL:GT:GQ 40,6,0:1/1:49 chr14 74877658 . C T 45 . DP=48;AF1=1;CI95=1,1;DP4=0,1,0,12;MQ=36;PV4=1,0.02,1,0.39 PL:GT:GQ 78,28,0:1/1:99 chr14 75546678 . C T 19.2 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=17 PL:GT:GQ 52,18,0:1/1:90 chr14 76439185 . T C 67.1 . DP=7;AF1=0.505;CI95=0.5,0.5;DP4=0,1,0,6;MQ=33;PV4=1,1,0.056,0.29 PL:GT:GQ 97,0,17:0/1:20 chr14 77313295 . T A 99 . DP=12;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=48 PL:GT:GQ 191,30,0:1/1:99 chr14 77673422 . G A 11.5 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=24 PL:GT:GQ 44,18,0:1/1:90 chr14 78646125 . T C 99 . DP=8;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=40 PL:GT:GQ 153,24,0:1/1:96 chr14 91702449 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr14 91769842 . G A 63 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 95,9,0:1/1:63 chr14 91775899 . C G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 73,6,0:1/1:49 chr14 91775924 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr14 93482918 . A C 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 93665819 . C T 75 . DP=7;AF1=0.5002;CI95=0.5,0.5;DP4=0,3,0,4;MQ=42;PV4=1,1,1,1 PL:GT:GQ 105,0,31:0/1:34 chr14 95422276 . A G 55.1 . DP=7;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=45 PL:GT:GQ 88,21,0:1/1:84 chr14 95731986 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr14 96045464 . A G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=33 PL:GT:GQ 44,6,0:1/1:49 chr14 97172020 . C T 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=51 PL:GT:GQ 100,9,0:1/1:63 chr14 100515480 . A G 6.98 . DP=3;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=45;PV4=1,0.14,0.085,0.33 PL:GT:GQ 36,0,30:0/1:32 chr14 100770214 . A T 8.69 . DP=20;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 41,21,0:1/1:84 chr14 101258303 . G A 82 . DP=15;AF1=1;CI95=1,1;DP4=0,0,15,0;MQ=26 PL:GT:GQ 115,45,0:1/1:99 chr14 101701492 . C G 66 . DP=10;AF1=1;CI95=1,1;DP4=0,0,10,0;MQ=49 PL:GT:GQ 99,30,0:1/1:99 chr14 102113772 . T C 3.98 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=30 PL:GT:GQ 33,6,0:1/1:49 chr14 102751431 . A C 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr14 103708033 . A G 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,0,12;MQ=27 PL:GT:GQ 141,36,0:1/1:99 chr14 104744582 . G A 3.52 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 33,9,0:1/1:63 chr14 105989100 . C T 3.14 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 33,15,0:1/1:75 chr14 105989162 . C T 3.65 . DP=12;AF1=0.7301;CI95=0.5,1;DP4=0,6,0,6;MQ=15;PV4=1,1,1,1 PL:GT:GQ 30,0,2:0/1:3 chr14 106234810 . G A 25.3 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=39 PL:GT:GQ 58,15,0:1/1:75 chr14 106995572 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr14 107283057 . T C 5.5 . DP=8;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=20 PL:GT:GQ 37,21,0:1/1:84 chr14 107285319 . T C 33 . DP=36;AF1=1;CI95=1,1;DP4=0,0,0,35;MQ=22 PL:GT:GQ 66,105,0:1/1:99 chr14 107640449 . A G 11.8 . DP=7;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 44,12,0:1/1:72 chr15 20082092 . T G 18.3 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=24 PL:GT:GQ 51,15,0:1/1:75 chr15 22955884 . T C 67 . DP=12;AF1=1;CI95=1,1;DP4=0,0,12,0;MQ=48 PL:GT:GQ 100,36,0:1/1:99 chr15 22971987 . A G 5.29 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=22 PL:GT:GQ 35,6,0:1/1:49 chr15 23233324 . C A 47 . DP=16;AF1=1;CI95=1,1;DP4=0,0,14,0;MQ=31 PL:GT:GQ 80,42,0:1/1:99 chr15 25175286 . C T 36.5 . DP=3;AF1=0.9998;CI95=0.5,1;DP4=1,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 66,2,0:1/1:37 chr15 25385709 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=48 PL:GT:GQ 40,6,0:1/1:49 chr15 27372396 . A G 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=40 PL:GT:GQ 76,9,0:1/1:63 chr15 35998093 . C T 9.53 . DP=9;AF1=1;CI95=1,1;DP4=0,0,9,0;MQ=17 PL:GT:GQ 42,27,0:1/1:99 chr15 36716538 . C G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr15 36793360 . G T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=42 PL:GT:GQ 76,9,0:1/1:63 chr15 53783097 . A G 10.5 . DP=31;AF1=1;CI95=1,1;DP4=0,0,7,0;MQ=16 PL:GT:GQ 43,21,0:1/1:84 chr15 54180175 . C T 10.4 . DP=7;AF1=0.5001;CI95=0.5,0.5;DP4=4,0,3,0;MQ=27;PV4=1,1.2e-05,1,1 PL:GT:GQ 40,0,32:0/1:34 chr15 54939306 . C T 99 . DP=34;AF1=0.5;CI95=0.5,0.5;DP4=0,18,0,16;MQ=49;PV4=1,1,0.18,1 PL:GT:GQ 172,0,181:0/1:99 chr15 59377916 . C T 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr15 59685961 . G C 68 . DP=11;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=36 PL:GT:GQ 101,33,0:1/1:99 chr15 60306384 . A G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr15 60345642 . G C 14.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 46,6,0:1/1:49 chr15 60367387 . G A 13.2 . DP=6;AF1=0.5001;CI95=0.5,0.5;DP4=3,0,3,0;MQ=34;PV4=1,0.098,0.24,1 PL:GT:GQ 43,0,35:0/1:37 chr15 60367446 . C T 44 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 76,9,0:1/1:63 chr15 61763755 . G A 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=45 PL:GT:GQ 100,9,0:1/1:63 chr15 61831362 . C G 11.3 . DP=5;AF1=0.5;CI95=0.5,0.5;DP4=0,2,0,3;MQ=30;PV4=1,0.00077,0.47,1 PL:GT:GQ 41,0,42:0/1:41 chr15 63978880 . G C 60 . DP=6;AF1=0.9999;CI95=0.5,1;DP4=2,0,4,0;MQ=35;PV4=1,1,1,1 PL:GT:GQ 90,3,0:1/1:41 chr15 64342445 . A G 12.2 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=18 PL:GT:GQ 44,9,0:1/1:63 chr15 65424859 . T C 11.3 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=21 PL:GT:GQ 44,30,0:1/1:99 chr15 65603698 . C T 60 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 92,9,0:1/1:63 chr15 67005078 . G A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr15 71133512 . G C 22.3 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 55,15,0:1/1:75 chr15 72619009 . A G 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr15 73272688 . C T 70.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=39 PL:GT:GQ 103,15,0:1/1:75 chr15 73699335 . T A 99 . DP=9;AF1=1;CI95=1,1;DP4=0,0,0,9;MQ=45 PL:GT:GQ 175,27,0:1/1:99 chr15 74513352 . C T 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,10;MQ=37 PL:GT:GQ 139,30,0:1/1:99 chr15 75540536 . G A 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr15 75822537 . C A 17.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=23 PL:GT:GQ 50,15,0:1/1:75 chr15 78554005 . T C 12 . DP=18;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=46 PL:GT:GQ 43,6,0:1/1:49 chr15 80089369 . G A 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=28 PL:GT:GQ 40,6,0:1/1:49 chr15 83089149 . C G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=33 PL:GT:GQ 40,6,0:1/1:49 chr15 86839307 . T C 90.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=43 PL:GT:GQ 123,15,0:1/1:75 chr15 89836258 . T C 99 . DP=10;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=39 PL:GT:GQ 141,24,0:1/1:96 chr15 89837706 . G A 4.13 . DP=8;AF1=0.4998;CI95=0.5,0.5;DP4=0,4,0,4;MQ=30;PV4=1,1,0.25,1 PL:GT:GQ 32,0,59:0/1:35 chr15 89857648 . T C 99 . DP=27;AF1=0.5;CI95=0.5,0.5;DP4=8,0,8,0;MQ=40;PV4=1,1,0.3,1 PL:GT:GQ 133,0,130:0/1:99 chr15 89864228 . A C 32 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=2,0,2,0;MQ=42;PV4=1,1,1,1 PL:GT:GQ 62,0,31:0/1:34 chr15 91261235 . G A 7.8 . DP=4;AF1=0.5002;CI95=0.5,0.5;DP4=1,0,2,0;MQ=44;PV4=1,1,0.32,1 PL:GT:GQ 37,0,30:0/1:32 chr16 256990 . A C 10.4 . DP=16;AF1=0.5008;CI95=0.5,0.5;DP4=4,0,3,0;MQ=23;PV4=1,0.34,1,1 PL:GT:GQ 40,0,25:0/1:28 chr16 260794 . T C 3.01 . DP=19;AF1=0.4999;CI95=0.5,0.5;DP4=13,0,2,0;MQ=24;PV4=1,1,1,1 PL:GT:GQ 30,0,32:0/1:31 chr16 419905 . A G 7.9 . DP=5;AF1=0.9966;CI95=0.5,1;DP4=0,2,0,3;MQ=22;PV4=1,1,1,1 PL:GT:GQ 36,1,0:1/1:23 chr16 824086 . T C 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=48 PL:GT:GQ 54,9,0:1/1:63 chr16 1085063 . C T 52 . DP=12;AF1=0.5;CI95=0.5,0.5;DP4=6,0,6,0;MQ=42;PV4=1,1,0.014,1 PL:GT:GQ 82,0,128:0/1:85 chr16 1221305 . T C 54 . DP=7;AF1=0.5;CI95=0.5,0.5;DP4=0,3,0,3;MQ=40;PV4=1,1,1,1 PL:GT:GQ 84,0,60:0/1:63 chr16 1411728 . A G 32.3 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=35 PL:GT:GQ 65,15,0:1/1:75 chr16 1443197 . C G 64 . DP=26;AF1=1;CI95=1,1;DP4=0,0,25,0;MQ=36 PL:GT:GQ 97,75,0:1/1:99 chr16 1478746 . A T 32 . DP=20;AF1=1;CI95=1,1;DP4=0,0,8,0;MQ=28 PL:GT:GQ 65,24,0:1/1:96 chr16 1514438 . A C 45 . DP=49;AF1=1;CI95=1,1;DP4=0,0,48,0;MQ=26 PL:GT:GQ 78,144,0:1/1:99 chr16 1601989 . T C 99 . DP=13;AF1=1;CI95=1,1;DP4=0,0,13,0;MQ=29 PL:GT:GQ 133,39,0:1/1:99 chr16 2043883 . C T 30 . DP=33;AF1=1;CI95=1,1;DP4=0,0,0,33;MQ=14 PL:GT:GQ 63,99,0:1/1:99 chr16 2137470 . A C 39 . DP=38;AF1=0.5016;CI95=0.5,0.5;DP4=4,0,6,0;MQ=34;PV4=1,0.02,1,1 PL:GT:GQ 69,0,22:0/1:25 chr16 2537260 . A G 99 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=40 PL:GT:GQ 177,33,0:1/1:99 chr16 2564737 . T C 99 . DP=25;AF1=1;CI95=1,1;DP4=0,0,0,22;MQ=41 PL:GT:GQ 199,66,0:1/1:99 chr16 2612605 . A T 62.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=28 PL:GT:GQ 95,15,0:1/1:75 chr16 2704518 . G A 41 . DP=48;AF1=0.5;CI95=0.5,0.5;DP4=0,17,0,12;MQ=48;PV4=1,1.9e-23,0.24,0.034 PL:GT:GQ 71,0,175:0/1:74 chr16 3274307 . G T 68 . DP=39;AF1=0.5;CI95=0.5,0.5;DP4=0,30,0,8;MQ=37;PV4=1,1,1,1 PL:GT:GQ 98,0,138:0/1:99 chr16 5467292 . G C 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr16 10079145 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 11483702 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 40,6,0:1/1:49 chr16 12038227 . A T 23 . DP=47;AF1=0.5;CI95=0.5,0.5;DP4=0,22,0,23;MQ=32;PV4=1,4.4e-66,0.47,0.028 PL:GT:GQ 53,0,135:0/1:56 chr16 21336880 . G C 55 . DP=35;AF1=0.5;CI95=0.5,0.5;DP4=0,12,0,19;MQ=47;PV4=1,5.6e-21,1,1 PL:GT:GQ 85,0,121:0/1:88 chr16 21980241 . C T 16.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=29 PL:GT:GQ 48,9,0:1/1:63 chr16 23275383 . C G 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 44,6,0:1/1:49 chr16 27546495 . G T 25 . DP=35;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=43 PL:GT:GQ 57,9,0:1/1:63 chr16 27700399 . A T 17.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=17 PL:GT:GQ 50,12,0:1/1:72 chr16 28021935 . A G 18.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=23 PL:GT:GQ 51,15,0:1/1:75 chr16 29070016 . G T 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr16 29478618 . C T 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=42 PL:GT:GQ 43,9,0:1/1:63 chr16 29718140 . C T 46.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=31 PL:GT:GQ 79,15,0:1/1:75 chr16 30700759 . T C 17.1 . DP=14;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=14 PL:GT:GQ 50,42,0:1/1:99 chr16 35139103 . A G 46.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=37 PL:GT:GQ 79,12,0:1/1:72 chr16 35473348 . G A 3.83 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 34,12,0:1/1:72 chr16 36213667 . A G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 73,6,0:1/1:49 chr16 36705528 . G A 14.4 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=32 PL:GT:GQ 47,15,0:1/1:75 chr16 43831353 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=42 PL:GT:GQ 102,12,0:1/1:72 chr16 44715166 . A C 25 . DP=18;AF1=1;CI95=1,1;DP4=0,0,0,8;MQ=32 PL:GT:GQ 58,24,0:1/1:96 chr16 44957661 . T C 7.03 . DP=23;AF1=1;CI95=1,1;DP4=0,0,0,7;MQ=18 PL:GT:GQ 39,21,0:1/1:84 chr16 44958698 . C T 42.3 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=49 PL:GT:GQ 75,15,0:1/1:75 chr16 44959163 . T C 33.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=48 PL:GT:GQ 66,12,0:1/1:72 chr16 45167959 . C T 4.45 . DP=16;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=24 PL:GT:GQ 35,12,0:1/1:72 chr16 50254956 . C T 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=36 PL:GT:GQ 45,6,0:1/1:49 chr16 52383122 . A C 46.5 . DP=19;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=42 PL:GT:GQ 79,12,0:1/1:72 chr16 55978159 . C T 10.7 . DP=20;AF1=0.5336;CI95=0.5,1;DP4=2,0,5,0;MQ=35;PV4=1,0.038,1,0.059 PL:GT:GQ 40,0,9:0/1:12 chr16 61358878 . T A 15.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=32 PL:GT:GQ 47,6,0:1/1:49 chr16 61392487 . G A 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 44,6,0:1/1:49 chr16 61621603 . G T 6.59 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=22 PL:GT:GQ 38,12,0:1/1:72 chr16 69120890 . G C 51.3 . DP=36;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=42 PL:GT:GQ 84,15,0:1/1:75 chr16 70778219 . A G 21.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=39 PL:GT:GQ 53,6,0:1/1:49 chr16 71899519 . T C 40 . DP=11;AF1=1;CI95=1,1;DP4=0,0,11,0;MQ=33 PL:GT:GQ 73,33,0:1/1:99 chr16 72079251 . A G 11.3 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=41 PL:GT:GQ 43,9,0:1/1:63 chr16 72093003 . G C 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 72672428 . A G 68 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=49 PL:GT:GQ 100,9,0:1/1:63 chr16 72864515 . A G 13.9 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=35 PL:GT:GQ 45,6,0:1/1:49 chr16 72890560 . G A 47.1 . DP=10;AF1=0.5064;CI95=0.5,0.5;DP4=0,1,0,7;MQ=49;PV4=1,0.0019,0.0033,1 PL:GT:GQ 77,0,16:0/1:19 chr16 73048929 . A G 6.29 . DP=4;AF1=0.9966;CI95=0.5,1;DP4=1,0,2,0;MQ=27;PV4=1,1,1,0.33 PL:GT:GQ 34,1,0:1/1:23 chr16 73177179 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr16 73191468 . C T 69.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=40 PL:GT:GQ 102,12,0:1/1:72 chr16 73367439 . A C 7.41 . DP=36;AF1=1;CI95=0.5,1;DP4=0,2,0,13;MQ=26;PV4=1,1,0.027,1 PL:GT:GQ 37,4,0:1/1:45 chr16 74259316 . C T 89.5 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=49 PL:GT:GQ 122,12,0:1/1:72 chr16 75271450 . C G 6.99 . DP=15;AF1=0.5015;CI95=0.5,0.5;DP4=0,1,0,3;MQ=44;PV4=1,0.065,0.31,1 PL:GT:GQ 36,0,22:0/1:25 chr16 76199870 . G A 26 . DP=14;AF1=0.5;CI95=0.5,0.5;DP4=8,0,6,0;MQ=47;PV4=1,1.2e-06,0.32,1 PL:GT:GQ 56,0,141:0/1:59 chr16 77723692 . A G 89.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=50 PL:GT:GQ 122,12,0:1/1:72 chr17 165875 . G A 40.8 . DP=11;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=42 PL:GT:GQ 72,6,0:1/1:49 chr17 1443809 . C G 9.31 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=50 PL:GT:GQ 40,6,0:1/1:49 chr17 1618253 . C T 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=39 PL:GT:GQ 54,9,0:1/1:63 chr17 2815309 . T G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 40,6,0:1/1:49 chr17 3537486 . T G 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=50 PL:GT:GQ 73,6,0:1/1:49 chr17 3734367 . C A 23.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=36 PL:GT:GQ 56,12,0:1/1:72 chr17 5634764 . T C 13 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=35 PL:GT:GQ 44,6,0:1/1:49 chr17 6408090 . C G 3.54 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=3,0,2,0;MQ=40;PV4=1,1,0.36,1 PL:GT:GQ 31,0,66:0/1:34 chr17 7089723 . A G 9.31 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=47 PL:GT:GQ 40,6,0:1/1:49 chr17 8731503 . G C 11.1 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 42,6,0:1/1:49 chr17 9282935 . T C,G 24.5 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=40 PL:GT:GQ 57,12,61,0,3,61:1/1:72 chr17 17284831 . T C 29 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=25 PL:GT:GQ 61,9,0:1/1:63 chr17 18439515 . G A 4.11 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=25 PL:GT:GQ 34,9,0:1/1:63 chr17 18602146 . C T 4.76 . DP=20;AF1=1;CI95=1,1;DP4=0,0,0,11;MQ=16 PL:GT:GQ 36,33,0:1/1:99 chr17 19427888 . C T 57 . DP=104;AF1=0.5;CI95=0.5,0.5;DP4=45,0,29,0;MQ=39;PV4=1,2.2e-12,1,1 PL:GT:GQ 87,0,131:0/1:90 chr17 19604159 . T C 9.31 . DP=5;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=45 PL:GT:GQ 40,6,0:1/1:49 chr17 19610366 . C T 13 . DP=13;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=48 PL:GT:GQ 44,6,0:1/1:49 chr17 20484706 . C G 51 . DP=35;AF1=0.5001;CI95=0.5,0.5;DP4=0,11,0,21;MQ=21;PV4=1,0.39,0.49,1 PL:GT:GQ 81,0,36:0/1:39 chr17 20555720 . A G 26.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,5;MQ=28 PL:GT:GQ 59,15,0:1/1:75 chr17 24328984 . A C 15.4 . DP=34;AF1=1;CI95=0.5,1;DP4=0,0,5,0;MQ=25 PL:GT:GQ 48,15,0:1/1:75 chr17 26237090 . G A 41.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=44 PL:GT:GQ 73,6,0:1/1:49 chr17 28394766 . C A 13.9 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=31 PL:GT:GQ 45,6,0:1/1:49 chr17 31218277 . A G 3.62 . DP=38;AF1=0.5161;CI95=0.5,0.5;DP4=0,1,0,2;MQ=38;PV4=1,0.26,1,1 PL:GT:GQ 31,0,12:0/1:15 chr17 31254021 . C T 15.1 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 47,9,0:1/1:63 chr17 32516798 . G A 37.8 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=49 PL:GT:GQ 69,6,0:1/1:49 chr17 32600253 . A G 16.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 49,12,0:1/1:72 chr17 34255214 . G C 19.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=21 PL:GT:GQ 52,18,0:1/1:90 chr17 34365900 . T C 93.1 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,6,0;MQ=38 PL:GT:GQ 126,18,0:1/1:90 chr17 35380386 . A T 6.79 . DP=44;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=46 PL:GT:GQ 37,6,0:1/1:49 chr17 41993344 . C T 64 . DP=41;AF1=1;CI95=1,1;DP4=0,0,0,41;MQ=16 PL:GT:GQ 97,123,0:1/1:99 chr17 42128201 . A G 4.13 . DP=5;AF1=0.4998;CI95=0.5,0.5;DP4=0,2,0,2;MQ=52;PV4=1,0.0041,1,1 PL:GT:GQ 32,0,62:0/1:35 chr17 42984490 . C A 56 . DP=33;AF1=0.5001;CI95=0.5,0.5;DP4=6,0,12,0;MQ=42;PV4=1,0.004,1,1 PL:GT:GQ 86,0,34:0/1:37 chr17 43419457 . G A 99 . DP=16;AF1=1;CI95=1,1;DP4=0,0,0,14;MQ=45 PL:GT:GQ 185,42,0:1/1:99 chr17 43421225 . A G 65.1 . DP=31;AF1=1;CI95=0.5,1;DP4=0,6,0,17;MQ=43;PV4=1,0.004,1,1 PL:GT:GQ 98,18,0:1/1:90 chr17 45206897 . G A 22 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=47 PL:GT:GQ 54,9,0:1/1:63 chr17 45381302 . T C 18.6 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,0,4;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 45530812 . C A 3.54 . DP=6;AF1=0.4998;CI95=0.5,0.5;DP4=0,3,0,2;MQ=40;PV4=1,1,0.37,1 PL:GT:GQ 31,0,58:0/1:34 chr17 50242633 . G A 44 . DP=42;AF1=0.5;CI95=0.5,0.5;DP4=0,25,0,13;MQ=32;PV4=1,0.084,0.14,1 PL:GT:GQ 74,0,154:0/1:77 chr17 51275317 . G A 14.9 . DP=10;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=31 PL:GT:GQ 46,6,0:1/1:49 chr17 52325530 . C T 29 . DP=19;AF1=1;CI95=1,1;DP4=0,0,0,18;MQ=24 PL:GT:GQ 62,54,0:1/1:99 chr17 52411748 . T G 18.6 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,4,0;MQ=25 PL:GT:GQ 51,12,0:1/1:72 chr17 53190746 . C G 62.1 . DP=20;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=40 PL:GT:GQ 95,18,0:1/1:90 chr17 58289916 . T C 18.2 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,0,6;MQ=22 PL:GT:GQ 51,18,0:1/1:90 chr17 59796875 . C T 42 . DP=6;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=35 PL:GT:GQ 74,9,0:1/1:63 pysam-0.7.7/tests/vcf-examples/13.vcf0000664000076400007650000015066111754437212017203 0ustar andreasandreas##fileformat=VCFv4.0 ##fileDate=2011-10-11 ##source=Platypus_Version_0.1.5 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT WTCHG_27173_05.bam WTCHG_27173_04.bam chr1 1451489 . T C 103 PASS ABPV=1.00e+00;FPV=7.56e-01;FR=0.2501;HP=7;MMLQ=30;NF=2;NR=18;PP=103;RMP=57.54;RPV=1.00e-00;SC=CCGGTGTGGGTGGGGAGGCCG;TC=42;TCF=7;TCR=35;TR=20;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.36;dbsnp=rs76717221 GT:GL:GQ:NR 0/0:-43.28,-51.0,-125.34:35:18 1/0:-135.58,-103.29,-138.87:100:24 chr1 1451490 . G A 73 PASS ABPV=1.00e+00;FPV=9.29e-01;FR=0.2501;HP=3;MMLQ=30;NF=3;NR=16;PP=73;RMP=58.79;RPV=9.98e-01;SC=CGGTGTGGGTGGGGAGGCCGG;TC=42;TCF=7;TCR=35;TR=19;func=intronic;gene=ATAD3A;segdup=0.91;1000g=0.33;dbsnp=rs9439460 GT:GL:GQ:NR 0/0:-43.28,-50.99,-127.79:35:18 0/1:-135.58,-110.35,-146.87:100:24 chr1 12939904 . A C 109 PASS ABPV=1.00e+00;FPV=7.66e-01;FR=0.2500;HP=1;MMLQ=37;NF=22;NR=1;PP=109;RMP=45.66;RPV=4.46e-06;SC=ATTGTGAGGAACTTTAACGAG;TC=132;TCF=79;TCR=53;TR=23 GT:GL:GQ:NR 0/0:-40.31,-50.48,-301.89:45:53 0/1:-121.0,-87.39,-396.61:100:79 chr1 16902943 . T C 50 PASS ABPV=1.00e+00;FPV=2.90e-01;FR=0.2506;HP=2;MMLQ=34;NF=30;NR=18;PP=50;RMP=46.42;RPV=8.84e-01;SC=GGGTCAGCTCTCGTTCCTGAG;TC=191;TCF=133;TCR=58;TR=48 GT:GL:GQ:NR 0/0:-337.26,-342.92,-618.53:26:93 0/1:-428.71,-408.75,-668.15:84:98 chr1 16902982 . G T 41 PASS ABPV=1.00e+00;FPV=5.26e-02;FR=0.2500;HP=1;MMLQ=36;NF=29;NR=10;PP=41;RMP=55.68;RPV=1.90e-02;SC=ATTGCCTAAGGTGAGACGGTA;TC=223;TCF=152;TCR=71;TR=39 GT:GL:GQ:NR 0/0:-282.16,-293.75,-760.18:52:108 0/1:-308.83,-290.99,-786.16:75:115 chr1 16918180 . C T 200 PASS ABPV=1.00e+00;FPV=7.60e-05;FR=0.2500;HP=1;MMLQ=37;NF=8;NR=11;PP=200;RMP=57.84;RPV=6.15e-01;SC=TACTTTGGTACCTCTGTCTTC;TC=134;TCF=91;TCR=43;TR=19 GT:GL:GQ:NR 0/0:-48.3,-68.7,-289.28:90:47 0/1:-194.28,-132.13,-452.09:100:87 chr1 17083652 . C T 200 PASS ABPV=3.06e-02;FPV=6.38e-13;FR=0.2500;HP=2;MMLQ=36;NF=29;NR=3;PP=200;RMP=38.16;RPV=2.05e-02;SC=AAATCTCAACCTTGAGTACAA;TC=350;TCF=317;TCR=33;TR=32;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.37;dbsnp=rs113710576 GT:GL:GQ:NR 0/0:-547.14,-559.85,-1017.76:56:159 0/1:-723.35,-656.42,-1167.76:100:191 chr1 17083776 . C A 79 PASS ABPV=1.08e-01;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=35;NF=1;NR=22;PP=79;RMP=76.99;RPV=1.13e-09;SC=CACAGAGACACGCGTGAAGAC;TC=238;TCF=4;TCR=234;TR=23;func=ncRNA;gene=MST1P9;cons46=632 Name=lod=492;segdup=0.99;1000g=0.20;dbsnp=rs56318124 GT:GL:GQ:NR 0/0:-442.45,-455.85,-790.66:59:121 0/1:-451.84,-425.21,-717.41:100:117 chr1 17575714 . G A 59 PASS ABPV=2.52e-01;FPV=3.10e-02;FR=0.2500;HP=1;MMLQ=31;NF=1;NR=4;PP=59;RMP=43.35;RPV=1.94e-02;SC=GACCCTCGTGGACATTTATGG;TC=58;TCF=19;TCR=39;TR=5 GT:GL:GQ:NR 0/0:-14.49,-33.87,-234.95:85:32 0/1:-39.36,-17.32,-168.9:93:26 chr1 21751228 . T TCGCGCCCGGC 66 PASS ABPV=3.86e-06;FPV=8.03e-37;FR=0.2500;HP=4;NF=1;NR=1;PP=66;RMP=15.56;RPV=1.98e-06;SC=CTCAAATGAGTAAAAGGCACT;TC=133;TCF=77;TCR=56;TR=2 GT:GL:GQ:NR 0/0:-178.34,-190.57,-398.5:54:72 0/1:-308.3,-271.14,-540.05:100:98 chr1 21755539 . C A 27 PASS ABPV=1.00e+00;FPV=9.84e-01;FR=0.2503;HP=1;MMLQ=31;NF=2;NR=1;PP=27;RMP=65.83;RPV=4.98e-02;SC=GGCCAACAACCGCCAGGTGCG;TC=20;TCF=3;TCR=17;TR=3;func=intergenic;gene=ECE1(dist=83505) NBPF3(dist=11092);cons46=807 Name=lod=2532;segdup=0.99;1000g=0.80;dbsnp=rs3855556 GT:GL:GQ:NR 0/0:0.0,-6.22,-62.68:28:10 1/0:-21.51,-6.92,-52.98:61:10 chr1 40798730 . A AT 59 PASS ABPV=1.00e+00;FPV=6.06e-01;FR=0.2504;HP=10;NF=7;NR=1;PP=59;RMP=50.29;RPV=7.38e-01;SC=GAAGTCTTCTATTTTTTTTTA;TC=28;TCF=24;TCR=4;TR=8;func=intergenic;gene=COL9A2(dist=15791) SMAP2(dist=40648);dbsnp=rs34372767 GT:GL:GQ:NR 0/0:0.0,-6.13,-39.37:28:12 0/1:-35.97,-10.49,-31.53:98:16 chr1 142803580 . TA T 145 PASS ABPV=1.00e+00;FPV=6.35e-02;FR=0.2500;HP=6;NF=1;NR=11;PP=145;RMP=65.89;RPV=8.29e-02;SC=TTCATAGATTTAAAAAATTAT;TC=81;TCF=16;TCR=65;TR=12 GT:GL:GQ:NR 0/0:-39.18,-49.93,-242.54:48:33 1/0:-80.12,-35.74,-249.72:100:48 chr1 144854799 . C T 50 PASS ABPV=1.00e+00;FPV=9.37e-01;FR=0.2504;HP=1;MMLQ=34;NF=1;NR=19;PP=50;RMP=60.89;RPV=9.86e-01;SC=GCCTCGGATACCTCCAGCTGA;TC=52;TCF=2;TCR=50;TR=20;func=intronic;gene=PDE4DIP;segdup=0.96;dbsnp=rs5004097 GT:GL:GQ:NR 0/0:-89.24,-95.22,-205.12:27:25 0/1:-177.25,-157.18,-246.67:85:27 chr1 145116027 . T C 127 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2501;HP=2;MMLQ=34;NF=0;NR=7;PP=127;RMP=54.07;RPV=5.14e-01;SC=AAAAGAGATGTCCTGAAAATG;TC=30;TCF=0;TCR=30;TR=7;func=UTR3;gene=SEC22B;cons46=340 Name=lod=32;1000g=0.45;dbsnp=rs7550440 GT:GL:GQ:NR 0/0:0.0,-7.61,-92.94:34:11 0/1:-56.84,-19.14,-106.99:100:19 chr1 146554532 . C T 57 PASS ABPV=1.00e+00;FPV=5.18e-01;FR=0.2501;HP=12;MMLQ=31;NF=4;NR=5;PP=57;RMP=66.19;RPV=4.68e-01;SC=CTTCTTCTTTCTTTTTTTTTA;TC=41;TCF=18;TCR=23;TR=9;func=intergenic;gene=LOC728989(dist=39933) PRKAB2(dist=72153);segdup=0.93;dbsnp=rs9662613 GT:GL:GQ:NR 0/0:-13.82,-21.42,-95.53:34:13 0/1:-131.76,-110.18,-223.87:91:28 chr1 148344564 . T C 34 PASS ABPV=3.69e-01;FPV=1.16e-03;FR=0.2500;HP=2;MMLQ=36;NF=24;NR=1;PP=34;RMP=22.65;RPV=1.98e-06;SC=TTCGTTCTTATTTCTCCCCGC;TC=218;TCF=162;TCR=56;TR=25 GT:GL:GQ:NR 0/0:-210.1,-224.84,-651.44:65:104 0/1:-232.74,-216.41,-586.14:69:114 chr1 148853862 . G T 37 PASS ABPV=3.79e-01;FPV=1.94e-02;FR=0.2500;HP=3;MMLQ=31;NF=6;NR=2;PP=37;RMP=50.34;RPV=2.58e-02;SC=CGCTCCTGGAGCCCAGCCCGG;TC=76;TCF=50;TCR=26;TR=8 GT:GL:GQ:NR 0/0:-247.75,-257.0,-317.61:41:35 1/0:-179.5,-162.62,-280.47:71:41 chr1 148854004 . C T 32 PASS ABPV=1.83e-01;FPV=3.17e-02;FR=0.2500;HP=1;MMLQ=34;NF=0;NR=3;PP=32;RMP=93.74;RPV=2.52e-02;SC=GCCCGCACTGCTGCAGCGCCC;TC=44;TCF=12;TCR=32;TR=3 GT:GL:GQ:NR 0/0:-75.02,-87.66,-197.34:56:26 1/0:-55.07,-39.25,-94.0:66:18 chr1 152187606 . G A 200 PASS ABPV=3.64e-01;FPV=4.08e-07;FR=0.2500;HP=2;MMLQ=32;NF=7;NR=16;PP=200;RMP=30.4;RPV=4.89e-02;SC=GAAGACTGACGGGAGCCAGAC;TC=202;TCF=109;TCR=93;TR=23;func=exonic;gene=HRNR;exon_func=nonsynonymous SNV;AAchange=NM_001009931:c.C6499T:p.R2167C;segdup=0.98;1000g=0.05;sift=0.2;pp2=0.269490;phylop=0.009549;mutT=0.062064;LRT=0.589002 GT:GL:GQ:NR 0/0:-190.82,-206.2,-650.62:68:98 0/1:-306.73,-239.37,-605.74:100:104 chr1 152281007 . A G 38 PASS ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=38;RMP=56.83;RPV=9.75e-01;SC=GCCTGATCATAATGGGATCCT;TC=370;TCF=169;TCR=201;TR=99 GT:GL:GQ:NR 0/0:-830.31,-842.03,-1695.93:52:178 0/1:-1104.87,-1087.65,-1851.72:72:192 chr1 152281008 . A G 56 PASS ABPV=1.00e+00;FPV=2.26e-01;FR=0.2500;HP=1;MMLQ=31;NF=37;NR=62;PP=56;RMP=57.69;RPV=9.75e-01;SC=CCTGATCATAATGGGATCCTT;TC=368;TCF=167;TCR=201;TR=99 GT:GL:GQ:NR 0/0:-836.29,-850.28,-1704.3:62:178 1/0:-1097.96,-1076.67,-1811.19:90:190 chr1 152281466 . C T 200 PASS ABPV=1.00e+00;FPV=3.99e-04;FR=0.2500;HP=2;MMLQ=33;NF=26;NR=66;PP=200;RMP=66.62;RPV=7.23e-01;SC=TGCCCGTGACCGGCTCTGTCT;TC=430;TCF=180;TCR=250;TR=92 GT:GL:GQ:NR 0/0:-912.94,-966.99,-1954.85:100:223 1/0:-939.3,-872.22,-1720.42:100:207 chr1 168549565 . T C 28 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2504;HP=2;MMLQ=37;NF=0;NR=8;PP=28;RMP=72.28;RPV=1.34e-01;SC=TCCTTATCAATCATGTCTTTC;TC=47;TCF=0;TCR=47;TR=8 GT:GL:GQ:NR 0/0:-27.57,-33.72,-167.32:28:21 1/0:-34.62,-19.62,-182.0:63:26 chr1 236647542 . G T 46 PASS ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=34;NF=16;NR=40;PP=46;RMP=62.31;RPV=1.00e-00;SC=GTGCAAGCTGGCCCAGGCCAA;TC=104;TCF=32;TCR=72;TR=56 GT:GL:GQ:NR 0/0:-318.17,-328.23,-521.3:45:54 1/0:-498.22,-479.17,-572.27:80:50 chr1 236647562 . T C 73 PASS ABPV=1.00e+00;FPV=9.95e-01;FR=0.2503;HP=2;MMLQ=37;NF=11;NR=36;PP=73;RMP=64.25;RPV=1.00e-00;SC=ATGGTTGGTGTGTCATGGTGC;TC=85;TCF=23;TCR=62;TR=47 GT:GL:GQ:NR 0/0:-240.39,-246.81,-405.51:29:42 0/1:-421.95,-396.59,-483.66:100:43 chr1 236700807 . T A 130 PASS ABPV=1.00e+00;FPV=5.12e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=7;PP=130;RMP=47.87;RPV=8.70e-01;SC=GTAATCCCGTTTGTTGGCACC;TC=55;TCF=34;TCR=21;TR=15;func=exonic;gene=LGALS8;exon_func=nonsynonymous SNV;AAchange=NM_201544:c.T56A:p.F19Y;cons46=463 Name=lod=102;1000g=0.62;dbsnp=rs2737713;pp2=0.0;phylop=0.983932;mutT=4.6E-5;LRT=0.999982 GT:GL:GQ:NR 0/0:-41.35,-48.14,-183.02:31:21 0/1:-204.57,-166.19,-295.14:100:34 chr1 236700823 . T C 200 PASS ABPV=1.00e+00;FPV=6.24e-01;FR=0.2504;HP=2;MMLQ=32;NF=9;NR=8;PP=200;RMP=58.62;RPV=8.49e-01;SC=GCACCATTCCTGATCAGCTGG;TC=60;TCF=35;TCR=25;TR=17;func=exonic;gene=LGALS8;exon_func=synonymous SNV;AAchange=NM_201544:c.T72C:p.P24P;cons46=463 Name=lod=102;1000g=0.61;dbsnp=rs1041934 GT:GL:GQ:NR 0/0:-41.35,-47.43,-173.43:28:22 1/0:-232.08,-183.12,-325.41:100:38 chr1 241663902 . TGA T 37 PASS ABPV=2.57e-03;FPV=3.07e-05;FR=0.2507;HP=2;NF=0;NR=3;PP=37;RMP=44.45;RPV=2.39e-06;SC=TTTGAGTGAGTGAGAGAGAGA;TC=90;TCF=18;TCR=72;TR=3;func=intronic;gene=FH GT:GL:GQ:NR 0/0:-115.58,-120.99,-206.17:25:29 1/0:-208.1,-188.38,-347.52:83:62 chr10 52420020 . G A 135 PASS ABPV=1.00e+00;FPV=2.24e-01;FR=0.2502;HP=2;MMLQ=35;NF=3;NR=3;PP=135;RMP=58.04;RPV=7.75e-01;SC=GAGAACTTCCGGCTGCAGTAC;TC=30;TCF=20;TCR=10;TR=6 GT:GL:GQ:NR 0/0:-65.01,-71.52,-138.01:30:16 0/1:-83.86,-44.38,-74.93:100:14 chr10 118380701 . G A 77 PASS ABPV=1.00e+00;FPV=5.15e-01;FR=0.2503;HP=3;MMLQ=32;NF=5;NR=0;PP=77;RMP=22.32;RPV=5.62e-01;SC=CCGGGTTGCGGGGCGTCTGTT;TC=24;TCF=22;TCR=2;TR=5 GT:GL:GQ:NR 0/0:-4.14,-10.38,-77.71:28:10 0/1:-51.41,-25.11,-83.53:100:14 chr11 1651169 . T C 84 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2502;HP=2;MMLQ=33;NF=8;NR=26;PP=84;RMP=71.99;RPV=1.00e-00;SC=GCTGTGGCTCTGGCTGTGGGG;TC=71;TCF=14;TCR=57;TR=34;func=exonic;gene=KRTAP5-5;exon_func=synonymous SNV;AAchange=NM_001001480:c.T99C:p.S33S;1000g=0.29;dbsnp=rs71454095 GT:GL:GQ:NR 0/0:-199.38,-206.33,-365.55:31:38 0/1:-226.68,-198.86,-282.14:100:33 chr11 3431576 . G A 33 PASS ABPV=4.46e-01;FPV=4.99e-05;FR=0.2500;HP=1;MMLQ=30;NF=13;NR=10;PP=33;RMP=62.67;RPV=1.90e-02;SC=TCGTGTGTGAGTCCTACAGTG;TC=194;TCF=123;TCR=71;TR=23 GT:GL:GQ:NR 0/0:-71.93,-106.62,-693.75:100:102 1/0:-110.6,-94.58,-543.82:67:92 chr11 43918703 . C CTTTTCATATTAT 36 PASS ABPV=4.61e-02;FPV=1.12e-04;FR=0.2500;HP=3;NF=2;NR=0;PP=36;RMP=5.0;RPV=1.00e+00;SC=CTGACAGTGGCTTTATATATA;TC=49;TCF=49;TCR=0;TR=2 GT:GL:GQ:NR 0/0:-14.5,-34.6,-394.96:89:42 1/0:-47.66,-15.24,-223.69:100:36 chr11 48366812 . A C 48 PASS ABPV=1.00e+00;FPV=9.80e-01;FR=0.2502;HP=1;MMLQ=35;NF=16;NR=2;PP=48;RMP=45.69;RPV=1.00e+00;SC=AGATAATTGAATGTCCCAAGT;TC=44;TCF=42;TCR=2;TR=18 GT:GL:GQ:NR 0/0:-92.79,-99.69,-183.18:31:18 0/1:-133.87,-114.4,-228.26:82:26 chr11 48387506 . A G 48 PASS ABPV=1.00e+00;FPV=6.15e-01;FR=0.2500;HP=3;MMLQ=34;NF=28;NR=52;PP=48;RMP=59.69;RPV=1.00e-00;SC=AAATCCCCCGACCCATGCCAT;TC=227;TCF=109;TCR=118;TR=80;func=intergenic;gene=OR4C45(dist=13507) OR4A47(dist=122839);dbsnp=rs72898882;sift=0.42 GT:GL:GQ:NR 0/0:-665.75,-691.04,-1124.95:100:117 0/1:-697.01,-677.56,-1037.3:82:110 chr11 56143357 . G A 91 PASS ABPV=1.00e+00;FPV=9.70e-04;FR=0.2500;HP=3;MMLQ=36;NF=7;NR=60;PP=91;RMP=66.63;RPV=1.00e-00;SC=GGAATTTCTTGTACAAACAAA;TC=221;TCF=72;TCR=149;TR=67;func=exonic;gene=OR8U1 OR8U8;exon_func=synonymous SNV;AAchange=NM_001005204:c.G258A:p.L86L;dbsnp=rs76949582 GT:GL:GQ:NR 0/0:-538.52,-560.54,-1080.28:97:104 1/0:-924.01,-894.57,-1497.61:100:131 chr11 56468493 . A G 86 PASS ABPV=1.00e+00;FPV=1.31e-03;FR=0.2500;HP=1;MMLQ=30;NF=23;NR=16;PP=86;RMP=49.16;RPV=3.74e-01;SC=TCTGCCCCGCAGTGCTCATCC;TC=227;TCF=156;TCR=71;TR=39 GT:GL:GQ:NR 0/0:-212.22,-234.78,-819.52:99:105 0/1:-472.13,-443.86,-1063.46:100:122 chr11 92592540 . T G 22 PASS ABPV=9.72e-03;FPV=5.62e-02;FR=0.2501;HP=3;MMLQ=35;NF=0;NR=3;PP=22;RMP=99.66;RPV=8.62e-06;SC=GTTAGTGTTTTGGCTCTTGGA;TC=77;TCF=10;TCR=67;TR=3 GT:GL:GQ:NR 0/0:-302.47,-309.64,-322.1:32:36 0/1:-338.7,-325.07,-335.6:52:41 chr11 123504959 . C G 200 PASS ABPV=1.00e+00;FPV=4.20e-01;FR=0.2508;HP=2;MMLQ=40;NF=0;NR=7;PP=200;RMP=63.62;RPV=9.72e-01;SC=CAGTGCCCAGCGTGGGAACAC;TC=19;TCF=3;TCR=16;TR=7;func=intronic;gene=SCN3B;1000g=0.72;dbsnp=rs1148110 GT:GL:GQ:NR 0/0:-1.61,-6.93,-61.43:24:8 1/0:-66.0,-7.62,-36.11:100:11 chr12 92675 . C T 152 PASS ABPV=1.00e+00;FPV=7.38e-01;FR=0.2500;HP=1;MMLQ=37;NF=1;NR=7;PP=152;RMP=66.0;RPV=3.57e-01;SC=GGACTGTTTCCTGCTTGTAGC;TC=38;TCF=4;TCR=34;TR=8 GT:GL:GQ:NR 0/0:-41.61,-49.75,-120.62:37:14 1/0:-68.65,-25.34,-113.9:100:24 chr12 11183642 . A G 154 PASS ABPV=1.00e+00;FPV=8.37e-01;FR=0.2500;HP=1;MMLQ=34;NF=47;NR=62;PP=154;RMP=57.25;RPV=1.00e-00;SC=GCTAGTAGCAAGCCAGTTGCT;TC=311;TCF=168;TCR=143;TR=109;func=exonic;gene=TAS2R31;exon_func=nonsynonymous SNV;AAchange=NM_176885:c.T293C:p.L98P;segdup=0.93;dbsnp=rs73049067 GT:GL:GQ:NR 0/0:-561.52,-579.71,-1246.3:80:152 0/1:-826.02,-782.04,-1401.37:100:159 chr12 29908580 . A ATTGTT 200 PASS ABPV=1.00e+00;FPV=9.78e-01;FR=0.2507;HP=3;NF=10;NR=0;PP=200;RMP=36.19;RPV=1.00e+00;SC=TTTGGAAACTATTAAGTAATT;TC=24;TCF=24;TCR=0;TR=10;func=intronic;gene=TMTC1;dbsnp=rs3830194 GT:GL:GQ:NR 0/0:0.0,-5.55,-96.69:25:9 1/0:-151.5,-15.23,-76.28:100:17 chr12 31282765 . A T 21 PASS ABPV=1.00e+00;FPV=8.68e-01;FR=0.2502;HP=2;MMLQ=35;NF=12;NR=5;PP=21;RMP=46.72;RPV=8.51e-01;SC=AATGAATACAAATTTTTTCAT;TC=53;TCF=38;TCR=15;TR=17 GT:GL:GQ:NR 0/0:-83.08,-89.72,-221.87:30:27 1/0:-63.64,-50.39,-170.59:55:26 chr12 52843779 . T C 52 PASS ABPV=1.00e+00;FPV=1.21e-05;FR=0.2500;HP=4;MMLQ=20;NF=8;NR=16;PP=52;RMP=64.54;RPV=6.52e-01;SC=TTTGAACCCCTGGCTTCATCT;TC=161;TCF=100;TCR=61;TR=24;func=intronic;gene=KRT6B;segdup=0.93;dbsnp=rs380379 GT:GL:GQ:NR 0/0:-109.82,-139.81,-567.08:100:82 0/1:-186.27,-165.75,-481.84:87:79 chr12 65471467 . A G 200 PASS ABPV=1.00e+00;FPV=6.42e-01;FR=0.2501;HP=2;MMLQ=36;NF=7;NR=0;PP=200;RMP=38.97;RPV=4.22e-01;SC=TGCATCTTAAATATTCTTATC;TC=30;TCF=27;TCR=3;TR=7;func=intronic;gene=WIF1;1000g=0.27;dbsnp=rs2289936 GT:GL:GQ:NR 0/0:0.0,-7.62,-98.02:34:12 1/0:-69.82,-23.48,-105.09:100:18 chr12 99175091 . AAC A 86 PASS ABPV=3.61e-01;FPV=7.09e-04;FR=0.2503;HP=1;NF=4;NR=0;PP=86;RMP=34.87;RPV=9.95e-03;SC=AAACAACAACAACACACACAC;TC=43;TCF=27;TCR=16;TR=4;func=intronic;gene=ANKS1B GT:GL:GQ:NR 0/0:-4.37,-10.61,-100.0:28:17 0/1:-72.08,-41.09,-136.47:100:27 chr12 104378526 . G GACACAGAAACT 200 PASS ABPV=2.37e-01;FPV=8.53e-03;FR=0.2500;HP=1;NF=5;NR=0;PP=200;RMP=8.25;RPV=5.63e-02;SC=TGTGATTCTAGCTCTGCTATG;TC=59;TCF=49;TCR=10;TR=5 GT:GL:GQ:NR 0/0:0.0,-15.25,-297.25:67:32 1/0:-137.95,-64.82,-429.82:100:44 chr13 25169091 . A G 41 PASS ABPV=1.00e+00;FPV=1.23e-02;FR=0.2501;HP=3;MMLQ=35;NF=18;NR=1;PP=41;RMP=17.52;RPV=3.10e-02;SC=AATAACCAAAACAGTTTTTTA;TC=133;TCF=114;TCR=19;TR=19 GT:GL:GQ:NR 0/0:-140.13,-147.81,-405.22:35:57 0/1:-204.4,-186.51,-512.07:75:76 chr13 37795039 . G T 20 PASS ABPV=5.69e-01;FPV=5.25e-01;FR=0.2502;HP=1;MMLQ=40;NF=2;NR=0;PP=20;RMP=33.0;RPV=7.49e-02;SC=TCCTTGGCCTGAGCTTCTTTG;TC=19;TCF=10;TCR=9;TR=2 GT:GL:GQ:NR 0/0:0.0,-6.93,-89.94:31:11 1/0:-22.03,-9.0,-57.23:54:8 chr13 100517209 . G A 21 PASS ABPV=2.00e-01;FPV=2.14e-03;FR=0.2500;HP=2;MMLQ=35;NF=6;NR=7;PP=21;RMP=94.07;RPV=9.71e-04;SC=GTGTGTGTGTGTATATGTGTG;TC=134;TCF=62;TCR=72;TR=13 GT:GL:GQ:NR 0/0:-265.23,-279.13,-623.6:62:70 1/0:-308.0,-294.6,-524.58:56:64 chr13 114540947 . C CTCTGCTCTT 45 PASS ABPV=1.42e-01;FPV=3.34e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=45;RMP=1.0;RPV=5.62e-01;SC=CCACAGGAACCCAGCCAGCAG;TC=37;TCF=35;TCR=2;TR=2 GT:GL:GQ:NR 0/0:0.0,-11.09,-214.96:49:19 1/0:-74.37,-43.34,-288.0:100:27 chr14 19118192 . A G 200 PASS ABPV=1.00e+00;FPV=1.32e-05;FR=0.2507;HP=2;MMLQ=32;NF=68;NR=76;PP=200;RMP=53.85;RPV=5.74e-02;SC=TGCTTGCCATATGTCATGGAT;TC=771;TCF=415;TCR=356;TR=144;func=intergenic;gene=NONE(dist=NONE) OR11H12(dist=259402);segdup=0.96;dbsnp=rs77434589 GT:GL:GQ:NR 0/0:-730.61,-736.03,-2441.78:25:349 1/0:-997.51,-891.65,-2847.93:100:422 chr14 19500081 . A G 22 PASS ABPV=1.00e+00;FPV=1.61e-01;FR=0.2505;HP=3;MMLQ=22;NF=3;NR=0;PP=22;RMP=47.77;RPV=1.00e+00;SC=GGTGCACACCACTGTGGACGT;TC=22;TCF=22;TCR=0;TR=3 GT:GL:GQ:NR 0/0:-15.46,-21.36,-64.18:27:10 0/1:-27.84,-14.25,-57.82:57:12 chr14 20137380 . C T 33 PASS ABPV=1.24e-02;FPV=1.12e-09;FR=0.2500;HP=1;MMLQ=31;NF=8;NR=17;PP=33;RMP=61.98;RPV=3.46e-06;SC=TCACTGCCCTCGCCGCATGCA;TC=303;TCF=142;TCR=161;TR=25 GT:GL:GQ:NR 0/0:-373.48,-389.86,-1035.03:72:144 0/1:-475.48,-459.41,-1121.57:68:159 chr14 64496872 . G C 96 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;MMLQ=37;NF=0;NR=4;PP=96;RMP=55.12;RPV=5.17e-01;SC=AGAAATTCCAGTGGTATTCAG;TC=18;TCF=0;TCR=18;TR=4;func=intronic;gene=SYNE2;1000g=0.90;dbsnp=rs3866737 GT:GL:GQ:NR 0/0:0.0,-6.24,-83.73:28:9 0/1:-36.8,-6.24,-45.77:100:9 chr14 106881425 . A G 71 PASS ABPV=1.00e+00;FPV=1.15e-01;FR=0.2500;HP=1;MMLQ=32;NF=4;NR=10;PP=71;RMP=49.71;RPV=2.88e-01;SC=CCATCCACTCAAGCCCTTGTC;TC=78;TCF=29;TCR=49;TR=14 GT:GL:GQ:NR 0/0:-39.35,-48.57,-258.02:41:30 1/0:-231.62,-206.72,-399.17:100:48 chr14 106881452 . T C 66 PASS ABPV=1.00e+00;FPV=3.03e-01;FR=0.2509;HP=1;MMLQ=27;NF=3;NR=10;PP=66;RMP=65.33;RPV=1.89e-01;SC=CTGGTCACACTGAATTCATAC;TC=71;TCF=18;TCR=53;TR=13 GT:GL:GQ:NR 0/0:-57.13,-62.37,-258.3:24:30 0/1:-168.08,-144.38,-338.93:100:41 chr14 107034967 . T C 105 PASS ABPV=1.00e+00;FPV=6.54e-01;FR=0.2500;HP=1;MMLQ=34;NF=6;NR=9;PP=105;RMP=58.51;RPV=6.64e-01;SC=ACAGGAGATCTTCAGAGACTC;TC=57;TCF=23;TCR=34;TR=15 GT:GL:GQ:NR 0/0:-163.23,-172.19,-255.57:40:20 1/0:-379.46,-346.84,-445.34:100:39 chr15 20083754 . G A 54 PASS ABPV=1.00e+00;FPV=5.67e-01;FR=0.2500;HP=2;MMLQ=36;NF=33;NR=5;PP=54;RMP=47.07;RPV=4.22e-01;SC=AAATCATTATGTGCTTTGAGA;TC=155;TCF=131;TCR=24;TR=38 GT:GL:GQ:NR 0/0:-122.79,-137.29,-483.11:64:64 1/0:-176.25,-155.43,-655.46:88:91 chr15 20446256 . G C 57 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2500;HP=2;MMLQ=34;NF=1;NR=7;PP=57;RMP=71.88;RPV=4.32e-01;SC=CATGCAAGAAGCTGGAAAGCC;TC=33;TCF=1;TCR=32;TR=8;func=intergenic;gene=NONE(dist=NONE) LOC646096(dist=41741);segdup=0.97;dbsnp=rs3907011 GT:GL:GQ:NR 0/0:-13.82,-23.14,-131.81:42:16 0/1:-45.04,-23.56,-104.26:91:17 chr15 20875055 . C G 154 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2504;HP=3;MMLQ=37;NF=0;NR=12;PP=154;RMP=60.19;RPV=1.71e-01;SC=AATTTAAACGCAAATTAGTAA;TC=64;TCF=1;TCR=63;TR=12;func=ncRNA;gene=NBEAP1;segdup=0.93;1000g=0.26;dbsnp=rs7496378 GT:GL:GQ:NR 0/0:-9.2,-15.25,-188.16:27:22 0/1:-137.96,-94.13,-342.43:100:42 chr15 20875100 . A G 21 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2502;HP=4;MMLQ=35;NF=0;NR=6;PP=21;RMP=81.39;RPV=2.77e-01;SC=AGAGGTTAAAAATAACTTTCT;TC=33;TCF=1;TCR=32;TR=6;func=ncRNA;gene=NBEAP1;cons46=243 Name=lod=13;segdup=0.93;1000g=0.28;dbsnp=rs7497715 GT:GL:GQ:NR 0/0:-7.83,-14.75,-92.12:31:10 1/0:-92.65,-79.35,-211.07:56:23 chr15 21140945 . C T 26 PASS ABPV=1.00e+00;FPV=1.00e-01;FR=0.2506;HP=2;MMLQ=33;NF=1;NR=3;PP=26;RMP=65.04;RPV=7.12e-01;SC=ACATGTACAGCGCCACACTTC;TC=25;TCF=14;TCR=11;TR=4;func=intergenic;gene=NF1P2(dist=6320) LOC348120(dist=4822);cons46=679 Name=lod=765;segdup=1.00;1000g=0.24;dbsnp=rs12324229 GT:GL:GQ:NR 0/0:-16.95,-22.6,-60.18:26:13 0/1:-36.66,-22.19,-44.85:61:12 chr15 28900400 . G T 133 PASS ABPV=1.00e+00;FPV=6.31e-01;FR=0.2502;HP=3;MMLQ=34;NF=14;NR=0;PP=133;RMP=36.99;RPV=4.21e-01;SC=GCTTGTCATTGTAAATTTTCT;TC=57;TCF=54;TCR=3;TR=14 GT:GL:GQ:NR 0/0:-26.38,-32.94,-192.24:30:27 1/0:-71.34,-32.36,-180.89:100:30 chr15 75656200 . G A 75 PASS ABPV=1.00e+00;FPV=6.28e-01;FR=0.2507;HP=6;MMLQ=37;NF=4;NR=0;PP=75;RMP=47.43;RPV=1.00e+00;SC=CCAGCCCCCCGGCCCCGTTTT;TC=16;TCF=16;TCR=0;TR=4 GT:GL:GQ:NR 0/0:-7.14,-12.68,-76.44:25:8 0/1:-34.75,-8.99,-31.71:100:8 chr15 76075732 . A C 29 PASS ABPV=1.00e+00;FPV=9.97e-01;FR=0.2501;HP=2;MMLQ=34;NF=11;NR=15;PP=29;RMP=61.41;RPV=9.58e-01;SC=ATCCCTATCTATCCAGGCCTT;TC=64;TCF=22;TCR=42;TR=26 GT:GL:GQ:NR 0/0:-89.15,-96.33,-237.9:32:31 1/0:-134.14,-119.09,-238.26:63:33 chr15 100340178 . C G 52 PASS ABPV=1.00e+00;FPV=1.76e-01;FR=0.2500;HP=1;MMLQ=31;NF=5;NR=5;PP=52;RMP=87.78;RPV=1.32e-01;SC=AGTGTCTTCTCGTTCCCACGC;TC=64;TCF=31;TCR=33;TR=10;func=ncRNA;gene=DNM1P46;cons46=699 Name=lod=923;segdup=0.97;sift=0.27 GT:GL:GQ:NR 0/0:-139.12,-149.96,-310.47:37:36 1/0:-206.67,-186.19,-317.68:87:38 chr15 102303399 . C T 65 PASS ABPV=1.00e+00;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=30;PP=65;RMP=65.58;RPV=1.00e-00;SC=AGAGCTGCTGCCCAACCTGCA;TC=90;TCF=40;TCR=50;TR=35;func=intergenic;gene=TARSL2(dist=38754) OR4F6(dist=42524);cons46=920 Name=lod=7327;segdup=0.98;1000g=0.50;dbsnp=rs71416239 GT:GL:GQ:NR 0/0:-129.26,-138.34,-250.21:41:46 0/1:-118.78,-95.27,-224.48:100:44 chr15 102506389 . C T 50 PASS ABPV=6.29e-01;FPV=1.27e-01;FR=0.2500;HP=1;MMLQ=34;NF=1;NR=3;PP=50;RMP=67.19;RPV=2.63e-01;SC=GGATGCCCTGCAGTACCTGCA;TC=32;TCF=13;TCR=19;TR=4 GT:GL:GQ:NR 0/0:-3.9,-15.65,-133.88:52:17 0/1:-31.25,-11.29,-72.06:84:15 chr16 9250260 . T G 22 PASS ABPV=1.00e+00;FPV=1.00e-02;FR=0.2500;HP=2;MMLQ=29;NF=0;NR=4;PP=22;RMP=37.36;RPV=8.85e-01;SC=CACCTATTATTCCATGAATTC;TC=27;TCF=16;TCR=11;TR=4;func=intergenic;gene=C16orf72(dist=36705) MIR548X(dist=78514);cons46=749 Name=lod=1471;1000g=0.73;dbsnp=rs12929693 GT:GL:GQ:NR 0/0:-1.84,-10.83,-100.69:40:14 0/1:-25.85,-12.37,-70.66:56:13 chr16 21747662 . G A 36 PASS ABPV=1.00e+00;FPV=2.01e-01;FR=0.2500;HP=1;MMLQ=34;NF=16;NR=6;PP=36;RMP=40.34;RPV=5.40e-05;SC=CTGTCTTTCAGTCTGTTCGGA;TC=159;TCF=79;TCR=80;TR=22 GT:GL:GQ:NR 0/0:-69.29,-88.69,-470.14:85:75 1/0:-171.53,-154.82,-534.35:70:84 chr16 28618446 . T C 36 PASS ABPV=1.00e+00;FPV=8.61e-01;FR=0.2500;HP=3;MMLQ=32;NF=6;NR=14;PP=36;RMP=63.74;RPV=5.40e-01;SC=ACACAGCCTGTCCCAGGCCAG;TC=75;TCF=18;TCR=57;TR=20 GT:GL:GQ:NR 0/0:-33.24,-41.67,-205.86:38:27 0/1:-113.92,-97.17,-312.83:70:48 chr16 33390329 . G C 24 PASS ABPV=6.16e-01;FPV=4.32e-02;FR=0.2500;HP=2;MMLQ=34;NF=5;NR=0;PP=24;RMP=54.47;RPV=1.00e+00;SC=TTAGAAACAGGTTCACAATTG;TC=40;TCF=40;TCR=0;TR=5;func=intergenic;gene=LOC390705(dist=91627) LINC00273(dist=570723);segdup=0.97;1000g=0.32;dbsnp=rs12232434 GT:GL:GQ:NR 0/0:-6.09,-14.55,-170.95:38:21 0/1:-47.14,-33.16,-147.34:58:19 chr16 33401967 . G A 116 PASS ABPV=1.00e+00;FPV=1.64e-02;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=15;PP=116;RMP=51.2;RPV=2.96e-01;SC=GAGGTCTGCCGACAGCTGCAC;TC=172;TCF=102;TCR=70;TR=31;func=intergenic;gene=LOC390705(dist=103265) LINC00273(dist=559085);cons46=611 Name=lod=406;segdup=0.97;dbsnp=rs8047578 GT:GL:GQ:NR 0/0:-133.55,-144.14,-490.22:47:76 1/0:-209.17,-173.99,-648.51:100:96 chr16 33407954 . C G 34 PASS ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=3;MMLQ=34;NF=0;NR=3;PP=34;RMP=61.08;RPV=5.19e-01;SC=GAAATTGTCTCGGGCCTGAAG;TC=17;TCF=3;TCR=14;TR=3 GT:GL:GQ:NR 0/0:-10.82,-16.36,-77.44:25:9 1/0:-63.55,-47.37,-59.15:58:8 chr16 46405120 . C G 37 PASS ABPV=3.94e-02;FPV=4.07e-03;FR=0.2510;HP=2;MMLQ=40;NF=2;NR=1;PP=37;RMP=51.27;RPV=3.18e-03;SC=CGATTCCATTCGATAATGATT;TC=62;TCF=34;TCR=28;TR=3 GT:GL:GQ:NR 0/0:-129.24,-134.38,-161.33:24:28 0/1:-205.7,-188.69,-196.8:42:34 chr16 58148083 . C CACACGCAGGTACA 31 PASS ABPV=1.69e-01;FPV=1.00e+00;FR=0.2500;HP=2;NF=0;NR=2;PP=31;RMP=88.0;RPV=3.34e-03;SC=CAGGGAAGCACCCACCCTTGT;TC=35;TCF=0;TCR=35;TR=2 GT:GL:GQ:NR 0/0:-11.28,-21.68,-223.8:46:16 0/1:-62.86,-30.44,-243.59:100:20 chr17 5036281 . G C 48 PASS ABPV=1.00e+00;FPV=8.00e-01;FR=0.2500;HP=1;MMLQ=32;NF=14;NR=49;PP=48;RMP=47.67;RPV=9.22e-01;SC=AAGCACAGTAGCAAAGTAATG;TC=214;TCF=48;TCR=166;TR=63 GT:GL:GQ:NR 0/0:-506.02,-514.23,-1090.2:37:117 0/1:-460.03,-440.62,-871.14:82:97 chr17 6328747 . T G 200 PASS ABPV=1.00e+00;FPV=8.77e-01;FR=0.2507;HP=4;MMLQ=32;NF=8;NR=5;PP=200;RMP=59.22;RPV=9.45e-01;SC=GGCCACTTGCTCCCTGCCTGG;TC=36;TCF=24;TCR=12;TR=13 GT:GL:GQ:NR 0/0:-4.84,-10.37,-69.24:25:8 0/1:-116.1,-23.7,-86.84:100:28 chr17 14140191 . G A 125 PASS ABPV=1.00e+00;FPV=3.98e-02;FR=0.2500;HP=1;MMLQ=34;NF=2;NR=11;PP=125;RMP=71.76;RPV=3.84e-02;SC=AGCTGTTTACGGCGCTGACTC;TC=95;TCF=24;TCR=71;TR=13;func=upstream;gene=CDRT15;segdup=0.99;1000g=0.17;dbsnp=rs28533558 GT:GL:GQ:NR 0/0:-146.51,-156.3,-338.05:44:40 0/1:-162.79,-125.58,-384.62:100:55 chr17 21904955 . G A 29 PASS ABPV=1.46e-01;FPV=3.00e-01;FR=0.2500;HP=2;MMLQ=33;NF=1;NR=7;PP=29;RMP=77.08;RPV=5.90e-05;SC=GTGGCACGGCGCTGTATCCTG;TC=95;TCF=9;TCR=86;TR=8 GT:GL:GQ:NR 0/0:-95.23,-110.26,-302.39:67:42 0/1:-104.15,-88.94,-334.7:64:53 chr17_gl000205_random 114392 . G GC 200 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2503;HP=1;NF=1;NR=9;PP=200;RMP=62.13;RPV=8.86e-01;SC=GAGCTTCTATGAGGCGTGGGG;TC=28;TCF=1;TCR=27;TR=10;func=intergenic;gene=NONE(dist=NONE) MGC70870(dist=2231) GT:GL:GQ:NR 0/0:0.0,-6.24,-93.01:28:9 0/1:-137.06,-63.68,-124.76:100:19 chr17_gl000205_random 118186 . TCGC T 157 PASS ABPV=1.00e+00;FPV=4.85e-02;FR=0.2506;HP=1;NF=4;NR=5;PP=157;RMP=51.77;RPV=1.51e-01;SC=CCATCATAAGTCGCATCCCGG;TC=55;TCF=23;TCR=32;TR=9;func=ncRNA;gene=MGC70870;cons46=824 Name=lod=2972;segdup=0.90 GT:GL:GQ:NR 0/0:-80.93,-86.51,-246.22:26:23 0/1:-151.92,-104.34,-309.99:100:34 chr17_gl000205_random 118289 . G A 30 PASS ABPV=1.00e+00;FPV=2.43e-02;FR=0.2500;HP=1;MMLQ=38;NF=1;NR=4;PP=30;RMP=51.3;RPV=5.18e-01;SC=TGAGCTCAGTGGTGCTACCTA;TC=38;TCF=20;TCR=18;TR=5 GT:GL:GQ:NR 0/0:-92.27,-100.53,-170.2:37:15 0/1:-193.59,-178.31,-262.43:64:23 chr17_gl000205_random 122791 . T C 124 PASS ABPV=1.00e+00;FPV=6.72e-01;FR=0.2504;HP=1;MMLQ=34;NF=8;NR=0;PP=124;RMP=54.5;RPV=1.00e+00;SC=GATATAAACTTCTAAAATTCA;TC=30;TCF=30;TCR=0;TR=8;func=intergenic;gene=MGC70870(dist=3059) NONE(dist=NONE) GT:GL:GQ:NR 0/0:-33.82,-39.98,-100.64:28:10 1/0:-177.82,-140.79,-190.46:100:20 chr18 14183747 . T C 115 PASS ABPV=1.00e+00;FPV=9.72e-01;FR=0.2500;HP=5;MMLQ=36;NF=49;NR=88;PP=115;RMP=54.47;RPV=9.86e-01;SC=ACAAAGAAAATAGAACGCCTT;TC=444;TCF=156;TCR=288;TR=137 GT:GL:GQ:NR 0/0:-919.95,-948.86,-1765.89:100:211 0/1:-1189.4,-1154.37,-1918.79:100:233 chr19 3611146 . A G 30 PASS ABPV=1.00e+00;FPV=5.15e-01;FR=0.2501;HP=1;MMLQ=24;NF=6;NR=1;PP=30;RMP=42.3;RPV=2.44e-01;SC=CCCTGTGCTCAGAGGTGGGGG;TC=36;TCF=26;TCR=10;TR=7;func=ncRNA;gene=C19orf29-AS1;1000g=0.56;dbsnp=rs2074786 GT:GL:GQ:NR 0/0:-27.63,-35.13,-121.04:34:15 0/1:-69.97,-54.53,-137.67:65:21 chr19 12543121 . C G 200 PASS ABPV=1.00e+00;FPV=7.14e-01;FR=0.2502;HP=7;MMLQ=40;NF=11;NR=0;PP=200;RMP=33.87;RPV=7.50e-01;SC=TTCTTTGCTTCTTTTTAAATT;TC=41;TCF=40;TCR=1;TR=11;func=intronic;gene=ZNF443;segdup=0.96;dbsnp=rs74181652 GT:GL:GQ:NR 0/0:-8.47,-15.46,-153.74:32:20 0/1:-71.21,-15.46,-97.4:100:21 chr19 15014189 . T C 90 PASS ABPV=1.00e+00;FPV=1.97e-01;FR=0.2500;HP=4;MMLQ=100;NF=2;NR=5;PP=90;RMP=90.56;RPV=4.68e-01;SC=GAGTGAGTTGTGGGTTGCAGC;TC=39;TCF=16;TCR=23;TR=7 GT:GL:GQ:NR 0/0:-190.71,-200.49,-255.11:44:24 1/0:-174.95,-145.84,-178.61:100:15 chr19 41515263 . A G 88 PASS ABPV=3.76e-01;FPV=1.82e-01;FR=0.2500;HP=2;MMLQ=33;NF=7;NR=3;PP=88;RMP=64.16;RPV=2.48e-04;SC=AGCGCCCCCAAGGACCTCATC;TC=93;TCF=40;TCR=53;TR=10;func=exonic;gene=CYP2B6;exon_func=nonsynonymous SNV;AAchange=NM_000767:c.A785G:p.K262R;segdup=0.92;1000g=0.20;dbsnp=rs2279343;pp2=0.0;phylop=0.086093;mutT=1.0E-6;LRT=0.999974 GT:GL:GQ:NR 0/0:-4.81,-28.32,-273.38:100:41 0/1:-65.82,-37.11,-263.4:100:52 chr19 42188037 . C T 114 PASS ABPV=1.00e+00;FPV=6.06e-02;FR=0.2500;HP=4;MMLQ=34;NF=2;NR=8;PP=114;RMP=98.9;RPV=1.54e-02;SC=GTGTGGCCCCCTTGGTTCCCC;TC=73;TCF=11;TCR=62;TR=10 GT:GL:GQ:NR 0/0:-205.49,-214.25,-251.15:29:29 0/1:-379.34,-343.91,-357.8:15:44 chr19 50474708 . T G 61 PASS ABPV=1.00e+00;FPV=7.17e-01;FR=0.2501;HP=2;MMLQ=30;NF=5;NR=1;PP=61;RMP=67.96;RPV=3.09e-02;SC=CTGGGCTCAGTGTCCCAGAGC;TC=37;TCF=18;TCR=19;TR=6 GT:GL:GQ:NR 0/0:-86.34,-93.74,-137.77:33:15 0/1:-129.81,-107.4,-147.05:95:22 chr19 52977823 . A G 102 PASS ABPV=1.00e+00;FPV=3.15e-01;FR=0.2507;HP=2;MMLQ=35;NF=0;NR=4;PP=102;RMP=41.58;RPV=8.84e-01;SC=GTTTCTCTCCAGTATGAATTC;TC=15;TCF=4;TCR=11;TR=4;func=intronic;gene=ZNF578;cons46=395 Name=lod=54;1000g=0.94;dbsnp=rs1673901 GT:GL:GQ:NR 0/0:0.0,-5.54,-65.87:25:9 1/0:-36.12,-4.16,-18.86:71:6 chr19 54726711 . G T 43 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2504;HP=3;MMLQ=31;NF=22;NR=2;PP=43;RMP=52.84;RPV=6.78e-01;SC=GTCCCCGCCCGGGTGCCTCCT;TC=53;TCF=45;TCR=8;TR=24 GT:GL:GQ:NR 0/0:-47.88,-54.03,-95.64:28:18 1/0:-164.89,-146.64,-206.88:77:35 chr2 905553 . G C 76 PASS ABPV=1.62e-02;FPV=5.75e-08;FR=0.2500;HP=2;MMLQ=31;NF=1;NR=7;PP=76;RMP=95.73;RPV=1.04e-02;SC=GCCTGCACTGGGTCTGGTGTT;TC=128;TCF=69;TCR=59;TR=8 GT:GL:GQ:NR 0/0:-314.19,-325.21,-450.94:49:57 0/1:-390.34,-364.48,-513.78:100:71 chr2 905595 . G C 24 PASS ABPV=1.21e-01;FPV=1.79e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=1;PP=24;RMP=13.0;RPV=6.96e-04;SC=GCCTGCACTGGGTCTGGTGTT;TC=79;TCF=45;TCR=34;TR=6 GT:GL:GQ:NR 0/0:-210.22,-219.58,-290.19:42:42 1/0:-197.49,-183.47,-250.46:59:38 chr2 91885842 . G A 37 PASS ABPV=1.00e+00;FPV=2.46e-01;FR=0.2502;HP=1;MMLQ=36;NF=4;NR=0;PP=37;RMP=71.85;RPV=4.22e-01;SC=CCAACATTACGGAATTTGGAT;TC=27;TCF=24;TCR=3;TR=4 GT:GL:GQ:NR 0/0:-11.45,-18.39,-83.47:31:11 0/1:-59.01,-41.99,-86.53:72:16 chr2 96525556 . C T 37 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2503;HP=1;MMLQ=37;NF=60;NR=2;PP=37;RMP=45.25;RPV=9.49e-01;SC=TCTCCTTATACGTCTTTAATA;TC=91;TCF=87;TCR=4;TR=62 GT:GL:GQ:NR 0/0:-304.4,-310.82,-406.42:29:43 0/1:-411.62,-394.62,-459.09:72:48 chr2 107042620 . C T 45 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=4;MMLQ=33;NF=0;NR=10;PP=45;RMP=77.64;RPV=2.94e-02;SC=GCAAGAGCTACAAATACAAAA;TC=69;TCF=1;TCR=68;TR=10;func=intronic;gene=RGPD3;cons46=333 Name=lod=30;segdup=0.99;dbsnp=rs2433787 GT:GL:GQ:NR 0/0:-9.17,-23.45,-154.19:63:21 1/0:-107.84,-88.96,-294.09:80:48 chr2 132860931 . G A 113 PASS ABPV=1.00e+00;FPV=5.61e-01;FR=0.2507;HP=1;MMLQ=38;NF=0;NR=8;PP=113;RMP=69.43;RPV=9.58e-01;SC=GAAGAATGTGGTAAAGCCTTT;TC=22;TCF=2;TCR=20;TR=8 GT:GL:GQ:NR 0/0:-12.66,-18.1,-56.72:25:9 1/0:-57.64,-23.24,-50.67:100:13 chr2 133020074 . G A 33 PASS ABPV=1.00e+00;FPV=9.94e-01;FR=0.2501;HP=2;MMLQ=36;NF=45;NR=12;PP=33;RMP=47.59;RPV=9.08e-01;SC=ATTTCAGAAGGGAAAATATCC;TC=167;TCF=131;TCR=36;TR=57;func=intergenic;gene=ANKRD30BL(dist=4532) GPR39(dist=154073);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs111959326 GT:GL:GQ:NR 0/0:-698.84,-706.52,-798.38:35:80 1/0:-786.87,-770.7,-903.5:68:87 chr2 133020186 . T C 66 PASS ABPV=1.00e+00;FPV=1.55e-01;FR=0.2500;HP=1;MMLQ=34;NF=52;NR=51;PP=66;RMP=46.69;RPV=9.65e-01;SC=TAGCTTTGTGTTCATACCACT;TC=402;TCF=237;TCR=165;TR=103;func=intergenic;gene=ANKRD30BL(dist=4644) GPR39(dist=153961);cons46=762 Name=lod=1662;segdup=0.91;dbsnp=rs112259198 GT:GL:GQ:NR 0/0:-1712.52,-1737.48,-1975.72:100:192 1/0:-1974.59,-1950.96,-2276.74:100:211 chr2 133020542 . G A 50 PASS ABPV=1.00e+00;FPV=1.14e-01;FR=0.2503;HP=1;MMLQ=32;NF=3;NR=6;PP=50;RMP=53.94;RPV=7.08e-02;SC=CTATCCAAGTGGATCCAAATT;TC=66;TCF=24;TCR=42;TR=9;func=intergenic;gene=ANKRD30BL(dist=5000) GPR39(dist=153605);cons46=762 Name=lod=1662;segdup=0.93;dbsnp=rs2257591 GT:GL:GQ:NR 0/0:-181.04,-187.42,-271.44:29:29 1/0:-243.98,-224.07,-313.1:84:37 chr2 166801924 . C G 78 PASS ABPV=1.00e+00;FPV=5.71e-01;FR=0.2507;HP=3;MMLQ=34;NF=4;NR=0;PP=78;RMP=67.75;RPV=7.49e-01;SC=TATTTACAAACTGGCAATAGA;TC=18;TCF=17;TCR=1;TR=4;func=ncRNA;gene=LOC100506134;1000g=0.64;dbsnp=rs6432853 GT:GL:GQ:NR 0/0:-34.05,-39.57,-91.24:25:8 1/0:-42.79,-16.34,-58.89:100:10 chr2 204055943 . T C 59 PASS ABPV=2.58e-01;FPV=8.29e-02;FR=0.2500;HP=2;MMLQ=33;NF=11;NR=2;PP=59;RMP=61.13;RPV=3.22e-06;SC=ATGGCCGCCATCCTCATGACA;TC=128;TCF=65;TCR=63;TR=13;func=intronic;gene=NBEAL1;cons46=702 Name=lod=950;dbsnp=rs4561645 GT:GL:GQ:NR 0/0:-41.52,-53.03,-440.53:51:70 1/0:-89.56,-67.55,-350.54:93:58 chr2 210594540 . A G 200 PASS ABPV=1.00e+00;FPV=9.70e-01;FR=0.2507;HP=1;MMLQ=30;NF=10;NR=1;PP=200;RMP=52.61;RPV=9.37e-01;SC=CGAATGCAAGATATAGTTAAA;TC=27;TCF=25;TCR=2;TR=11;func=intronic;gene=MAP2;1000g=0.88;dbsnp=rs4673486 GT:GL:GQ:NR 0/0:0.0,-5.54,-62.54:25:8 0/1:-93.19,-14.77,-63.29:100:19 chr2 211444533 . GGT G 32 PASS ABPV=1.78e-01;FPV=1.96e-01;FR=0.2503;HP=2;NF=1;NR=3;PP=32;RMP=50.82;RPV=2.40e-03;SC=TGTTTCTTCGGGTGTGTGTGT;TC=54;TCF=11;TCR=43;TR=4 GT:GL:GQ:NR 0/0:-4.14,-10.38,-103.02:28:17 1/0:-41.6,-23.06,-172.26:78:37 chr2 227659818 . T TCAAGTGAGGA 93 PASS ABPV=3.68e-02;FPV=2.37e-01;FR=0.2500;HP=1;NF=0;NR=3;PP=93;RMP=91.0;RPV=7.64e-05;SC=CTCTCACCGCTGCCCAGGGGT;TC=63;TCF=5;TCR=58;TR=3 GT:GL:GQ:NR 0/0:-17.96,-35.28,-330.9:77:30 0/1:-94.07,-50.73,-458.79:100:41 chr2 227954599 . G A 200 PASS ABPV=1.00e+00;FPV=9.19e-01;FR=0.2507;HP=2;MMLQ=31;NF=6;NR=4;PP=200;RMP=46.35;RPV=9.51e-01;SC=TCTCCTTTTGGGCCTCTTCCT;TC=25;TCF=16;TCR=9;TR=10;func=exonic;gene=COL4A4;exon_func=nonsynonymous SNV;AAchange=NM_000092:c.C1444T:p.P482S;1000g=0.55;dbsnp=rs2229814;sift=0.44;pp2=0.0;phylop=0.897442;mutT=9.0E-5;LRT=0.824593 GT:GL:GQ:NR 0/0:0.0,-5.54,-68.56:25:9 0/1:-80.77,-11.53,-34.97:100:16 chr2 233273018 . G A 32 PASS ABPV=1.00e+00;FPV=3.62e-01;FR=0.2500;HP=3;MMLQ=34;NF=13;NR=4;PP=32;RMP=56.47;RPV=8.89e-03;SC=TTCCCATGGGGACCCCAGACC;TC=102;TCF=59;TCR=43;TR=17 GT:GL:GQ:NR 0/0:-50.24,-59.48,-309.03:41:45 0/1:-159.89,-144.07,-409.74:66:57 chr20 29633938 . A G 28 PASS ABPV=1.00e+00;FPV=1.27e-01;FR=0.2500;HP=2;MMLQ=34;NF=16;NR=24;PP=28;RMP=56.91;RPV=2.94e-01;SC=AAATGACTGGAATTTTTGTTT;TC=192;TCF=84;TCR=108;TR=40;func=ncRNA;gene=FRG1B;cons46=514 Name=lod=163;segdup=0.96;dbsnp=rs4006818 GT:GL:GQ:NR 0/0:-963.63,-978.07,-1139.59:64:101 1/0:-1046.34,-1031.41,-1112.07:63:91 chr20 33356511 . C T 44 PASS ABPV=1.00e+00;FPV=7.49e-01;FR=0.2507;HP=1;MMLQ=37;NF=0;NR=4;PP=44;RMP=57.46;RPV=6.28e-01;SC=AGTTTACCACCAGAAAAATGG;TC=17;TCF=1;TCR=16;TR=4;func=intronic;gene=NCOA6;cons46=243 Name=lod=13;1000g=0.36;dbsnp=rs2295353 GT:GL:GQ:NR 0/0:0.0,-5.54,-70.65:25:8 0/1:-49.75,-31.07,-63.51:79:9 chr21 14424170 . C G 200 PASS ABPV=1.00e+00;FPV=7.37e-05;FR=0.2502;HP=1;MMLQ=31;NF=51;NR=68;PP=200;RMP=55.06;RPV=7.01e-02;SC=GGAAAGAACACCTGACACGGC;TC=637;TCF=318;TCR=319;TR=119 GT:GL:GQ:NR 0/0:-1068.97,-1075.78,-2090.04:31:272 1/0:-1608.82,-1559.51,-2814.14:100:365 chr22 16256578 . G T 200 PASS ABPV=2.18e-01;FPV=6.87e-08;FR=0.2502;HP=4;MMLQ=34;NF=19;NR=8;PP=200;RMP=40.16;RPV=2.46e-02;SC=TGGCTCTGATGTTTCATTATG;TC=253;TCF=194;TCR=59;TR=27 GT:GL:GQ:NR 0/0:-139.12,-145.98,-745.94:31:118 0/1:-324.53,-220.54,-788.14:100:135 chr22 24640438 . TCA T 58 PASS ABPV=5.57e-01;FPV=3.19e-02;FR=0.2503;HP=2;NF=2;NR=1;PP=58;RMP=48.68;RPV=9.37e-01;SC=ATACATTCACTCACACACACA;TC=27;TCF=25;TCR=2;TR=3 GT:GL:GQ:NR 0/0:-4.37,-10.61,-107.94:28:12 0/1:-47.48,-22.82,-120.6:100:15 chr22 42524924 . A G 32 PASS ABPV=1.00e+00;FPV=1.78e-02;FR=0.2500;HP=2;MMLQ=35;NF=0;NR=4;PP=32;RMP=71.83;RPV=5.74e-01;SC=TGTCCAAGAGACCGTTGGGGC;TC=31;TCF=14;TCR=17;TR=4 GT:GL:GQ:NR 0/0:-1.84,-12.87,-112.28:49:17 1/0:-35.2,-19.47,-73.62:66:14 chr3 6522043 . G A 62 PASS ABPV=1.00e+00;FPV=5.16e-01;FR=0.2507;HP=3;MMLQ=37;NF=4;NR=0;PP=62;RMP=44.82;RPV=7.49e-01;SC=TAACTGCAAAGTAGGAACACG;TC=19;TCF=18;TCR=1;TR=4 GT:GL:GQ:NR 0/0:0.0,-5.54,-65.36:25:9 1/0:-46.21,-23.49,-68.33:96:10 chr3 135742089 . GAAAATA G 56 PASS ABPV=2.53e-02;FPV=5.62e-01;FR=0.2500;HP=4;NF=0;NR=2;PP=56;RMP=97.0;RPV=4.10e-05;SC=GTTTTGTTTTGAAAATATTTT;TC=55;TCF=2;TCR=53;TR=2 GT:GL:GQ:NR 0/0:-171.19,-180.69,-401.53:43:27 1/0:-163.7,-138.73,-368.83:100:28 chr3 195453014 . G A 73 PASS ABPV=1.00e+00;FPV=9.99e-01;FR=0.2500;HP=3;MMLQ=31;NF=44;NR=44;PP=73;RMP=52.04;RPV=1.00e-00;SC=GACAGCACCCGGGGCCACGAC;TC=210;TCF=115;TCR=95;TR=88 GT:GL:GQ:NR 0/0:-596.82,-608.68,-929.74:53:99 0/1:-825.59,-800.41,-1040.36:100:111 chr3 195453412 . C T 21 PASS ABPV=1.00e+00;FPV=1.25e-02;FR=0.2502;HP=2;MMLQ=25;NF=13;NR=52;PP=21;RMP=62.2;RPV=1.00e-00;SC=CCACGACTGCCCGGACGAGGC;TC=219;TCF=89;TCR=130;TR=65 GT:GL:GQ:NR 0/0:-275.62,-282.43,-681.47:31:103 0/1:-362.65,-349.41,-719.87:55:117 chr3 195506775 . G A 87 PASS ABPV=1.00e+00;FPV=8.81e-01;FR=0.2500;HP=1;MMLQ=34;NF=11;NR=4;PP=87;RMP=30.23;RPV=4.10e-02;SC=AGGAAGTGTCGGTGACAGGAA;TC=69;TCF=34;TCR=35;TR=15;func=exonic;gene=MUC4;exon_func=synonymous SNV;AAchange=NM_018406:c.C11676T:p.H3892H;cons46=381 Name=lod=47;segdup=0.92;1000g=0.48;dbsnp=rs79609066 GT:GL:GQ:NR 0/0:-215.78,-225.62,-329.97:44:31 0/1:-253.55,-225.09,-324.19:100:38 chr3 195507372 . C A 72 PASS ABPV=1.00e+00;FPV=9.50e-01;FR=0.2510;HP=1;MMLQ=31;NF=12;NR=10;PP=72;RMP=82.02;RPV=4.71e-01;SC=GAGGGGTGGCCTGACCTGTGG;TC=76;TCF=33;TCR=43;TR=22 GT:GL:GQ:NR 0/0:-85.59,-90.71,-175.03:23:27 0/1:-302.0,-277.02,-435.24:100:49 chr3 195509974 . A G 107 PASS ABPV=1.00e+00;FPV=4.52e-02;FR=0.2501;HP=1;MMLQ=33;NF=7;NR=15;PP=107;RMP=66.83;RPV=1.62e-01;SC=ATGACCTGTGAACACTGAGGA;TC=127;TCF=50;TCR=77;TR=22 GT:GL:GQ:NR 0/0:-281.04,-289.1,-469.31:36:51 0/1:-474.46,-441.44,-679.46:100:76 chr4 3589510 . G A 82 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=35;NF=28;NR=15;PP=82;RMP=39.79;RPV=1.00e-00;SC=ACTTCCAGATGAGACTTCCTG;TC=89;TCF=62;TCR=27;TR=43;func=ncRNA;gene=FLJ35424 GT:GL:GQ:NR 0/0:-202.17,-216.0,-372.38:61:36 0/1:-618.94,-591.66,-690.1:100:53 chr4 5747131 . C A 40 PASS ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=33;NF=1;NR=19;PP=40;RMP=63.27;RPV=9.99e-01;SC=AAATTGGCTACATTAGAGAGA;TC=45;TCF=5;TCR=40;TR=20 GT:GL:GQ:NR 0/0:-175.23,-182.17,-227.63:31:19 1/0:-264.71,-246.95,-301.81:75:26 chr4 70261725 . G A 25 PASS ABPV=1.00e+00;FPV=8.43e-01;FR=0.2503;HP=3;MMLQ=36;NF=1;NR=5;PP=25;RMP=77.58;RPV=8.09e-01;SC=TGTGGCCCTGGGGTAGTTACT;TC=19;TCF=3;TCR=16;TR=6 GT:GL:GQ:NR 0/0:-25.09,-31.31,-100.1:28:11 1/0:-62.48,-48.33,-68.8:59:8 chr5 837488 . C A 84 PASS ABPV=3.03e-01;FPV=2.26e-02;FR=0.2502;HP=2;MMLQ=35;NF=22;NR=3;PP=84;RMP=67.65;RPV=4.45e-09;SC=ACCTGGAGAACTCCTTTGTCC;TC=225;TCF=128;TCR=97;TR=25 GT:GL:GQ:NR 0/0:-71.02,-77.56,-596.34:30:92 0/1:-157.13,-129.33,-794.35:100:133 chr5 34192944 . A G 136 PASS ABPV=3.53e-01;FPV=1.29e-04;FR=0.2500;HP=1;MMLQ=31;NF=17;NR=13;PP=136;RMP=51.73;RPV=7.15e-05;SC=GCAGTGGATGAAGGCCCCTCA;TC=261;TCF=140;TCR=121;TR=30 GT:GL:GQ:NR 0/0:-120.41,-138.2,-806.35:79:120 0/1:-199.6,-159.91,-913.41:100:141 chr5 36200413 . G A 33 PASS ABPV=1.25e-02;FPV=1.03e-02;FR=0.2511;HP=3;MMLQ=34;NF=2;NR=4;PP=33;RMP=98.68;RPV=2.69e-06;SC=GAAAATGTATGTTATAAATAT;TC=109;TCF=30;TCR=79;TR=6 GT:GL:GQ:NR 0/0:-295.77,-300.82,-490.03:23:53 1/0:-290.08,-274.08,-469.93:67:56 chr5 41909830 . C T 27 PASS ABPV=5.28e-01;FPV=2.35e-03;FR=0.2504;HP=18;MMLQ=0;NF=0;NR=3;PP=27;RMP=14.14;RPV=9.29e-01;SC=AGATATCTTTCTTTTTTTTTT;TC=28;TCF=21;TCR=7;TR=3 GT:GL:GQ:NR 0/0:-4.61,-10.58,-40.73:26:11 0/1:-41.44,-26.72,-53.62:62:17 chr5 54329850 . C CTGCTTTACTTA 68 PASS ABPV=5.01e-01;FPV=1.00e+00;FR=0.2503;HP=1;NF=0;NR=2;PP=68;RMP=90.0;RPV=7.41e-02;SC=CATATGGGGTCCATTTTTGCA;TC=21;TCF=0;TCR=21;TR=2 GT:GL:GQ:NR 0/0:0.0,-6.24,-122.94:28:9 1/0:-45.59,-6.93,-110.5:100:12 chr5 58121059 . G A 112 PASS ABPV=1.00e+00;FPV=4.22e-01;FR=0.2501;HP=2;MMLQ=35;NF=0;NR=5;PP=112;RMP=75.51;RPV=4.68e-01;SC=TACAGAGTCCGAGCTAATTGT;TC=26;TCF=3;TCR=23;TR=5 GT:GL:GQ:NR 0/0:-31.77,-39.38,-124.25:34:12 0/1:-43.94,-9.7,-79.61:100:15 chr5 169535734 . C A 20 PASS ABPV=1.00e+00;FPV=1.00e+00;FR=0.2507;HP=1;MMLQ=34;NF=0;NR=2;PP=20;RMP=68.72;RPV=3.31e-01;SC=CAGGAGCCTCCGAGGAATCCA;TC=13;TCF=0;TCR=13;TR=2;func=UTR3;gene=FOXI1;1000g=0.35;dbsnp=rs6873124 GT:GL:GQ:NR 0/0:-5.3,-10.84,-76.27:25:8 1/0:-15.88,-2.77,-16.56:54:5 chr5 175467765 . A C 34 PASS ABPV=1.00e+00;FPV=6.86e-01;FR=0.2503;HP=3;MMLQ=37;NF=4;NR=7;PP=34;RMP=58.23;RPV=9.60e-01;SC=AGGAAAGCAGATTTGTACATC;TC=32;TCF=15;TCR=17;TR=11 GT:GL:GQ:NR 0/0:-48.25,-54.62,-116.89:29:16 0/1:-64.43,-48.26,-102.15:68:18 chr5 180047739 . CGT C 40 PASS ABPV=3.01e-01;FPV=4.20e-02;FR=0.2503;HP=3;NF=0;NR=2;PP=40;RMP=66.37;RPV=1.63e-01;SC=AAGGGGCCGGCGTGTGTGTGT;TC=28;TCF=11;TCR=17;TR=2 GT:GL:GQ:NR 0/0:-15.43,-21.66,-115.16:28:17 0/1:-35.79,-15.44,-86.67:86:11 chr6 26370657 . A G 26 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=1;MMLQ=34;NF=25;NR=18;PP=26;RMP=46.67;RPV=9.65e-01;SC=ACAGTGGAGCAACGCCAAGGG;TC=112;TCF=61;TCR=51;TR=43 GT:GL:GQ:NR 0/0:-408.78,-416.97,-671.27:37:70 1/0:-270.25,-255.76,-422.39:61:42 chr6 26370659 . C T 32 PASS ABPV=1.00e+00;FPV=9.98e-01;FR=0.2500;HP=2;MMLQ=34;NF=25;NR=17;PP=32;RMP=48.69;RPV=9.08e-01;SC=AGTGGAGCAACGCCAAGGGAG;TC=114;TCF=61;TCR=53;TR=42 GT:GL:GQ:NR 0/0:-408.78,-419.23,-664.68:47:70 1/0:-278.07,-262.18,-440.62:67:44 chr6 35838820 . A ATTCTTACTTGG 44 PASS ABPV=1.42e-01;FPV=7.50e-01;FR=0.2500;HP=1;NF=0;NR=2;PP=44;RMP=90.0;RPV=2.64e-03;SC=CTCTACCAGAATGAAAAGTCT;TC=37;TCF=1;TCR=36;TR=2 GT:GL:GQ:NR 0/0:-22.8,-33.89,-243.84:49:19 1/0:-50.19,-17.08,-221.97:100:21 chr6 58777098 . A T 42 PASS ABPV=1.00e+00;FPV=2.57e-03;FR=0.2500;HP=2;MMLQ=34;NF=14;NR=25;PP=42;RMP=50.5;RPV=1.85e-01;SC=GTAACTCTAGATTGAAGAATT;TC=224;TCF=105;TCR=119;TR=39;func=intergenic;gene=GUSBP4(dist=489374) NONE(dist=NONE);dbsnp=rs4330557 GT:GL:GQ:NR 0/0:-1161.42,-1180.18,-1411.53:83:106 0/1:-1283.78,-1265.72,-1460.11:76:119 chr6 116774635 . C G 38 PASS ABPV=1.00e+00;FPV=3.66e-01;FR=0.2504;HP=1;MMLQ=36;NF=4;NR=12;PP=38;RMP=76.7;RPV=4.76e-01;SC=CTTTTTCCACCACAAATTCTT;TC=72;TCF=21;TCR=51;TR=16 GT:GL:GQ:NR 0/0:-45.72,-51.81,-228.46:28:30 0/1:-179.58,-162.43,-353.98:72:42 chr6 136599000 . T TCATCTGTGA 73 PASS ABPV=2.21e-05;FPV=2.55e-09;FR=0.2505;HP=4;NF=2;NR=0;PP=73;RMP=1.41;RPV=3.11e-04;SC=TTTTAGTTTTTACCTTTTTAA;TC=118;TCF=90;TCR=28;TR=2;func=intronic;gene=BCLAF1;cons46=573 Name=lod=284;segdup=0.97 GT:GL:GQ:NR 0/0:-44.16,-49.89,-603.4:26:61 1/0:-105.25,-67.59,-750.95:100:79 chr6 155757781 . T A 106 PASS ABPV=1.00e+00;FPV=3.16e-01;FR=0.2504;HP=2;MMLQ=36;NF=0;NR=5;PP=106;RMP=66.42;RPV=6.16e-01;SC=TACAGTGAGCTCTGAAATATC;TC=24;TCF=4;TCR=20;TR=5;func=intronic;gene=NOX3;1000g=0.22;dbsnp=rs231961 GT:GL:GQ:NR 0/0:0.0,-6.09,-69.03:28:9 0/1:-48.54,-15.69,-84.63:100:15 chr7 65159983 . A G 128 PASS ABPV=1.00e+00;FPV=5.13e-01;FR=0.2500;HP=2;MMLQ=33;NF=9;NR=0;PP=128;RMP=42.05;RPV=1.33e-01;SC=TTGCTTAGTTACCAGGTAGAA;TC=45;TCF=38;TCR=7;TR=9;func=ncRNA;gene=INTS4L2 LOC441242;cons46=439 Name=lod=81;segdup=0.99;1000g=0.26;dbsnp=rs2949280 GT:GL:GQ:NR 0/0:0.0,-9.67,-99.87:43:16 0/1:-63.32,-25.43,-98.84:100:29 chr7 100552044 . T G 46 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=133;NR=185;PP=46;RMP=54.24;RPV=1.00e-00;SC=CTGTTCCTTCTTCACCATACA;TC=776;TCF=387;TCR=389;TR=318 GT:GL:GQ:NR 0/0:-2768.08,-2799.9,-3980.82:100:373 0/1:-3148.55,-3129.5,-4372.1:80:403 chr7 102319079 . G A 34 PASS ABPV=4.40e-01;FPV=1.00e+00;FR=0.2500;HP=1;MMLQ=38;NF=0;NR=6;PP=34;RMP=53.53;RPV=6.65e-03;SC=TGTGAGATGCGTGTGAAAATG;TC=56;TCF=0;TCR=56;TR=6;func=intergenic;gene=POLR2J2(dist=6903) FAM185A(dist=70320);segdup=1.00;1000g=0.17;dbsnp=rs62458736 GT:GL:GQ:NR 0/0:-9.39,-20.95,-166.2:51:26 0/1:-46.26,-30.07,-176.58:68:30 chr7 106272259 . C T 200 PASS ABPV=1.00e+00;FPV=1.51e-04;FR=0.2501;HP=2;MMLQ=31;NF=27;NR=25;PP=200;RMP=18.87;RPV=1.08e-05;SC=CTCATTCCAACCTCTGCTTCC;TC=391;TCF=192;TCR=199;TR=52 GT:GL:GQ:NR 0/0:-1599.11,-1606.25,-1841.06:32:195 0/1:-1703.84,-1621.18,-1787.33:100:196 chr7 128492558 . G A 32 PASS ABPV=1.00e+00;FPV=9.80e-01;FR=0.2501;HP=6;MMLQ=35;NF=15;NR=1;PP=32;RMP=45.11;RPV=5.34e-01;SC=TGAGTCCAGGGGGGGCTGCTC;TC=45;TCF=39;TCR=6;TR=16 GT:GL:GQ:NR 0/0:-82.82,-89.89,-214.44:32:24 0/1:-137.27,-121.35,-194.99:67:21 chr7 142223942 . A G 200 PASS ABPV=1.00e+00;FPV=1.00e-00;FR=0.2500;HP=1;MMLQ=33;NF=86;NR=42;PP=200;RMP=48.5;RPV=9.93e-01;SC=ACTGTGAATCATCTACTACAC;TC=282;TCF=160;TCR=122;TR=128 GT:GL:GQ:NR 0/0:-840.21,-856.54,-1228.56:72:124 1/0:-1069.18,-1023.08,-1489.98:100:158 chr7 142498735 . A C 51 PASS ABPV=1.00e+00;FPV=9.39e-01;FR=0.2500;HP=4;MMLQ=34;NF=23;NR=20;PP=51;RMP=54.1;RPV=9.74e-01;SC=AGGACCTGAAAAACGTGTTCC;TC=127;TCF=71;TCR=56;TR=43;func=intergenic;gene=TRY6(dist=16336) EPHB6(dist=54057);sift=0.35 GT:GL:GQ:NR 0/0:-407.53,-415.97,-666.18:38:67 0/1:-407.94,-387.73,-626.55:86:62 chr7 143295456 . A C 200 PASS ABPV=1.00e+00;FPV=7.75e-01;FR=0.2500;HP=1;MMLQ=26;NF=24;NR=7;PP=200;RMP=70.65;RPV=6.11e-02;SC=GCCTCCTCGCAGTGGGGGGCA;TC=135;TCF=87;TCR=48;TR=31 GT:GL:GQ:NR 0/0:-28.78,-39.63,-253.37:48:66 0/1:-158.76,-57.73,-187.94:100:69 chr7 143453710 . T A 66 PASS ABPV=1.00e+00;FPV=5.62e-01;FR=0.2501;HP=3;MMLQ=36;NF=0;NR=15;PP=66;RMP=54.55;RPV=5.68e-01;SC=TCTTCCTTTGTTTTGTCCACT;TC=62;TCF=2;TCR=60;TR=15 GT:GL:GQ:NR 0/0:-65.41,-73.41,-216.2:36:31 0/1:-102.8,-79.18,-187.97:100:31 chr7 143956461 . T C 37 PASS ABPV=1.00e+00;FPV=8.34e-02;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=0;PP=37;RMP=48.38;RPV=1.00e+00;SC=TGGGCTTGGCTGGATGCAGGA;TC=36;TCF=36;TCR=0;TR=5 GT:GL:GQ:NR 0/0:-6.63,-15.42,-125.53:39:20 1/0:-33.93,-16.96,-77.4:71:16 chr7 157367205 . TGA T 52 PASS ABPV=3.26e-01;FPV=5.62e-01;FR=0.2503;HP=2;NF=0;NR=2;PP=52;RMP=55.44;RPV=3.19e-02;SC=AGAGTAATAATGAGAGAGAGA;TC=27;TCF=2;TCR=25;TR=2;func=intronic;gene=PTPRN2 GT:GL:GQ:NR 0/0:-10.36,-16.59,-113.87:28:16 1/0:-39.42,-16.12,-59.64:99:12 chr8 8095880 . C T 131 PASS ABPV=1.00e+00;FPV=2.37e-01;FR=0.2500;HP=3;MMLQ=37;NF=0;NR=10;PP=131;RMP=64.63;RPV=8.71e-01;SC=GCCACATGGCCCCAGGCCCAA;TC=36;TCF=5;TCR=31;TR=10;func=ncRNA;gene=FLJ10661;segdup=0.98 GT:GL:GQ:NR 0/0:-78.8,-87.2,-171.27:38:18 0/1:-81.81,-43.3,-81.08:100:18 chr8 12236123 . T G 111 PASS ABPV=1.00e+00;FPV=1.38e-39;FR=0.2500;HP=2;MMLQ=30;NF=16;NR=9;PP=111;RMP=18.14;RPV=9.45e-01;SC=GTATTTGTGTTTGTGTGTGTG;TC=103;TCF=79;TCR=24;TR=25 GT:GL:GQ:NR 0/0:-265.16,-270.76,-457.35:100:49 1/0:-317.4,-305.02,-585.97:25:76 chr8 12428634 . C T 69 PASS ABPV=1.00e+00;FPV=7.50e-01;FR=0.2500;HP=1;MMLQ=36;NF=0;NR=5;PP=69;RMP=63.98;RPV=2.03e-01;SC=TCTTAACAACCGCCATGGTGC;TC=31;TCF=1;TCR=30;TR=5 GT:GL:GQ:NR 0/0:-10.77,-21.63,-134.62:48:17 1/0:-41.03,-16.59,-80.89:100:14 chr8 35608374 . T C 24 PASS ABPV=1.00e+00;FPV=6.32e-01;FR=0.2502;HP=2;MMLQ=34;NF=1;NR=34;PP=24;RMP=69.53;RPV=1.00e-00;SC=TGAAAGTGTGTGTTTTCCAAA;TC=62;TCF=5;TCR=57;TR=35 GT:GL:GQ:NR 0/0:-248.65,-255.21,-376.27:30:35 1/0:-265.91,-251.92,-307.04:58:27 chr8 121500323 . A AGTGGGATTGC 40 PASS ABPV=2.19e-01;FPV=8.43e-03;FR=0.2500;HP=2;NF=2;NR=0;PP=40;RMP=1.0;RPV=7.50e-01;SC=ATTATATCCTATGGATCAAAT;TC=32;TCF=31;TCR=1;TR=2 GT:GL:GQ:NR 0/0:-2.07,-11.08,-162.96:40:13 1/0:-47.66,-16.63,-264.67:100:25 chr9 14510 . CTGT C 200 PASS ABPV=2.20e-01;FPV=4.66e-14;FR=0.2500;HP=1;NF=12;NR=0;PP=200;RMP=43.31;RPV=1.00e-02;SC=TAAAAGCACACTGTTGGTTTC;TC=123;TCF=107;TCR=16;TR=12 GT:GL:GQ:NR 0/0:-22.04,-38.67,-350.71:73:53 0/1:-133.83,-67.48,-425.73:100:75 chr9 34724786 . G A 54 PASS ABPV=1.00e+00;FPV=5.46e-01;FR=0.2503;HP=2;MMLQ=31;NF=10;NR=18;PP=54;RMP=64.11;RPV=9.71e-01;SC=GGATTTCCACGGGACTAGGCT;TC=91;TCF=41;TCR=50;TR=28 GT:GL:GQ:NR 0/0:-77.92,-84.2,-224.15:29:46 1/0:-101.32,-80.48,-207.58:88:45 chr9 44118498 . G C 200 PASS ABPV=1.00e+00;FPV=9.49e-01;FR=0.2503;HP=2;MMLQ=34;NF=2;NR=7;PP=200;RMP=65.44;RPV=6.41e-01;SC=GAGGGCAGCTGCCTGTCACCT;TC=31;TCF=4;TCR=27;TR=9;func=intergenic;gene=CNTNAP3B(dist=196025) FAM27C(dist=871738);segdup=0.98;1000g=0.77;dbsnp=rs28610048 GT:GL:GQ:NR 0/0:-11.97,-18.32,-91.33:29:13 0/1:-73.63,-27.61,-81.59:100:18 chr9 67281836 . T G 200 PASS ABPV=1.00e+00;FPV=3.12e-01;FR=0.2500;HP=2;MMLQ=34;NF=6;NR=21;PP=200;RMP=63.02;RPV=5.58e-01;SC=GTGGACCTGATACAGTGGCCC;TC=115;TCF=31;TCR=84;TR=27;func=ncRNA;gene=AQP7P1;segdup=0.99;1000g=0.26;dbsnp=rs75812522 GT:GL:GQ:NR 0/0:-227.43,-240.42,-365.47:58:50 0/1:-353.09,-303.78,-464.7:100:65 chr9 67293649 . T G 200 PASS ABPV=1.00e+00;FPV=2.40e-02;FR=0.2509;HP=2;MMLQ=32;NF=8;NR=20;PP=200;RMP=65.85;RPV=6.29e-01;SC=GTGTGCCAAGTGACTTCATCT;TC=136;TCF=59;TCR=77;TR=28 GT:GL:GQ:NR 0/0:-52.46,-57.7,-399.51:24:62 0/1:-141.44,-82.05,-400.07:100:74 chr9 68358140 . T C 101 PASS ABPV=1.00e+00;FPV=4.09e-01;FR=0.2501;HP=2;MMLQ=31;NF=10;NR=13;PP=101;RMP=52.55;RPV=9.14e-01;SC=CCGCTTCAGATAGTGAAGAAG;TC=84;TCF=45;TCR=39;TR=23;func=intergenic;gene=ANKRD20A3(dist=387847) LOC642236(dist=69643);cons46=780 Name=lod=1967;segdup=0.98;dbsnp=rs62544188 GT:GL:GQ:NR 0/0:-99.49,-107.4,-306.63:36:46 0/1:-122.69,-91.06,-221.21:100:38 chr9 92995102 . C T 25 PASS ABPV=1.74e-02;FPV=2.34e-06;FR=0.2500;HP=3;MMLQ=33;NF=11;NR=10;PP=25;RMP=36.17;RPV=2.75e-07;SC=ATAAAATTGTCCCCTCCATTC;TC=258;TCF=127;TCR=131;TR=21;func=intergenic;gene=LOC286370(dist=191321) LOC340515(dist=229612);segdup=0.96 GT:GL:GQ:NR 0/0:-127.8,-170.89,-839.43:100:127 1/0:-164.37,-150.07,-829.28:60:131 chr9 139572068 . C G 44 PASS ABPV=1.00e+00;FPV=4.21e-01;FR=0.2507;HP=2;MMLQ=29;NF=0;NR=3;PP=44;RMP=57.58;RPV=7.11e-01;SC=GGCTGGGGCGCGAAGGCCTGG;TC=14;TCF=3;TCR=11;TR=3;func=intronic;gene=AGPAT2;1000g=0.57;dbsnp=rs2236514 GT:GL:GQ:NR 0/0:0.0,-5.54,-62.14:25:9 1/0:-29.67,-11.06,-23.48:61:5 chr9 140777194 . A AGAGCGGCT 200 PASS ABPV=7.76e-05;FPV=4.77e-24;FR=0.2500;HP=2;NF=2;NR=1;PP=200;RMP=4.36;RPV=2.92e-05;SC=CGCTTCTCCTAGGACGACACG;TC=123;TCF=77;TCR=46;TR=3;func=splicing;gene=CACNA1B(NM_000718:c.390-2->CATGTCCGAGCGGCT NM_001243812:c.390-2->CATGTCCGAGCGGCT);cons46=573 Name=lod=285 GT:GL:GQ:NR 0/0:-260.4,-275.23,-819.04:71:85 0/1:-510.15,-408.95,-886.86:3:93 chrUn_gl000214 53458 . T A 82 PASS ABPV=4.34e-01;FPV=7.36e-06;FR=0.2500;HP=4;MMLQ=34;NF=22;NR=0;PP=82;RMP=47.4;RPV=5.62e-01;SC=AAACACTATATAAATATAATT;TC=187;TCF=185;TCR=2;TR=22;func=intergenic;gene=NONE(dist=NONE) NONE(dist=NONE);segdup=0.98 GT:GL:GQ:NR 0/0:-154.3,-180.61,-694.01:100:88 1/0:-304.62,-277.18,-752.95:100:99 chrUn_gl000214 61035 . A G 25 PASS ABPV=2.68e-01;FPV=1.27e-06;FR=0.2500;HP=2;MMLQ=34;NF=20;NR=0;PP=25;RMP=60.63;RPV=4.22e-01;SC=ATGTTTACCTATATAACAAAC;TC=187;TCF=184;TCR=3;TR=20 GT:GL:GQ:NR 0/0:-517.15,-538.58,-910.78:94:80 0/1:-812.82,-798.54,-1242.08:60:107 chrUn_gl000214 74804 . T C 45 PASS ABPV=5.69e-01;FPV=4.33e-02;FR=0.2500;HP=2;MMLQ=35;NF=5;NR=0;PP=45;RMP=36.66;RPV=5.62e-01;SC=ATCACTTGAATGCAGTAGGCA;TC=42;TCF=40;TCR=2;TR=5 GT:GL:GQ:NR 0/0:-65.35,-75.06,-177.61:43:16 0/1:-180.67,-161.94,-279.38:79:26 chrUn_gl000220 121703 . T C 75 PASS ABPV=9.31e-02;FPV=1.94e-05;FR=0.2500;HP=2;MMLQ=31;NF=5;NR=8;PP=75;RMP=52.13;RPV=2.81e-03;SC=GTGGGCACGGTACGCTCTGGT;TC=150;TCF=78;TCR=72;TR=13 GT:GL:GQ:NR 0/0:-64.92,-78.18,-505.13:59:80 1/0:-102.59,-76.78,-453.86:100:70 chrUn_gl000220 128026 . C T 73 PASS ABPV=1.00e+00;FPV=1.39e-05;FR=0.2500;HP=1;MMLQ=37;NF=12;NR=5;PP=73;RMP=48.23;RPV=2.65e-03;SC=TCTCTGTCTCCGTCTCTGTCT;TC=117;TCF=62;TCR=55;TR=17 GT:GL:GQ:NR 0/0:-175.58,-193.94,-521.81:81:62 1/0:-151.61,-126.36,-397.61:100:57 chrUn_gl000220 132074 . G A 200 PASS ABPV=1.00e+00;FPV=2.39e-03;FR=0.2500;HP=2;MMLQ=34;NF=10;NR=11;PP=200;RMP=61.51;RPV=6.72e-03;SC=CTCTCTGTCCGTCTCTGTCTT;TC=167;TCF=84;TCR=83;TR=21;func=intergenic;gene=LOC100507412(dist=5378) RN5-8S1(dist=23923);segdup=0.95 GT:GL:GQ:NR 0/0:-248.2,-257.69,-615.12:42:77 0/1:-290.71,-234.79,-658.31:100:90 chrUn_gl000220 145002 . C T 28 PASS ABPV=3.17e-02;FPV=7.56e-08;FR=0.2500;HP=4;MMLQ=31;NF=1;NR=3;PP=28;RMP=65.86;RPV=4.70e-03;SC=ACTAGCCGGGCGCGGTGGCAC;TC=76;TCF=36;TCR=40;TR=4 GT:GL:GQ:NR 0/0:-17.73,-43.17,-320.69:100:46 1/0:-67.96,-52.99,-236.43:63:37 chrUn_gl000220 145368 . T C 30 PASS ABPV=1.09e-01;FPV=1.31e-02;FR=0.2500;HP=1;MMLQ=29;NF=8;NR=2;PP=30;RMP=72.81;RPV=1.92e-05;SC=AGCCGGGCGCTGTGCTGTGCT;TC=119;TCF=63;TCR=56;TR=10;func=intergenic;gene=LOC100507412(dist=18672) RN5-8S1(dist=10629);dbsnp=rs3878955 GT:GL:GQ:NR 0/0:-48.56,-59.69,-409.13:50:53 0/1:-66.74,-51.46,-448.03:64:66 chrUn_gl000225 30398 . C T 29 PASS ABPV=1.13e-01;FPV=3.15e-04;FR=0.2502;HP=1;MMLQ=33;NF=1;NR=5;PP=29;RMP=58.12;RPV=2.55e-02;SC=CCTGCTCCTCCGAGCCTTTGA;TC=80;TCF=37;TCR=43;TR=6 GT:GL:GQ:NR 0/0:-195.73,-202.53,-342.72:31:35 1/0:-230.45,-215.31,-371.74:63:45 chrUn_gl000225 43193 . C T 46 PASS ABPV=1.00e+00;FPV=7.84e-02;FR=0.2507;HP=3;MMLQ=31;NF=8;NR=12;PP=46;RMP=44.42;RPV=4.19e-02;SC=GCCAGAGAGACGGGCCTCCCG;TC=126;TCF=51;TCR=75;TR=20 GT:GL:GQ:NR 0/0:-577.5,-583.01,-743.98:25:63 1/0:-604.31,-585.16,-703.98:81:63 chrX 106390898 . G A 65 PASS ABPV=4.78e-01;FPV=1.49e-02;FR=0.2500;HP=1;MMLQ=39;NF=5;NR=0;PP=65;RMP=43.16;RPV=1.00e+00;SC=GTTTGGTCATGGAGCATACAA;TC=46;TCF=46;TCR=0;TR=5 GT:GL:GQ:NR 0/0:0.0,-11.78,-148.84:52:17 1/0:-49.23,-25.85,-211.17:99:29 pysam-0.7.7/tests/vcf-examples/4.vcf0000664000076400007650000123202011754437212017112 0ustar andreasandreas##fileformat=VCFv4.1 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##fileDate=20110524 ##reference=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz ##source=EricBanksValidationQC;fromGoncaloAbecasisValidationSelection #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00127 HG00128 HG00136 HG00137 HG00138 HG00139 HG00152 HG00156 HG00234 HG00235 HG00237 HG00242 HG00244 HG00262 HG01055 HG01079 NA19138 NA18974 NA18523 NA12717 NA19209 NA18577 NA18973 NA18943 NA12873 NA18623 NA18622 NA18948 NA19171 NA19204 NA06994 NA18563 NA18547 NA18861 NA18608 NA12282 NA12751 NA18959 NA19331 NA19453 NA20537 NA12046 NA20515 NA20516 NA20521 NA20524 NA20528 NA20759 NA20768 NA20769 NA20774 NA20775 NA20783 NA20787 NA20790 NA20800 NA20819 NA20812 NA20505 NA20530 NA20540 NA20538 NA20581 NA20815 NA20544 NA20810 NA20807 NA20816 NA20504 NA20753 NA20502 NA12342 NA19150 NA19468 NA20336 NA19395 NA19257 NA19360 NA19700 NA18867 NA20317 NA18968 NA19107 HG00111 HG00108 NA19077 NA19684 NA18511 NA12044 NA19382 NA19457 NA18933 NA18923 NA18965 HG00141 NA20341 NA18740 HG00537 HG00346 HG01173 HG00702 HG00313 HG00150 NA18612 HG00339 NA12273 HG00250 NA18593 NA18621 HG00478 HG00251 HG01070 NA19160 NA18995 NA10851 NA18976 NA18603 NA19200 HG01204 HG01191 HG01101 HG00146 HG00306 NA18985 HG00160 HG00635 HG00372 HG00357 HG00634 NA18541 NA18950 NA19759 HG00351 HG00257 HG00118 HG00336 HG00448 HG01354 NA18609 HG00428 HG00326 NA11894 NA18956 HG00173 HG00117 NA11893 HG01251 HG01441 HG01437 HG00182 HG00330 HG01060 HG00329 NA18960 NA18856 NA07346 NA18871 NA19057 NA18868 NA18636 NA12830 NA19007 NA18910 NA18874 NA19056 NA19064 NA19066 NA18487 NA18642 NA19236 NA07056 NA18637 NA19235 NA19309 NA19311 NA19334 NA19346 NA19347 NA19372 NA19376 NA19383 NA19384 NA19394 NA19428 NA19430 NA19451 NA19466 NA19313 NA19321 NA19324 NA19332 HG00479 HG00608 NA18573 HG00375 NA19248 NA19093 HG01170 HG00534 HG01171 HG01522 NA18624 HG00683 HG01521 NA19005 NA20412 NA18971 HG00446 NA12748 HG00530 HG00690 HG01356 HG01516 NA20532 HG00344 HG00328 NA18542 HG00254 HG00321 HG00577 HG00656 HG00342 HG00524 HG00650 HG00557 HG00319 HG00457 HG00125 HG00578 HG00543 HG00638 HG00171 HG00699 HG00595 HG00187 HG00704 HG00533 HG00596 HG00268 HG01083 HG00651 HG01133 HG00671 HG00327 HG01148 HG00246 HG00672 HG00556 HG00436 HG00554 NA18633 NA20344 NA11993 NA07037 NA11930 HG01366 HG01389 HG00620 NA19740 HG00190 HG00419 NA18535 HG01495 NA18592 HG01497 HG00174 HG01140 NA12287 HG00689 HG01550 HG00334 HG01375 HG00637 NA18507 HG01113 NA18550 NA19129 HG01551 HG01462 HG00331 NA12413 HG01456 HG01360 HG00708 HG01350 HG00684 NA19099 HG00284 NA12399 NA12286 NA12777 HG00277 HG00266 NA19985 HG00353 HG01102 NA07347 NA07051 NA19900 NA18984 NA07048 HG00640 HG01066 NA12812 HG01174 HG01188 NA19390 NA19436 NA19439 NA19440 NA19463 NA19470 NA19471 NA19472 NA19676 NA19660 NA19661 NA19663 NA19722 NA19725 NA19728 NA19729 NA19731 NA19749 NA19755 NA19756 NA19758 NA19770 NA19773 NA19777 NA19780 NA19783 NA20525 NA20589 NA20765 NA20802 NA20804 NA18544 NA18602 NA18546 NA18610 NA18957 NA18615 NA18616 NA19010 NA18638 NA18639 NA18627 NA19072 NA18630 NA19074 NA19080 NA19081 NA19083 NA19085 NA19088 NA20287 NA19835 NA20276 NA19818 NA20278 NA20282 NA20342 NA20296 NA20314 NA20346 NA19712 NA19198 NA19108 NA18934 NA18916 NA18907 NA18917 NA06989 NA12058 NA12341 NA12546 NA12489 HG01197 NA18983 NA11843 NA11892 NA12749 20 82176 rs11906362 T C 318 NOT_TYPED;PQ10 BCM.AC=16;DB;SRC=VQSR+2-OF-7;PQ=0 20 249843 rs112456910 C T 1304 PASS BCM.AC=14;DB;SEQUENOM.AC=12;SRC=VQSR+INTERSECTION;PQ=29 GT 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 . . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . . 0/0 0/1 . . 0/0 0/0 . 0/0 . . . 0/0 . 0/0 0/0 0/1 0/0 . . . 0/0 . 0/0 . . . . . . . . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 . . 0/0 . . 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 . 0/0 . . . . . 0/0 0/0 . . 0/1 . . 0/0 . 0/1 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 . . . . . 0/0 . . . . . 0/0 . 0/1 . . . . 0/0 . . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . . . 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 . . . 0/0 0/1 0/0 . . . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . . . . 0/0 . 0/0 0/0 0/0 . . . . . . . 0/0 . 0/0 . . . . . . . . . . 0/0 . 0/0 . . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . 0/0 . . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 . 0/1 0/1 0/0 . . 0/0 0/0 . . 0/0 0/1 . . 0/1 . . . 0/0 0/0 0/0 . . . . . 0/0 . 20 688672 rs116071340 C T 56 PASS BCM.AC=1;DB;SEQUENOM.AC=2;SRC=VQSR+2-OF-7;PQ=52 GT . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 987773 rs6077519 T G 474 PASS DB;SEQUENOM.AC=73;SRC=VQSR-ONLY;PQ=42 GT . 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/1 0/0 0/0 0/0 1/1 1/1 0/0 1/1 0/0 0/0 0/0 0/0 1/1 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 1/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/1 . 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/1 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 20 1166164 . G T 26 NOT_DESIGNED BCM.AC=20;SRC=VQSR+2-OF-7 20 1333317 . 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C T 100 PASS SEQUENOM.AC=3;SRC=2-OF-7-ONLY;PQ=19 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 1577285 . G A 4 HIGH_NO_CALL_RATE SEQUENOM.AC=0;SRC=VQSR-ONLY;PQ=57 GT . . . 0/0 0/0 . 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . . 0/0 . 0/0 . . . 0/0 . . . . . . 0/0 . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . . . 0/0 0/0 . . . . 0/0 0/0 . 0/0 . . 0/0 0/0 . . . . . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 . . . 0/0 . . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 . . . . . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . . . 0/0 . . . . . . . . 0/0 . . . 0/0 . . . . . . . . . . . . 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . . . 0/0 . . . 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . . 0/0 . 0/0 0/0 . . 0/0 . . . . . . 0/0 . 0/0 0/0 . 0/0 . . . 0/0 . . . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . . 0/0 0/0 . . . . . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 . . . . 0/0 0/0 0/0 . 0/0 . 0/0 . 0/0 0/0 . 0/0 . 0/0 . 0/0 . 0/0 . . . . . 0/0 0/0 0/0 . . 0/0 0/0 20 1577845 . G A 267 HIGH_NO_CALL_RATE BCM.AC=42;SEQUENOM.AC=5;SRC=VQSR+2-OF-7;PQ=37 GT 0/0 . . 0/0 . . . . . . 0/0 . . 0/0 . . 0/0 0/0 . . . . 0/0 0/0 . 0/0 . 0/0 . . 0/0 0/0 . 1/1 0/0 0/0 . 0/0 . 0/0 0/0 . . 0/0 . . . . . 0/0 . 0/0 . 0/0 . . . . . . 0/0 . 0/0 . 0/0 . . 0/0 . . . 0/0 . . . . . . . . . . . 0/0 0/0 . 0/0 . . 0/0 0/0 0/0 . . . 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . 0/0 . . 0/0 . . 0/0 . . 0/0 0/0 . . 0/0 . . . 0/0 0/0 0/0 0/0 0/0 . . 0/0 0/0 0/0 . 0/0 0/0 . . . 0/0 0/0 . 0/0 0/0 . 0/0 . 0/0 0/0 0/0 . . . . . . 0/0 . 0/0 . 0/0 . . . 0/0 0/0 0/0 0/0 . . . . 0/0 . . 0/0 . . . . . 0/0 . . . . 0/0 . . . . . . . . . . . 0/0 . . 0/0 0/0 . 0/0 . . 0/0 . 0/0 . 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 . 0/0 0/0 . 0/0 . . . 0/0 0/0 . . 0/0 0/0 . 0/0 0/0 . . 0/0 0/0 0/0 . . 0/0 . 0/0 0/0 . . . . . 0/0 0/0 0/0 0/0 . 0/0 . . 0/0 0/0 . . . 0/0 . 0/0 . . . 0/0 . 0/0 0/0 . 0/0 0/0 0/0 . 0/0 . . 0/0 . 0/0 . . . . . . 0/0 0/0 . 0/0 . . . 0/0 . . 0/0 0/0 0/0 . . . . . 0/0 0/0 0/0 0/0 0/0 . . . 0/0 0/0 . . . . 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . . 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 . . . . 0/0 0/0 0/0 . . . . 0/0 0/0 0/1 . 0/0 . . . 0/0 . 1/1 . . 0/0 . 0/0 0/0 . 0/0 . . 0/0 0/0 20 1590306 . 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G A 9 NOT_DESIGNED BCM.AC=4;SRC=VQSR+2-OF-7 20 2280790 rs214779 T A 57436 NOT_DESIGNED BCM.AC=758;DB;SRC=VQSR+2-OF-7 20 2843004 rs118020362 T C 131 PASS BCM.AC=4;DB;SEQUENOM.AC=4;SRC=VQSR+INTERSECTION;PQ=57 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2854191 . C T 78 POSSIBLE_PROBE_FAILURE BCM.AC=25;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=60 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 2999522 . 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T G 86 NOT_TYPED;PQ10 BCM.AC=493;SRC=VQSR-ONLY;PQ=0 20 25751184 . G C 100 NOT_TYPED;PQ10 BCM.AC=180;SRC=2-OF-7-ONLY;PQ=0 20 25766473 . T A 124 NOT_TYPED;PQ10 SRC=VQSR+2-OF-7;PQ=0 20 25789517 . A T 40 NOT_TYPED;PQ10 BCM.AC=319;SRC=VQSR+2-OF-7;PQ=0 20 25794555 . G A 18 NOT_TYPED;PQ10 BCM.AC=181;SRC=VQSR-ONLY;PQ=0 20 25922316 . T C 26 PASS BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=18 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 25999667 . 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G A 26 NOT_TYPED;PQ10 BCM.AC=354;SRC=VQSR-ONLY;PQ=0 20 26057903 . G A 100 NOT_TYPED;PQ10 SRC=2-OF-7-ONLY;PQ=0 20 26071009 . 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0/0 0/0 0/0 0/0 0/0 20 29574811 rs73620522 G A 16281 HIGH_NO_CALL_RATE DB;SEQUENOM.AC=24;SRC=VQSR-ONLY;PQ=15 GT 0/1 1/1 1/1 . 1/1 1/1 0/1 1/1 1/1 . 1/1 1/1 . . 0/0 . . 1/1 . 1/1 1/1 . 1/1 1/1 0/1 1/1 . . 1/1 0/0 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . 1/1 . . 1/1 . . . . 1/1 1/1 . . . . . . . . . . . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . . . . . 1/1 . 1/1 . 0/1 . . . 0/1 . 1/1 . 1/1 . 1/1 1/1 0/1 1/1 . . 1/1 . 1/1 . . . 1/1 1/1 . . 1/1 . . . 1/1 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 . 0/1 1/1 1/1 . 1/1 . . 1/1 1/1 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . . 1/1 . 1/1 1/1 . . . . . 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 1/1 . 1/1 . . 1/1 1/1 . 1/1 . . 1/1 . . . 0/0 . 1/1 1/1 . . . . 1/1 1/1 . 1/1 1/1 . 1/1 . . . 1/1 . 1/1 1/1 . 1/1 . . . 1/1 1/1 1/1 1/1 . 1/1 . 1/1 . . . . . . . 1/1 . . . . . . . . . . 1/1 1/1 1/1 1/1 1/1 1/1 . . . . . 1/1 1/1 1/1 . 1/1 . . . . . . . 1/1 1/1 1/1 1/1 1/1 . 1/1 . . . . . . 1/1 1/1 1/1 . 1/1 0/0 . . . . . 1/1 1/1 1/1 1/1 1/1 . . 1/1 . 1/1 . 0/1 1/1 1/1 . 1/1 1/1 1/1 . . . . 1/1 . . . . . . . . . . . 1/1 1/1 . . 1/1 1/1 . 1/1 . 0/0 . . . . . . . 0/0 . . . . 1/1 . 1/1 1/1 1/1 1/1 1/1 1/1 . 1/1 . . . . 1/1 1/1 1/1 1/1 0/0 . . . 1/1 . . 1/1 . 1/1 1/1 1/1 1/1 1/1 . 1/1 1/1 . 1/1 . 1/1 . . 1/1 1/1 1/1 0/0 20 29598472 rs73612735 T G 10639 NOT_TYPED;PQ10 DB;SRC=VQSR-ONLY;PQ=0 20 29632410 . T C 5.11 NOT_TYPED;PQ10 SRC=2-OF-7-ONLY;PQ=0 20 29642272 rs77298479 T A 100 NOT_TYPED;PQ10 DB;SRC=2-OF-7-ONLY;PQ=9 20 29827087 rs62641496 G C 100 NOT_DESIGNED DB;SRC=2-OF-7-ONLY 20 30120025 . C G 1113 POSSIBLE_PROBE_FAILURE;PQ10 BCM.AC=9;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 30595334 rs62206358 C A 62 PASS BCM.AC=3;DB;SEQUENOM.AC=1;SRC=VQSR+2-OF-7;PQ=20 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 30616314 . 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T C 5 NOT_DESIGNED SRC=VQSR-ONLY 20 41137712 rs230167 C T 24 NOT_DESIGNED DB;SRC=VQSR+2-OF-7 20 41311175 . 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T C 198 NOT_DESIGNED BCM.AC=9;SRC=VQSR+2-OF-7 20 54313664 rs112885916 A T 98 PASS BCM.AC=10;DB;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=57 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54424603 . T C 116 PQ10 BCM.AC=8;SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54542220 . C T 33 NOT_DESIGNED SRC=VQSR-ONLY 20 54628591 . G A 87 POLYMORPHIC_SAMPLES_FAILED;PQ10 BCM.AC=2;SEQUENOM.AC=4;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 20 54793377 . C T 8 HIGH_NO_CALL_RATE BCM.AC=1;SEQUENOM.AC=0;SRC=VQSR-ONLY;PQ=60 GT . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 0/0 . . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0/0 0/0 . . . . . . . . . . 0/0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 55067830 . 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T C 17 AMBIGUOUS_SEQUENOM_CALLS;PQ10 SEQUENOM.AC=0;SRC=VQSR+2-OF-7;PQ=0 GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 pysam-0.7.7/tests/example_btag.bam0000664000076400007650000000140312075110102016743 0ustar andreasandreasBCCsred``p22`?"C.F$+8 ^s|2BCVMOQ=::%D1liFR4Xĸ1Ec ,Lܺ4Y_Fjb {=%B׻g{q4ݛ;7{j`4^t*J2#Wte+YʝNJTӕjED28N,ql gP ;yF~!i"" 065H`K@9n`O{S>%V|_/%ֱ(M9.%fa/Ipz~xMQ`7yO â6Yl˓ a?Qƨ!Yd+pe?Rd'>̡F=)8 ~]v)ƺB %>pO܁s=ю紃x Yne'H=!B8["9#F.kcaSʝ51%5_^՝vSvi^hV|O0|gKpthwff_JBCpysam-0.7.7/tests/ex7.sam0000664000076400007650000000046711700526652015067 0ustar andreasandreasread_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 PG:Z:P1 XT:A:U read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 PG:Z:P2 XT:A:R pysam-0.7.7/tests/example_user_header.sam0000664000076400007650000000056012052742477020365 0ustar andreasandreas@HD VN:1.0 @SQ SN:chr1 LN:1575 @SQ SN:chr2 LN:1584 @x1 A:2 B:5 @x2 A:4 B:5 @x3 A:6 B:5 read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 pysam-0.7.7/tests/ex8.sam0000664000076400007650000000100411700526652015054 0ustar andreasandreas@HD VN:1.0 @SQ SN:2 LN:48297693 GJP00TM04CAQ5W 0 2 38297693 60 45H51M1D13M1D12M1D9M2D5M1D7M4D2M1I6M1D28M1D5M1D2M1D18M55H * 0 0 CATGAAGAACCGCTGGGTATGGAGCACACCTCACCTGATGGACAGTTGATTATGCTCACCTTAACGCTAATTGAGAGCAGCACAAGAGGACTGGAAACTAGAATTTACTCCTCATCTCCGAAGATGTGAATATTCTAAATTCAGCTTGCCTCTTGCTTC IID7757111/=;?///:D>777;EEGAAAEEIHHIIIIIIIIIIIIIIBBBIIIIH==<<<<>>D?1112544556::03---//25.22=;DD?;;;>BDDDEEEGGGA<888= 3 if IS_PYTHON3: from itertools import zip_longest else: from itertools import izip as zip_longest SAMTOOLS="samtools" WORKDIR="pysam_test_work" def checkBinaryEqual( filename1, filename2 ): '''return true if the two files are binary equal.''' if os.path.getsize( filename1 ) != os.path.getsize( filename2 ): return False infile1 = open(filename1, "rb") infile2 = open(filename2, "rb") def chariter( infile ): while 1: c = infile.read(1) if c == b"": break yield c found = False for c1,c2 in zip_longest( chariter( infile1), chariter( infile2) ): if c1 != c2: break else: found = True infile1.close() infile2.close() return found def runSamtools( cmd ): '''run a samtools command''' try: retcode = subprocess.call(cmd, shell=True, stderr = subprocess.PIPE) if retcode < 0: print("Child was terminated by signal", -retcode) except OSError as e: print("Execution failed:", e) def getSamtoolsVersion(): '''return samtools version''' with subprocess.Popen(SAMTOOLS, shell=True, stderr=subprocess.PIPE).stderr as pipe: lines = b"".join(pipe.readlines()) if IS_PYTHON3: lines = lines.decode('ascii') return re.search( "Version:\s+(\S+)", lines).groups()[0] class BinaryTest(unittest.TestCase): '''test samtools command line commands and compare against pysam commands. Tests fail, if the output is not binary identical. ''' first_time = True # a dictionary of commands to test # first entry: (samtools output file, samtools command) # second entry: (pysam output file, (pysam function, pysam options) ) commands = \ { "view" : ( ("ex1.view", "view ex1.bam > ex1.view"), ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ), ), "view2" : ( ("ex1.view", "view -bT ex1.fa -o ex1.view2 ex1.sam"), # note that -o ex1.view2 throws exception. ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ), ), "sort" : ( ( "ex1.sort.bam", "sort ex1.bam ex1.sort" ), ( "pysam_ex1.sort.bam", (pysam.sort, "ex1.bam pysam_ex1.sort" ) ), ), "mpileup" : ( ("ex1.pileup", "mpileup ex1.bam > ex1.pileup" ), ("pysam_ex1.mpileup", (pysam.mpileup, "ex1.bam" ) ), ), "depth" : ( ("ex1.depth", "depth ex1.bam > ex1.depth" ), ("pysam_ex1.depth", (pysam.depth, "ex1.bam" ) ), ), "faidx" : ( ("ex1.fa.fai", "faidx ex1.fa"), ("pysam_ex1.fa.fai", (pysam.faidx, "ex1.fa") ), ), "index": ( ("ex1.bam.bai", "index ex1.bam" ), ("pysam_ex1.bam.bai", (pysam.index, "pysam_ex1.bam" ) ), ), "idxstats" : ( ("ex1.idxstats", "idxstats ex1.bam > ex1.idxstats" ), ("pysam_ex1.idxstats", (pysam.idxstats, "pysam_ex1.bam" ) ), ), "fixmate" : ( ("ex1.fixmate", "fixmate ex1.bam ex1.fixmate" ), ("pysam_ex1.fixmate", (pysam.fixmate, "pysam_ex1.bam pysam_ex1.fixmate") ), ), "flagstat" : ( ("ex1.flagstat", "flagstat ex1.bam > ex1.flagstat" ), ("pysam_ex1.flagstat", (pysam.flagstat, "pysam_ex1.bam") ), ), "calmd" : ( ("ex1.calmd", "calmd ex1.bam ex1.fa > ex1.calmd" ), ("pysam_ex1.calmd", (pysam.calmd, "pysam_ex1.bam ex1.fa") ), ), "merge" : ( ("ex1.merge", "merge -f ex1.merge ex1.bam ex1.bam" ), # -f option does not work - following command will cause the subsequent # command to fail ("pysam_ex1.merge", (pysam.merge, "pysam_ex1.merge pysam_ex1.bam pysam_ex1.bam") ), ), "rmdup" : ( ("ex1.rmdup", "rmdup ex1.bam ex1.rmdup" ), ("pysam_ex1.rmdup", (pysam.rmdup, "pysam_ex1.bam pysam_ex1.rmdup" )), ), "reheader" : ( ( "ex1.reheader", "reheader ex1.bam ex1.bam > ex1.reheader"), ( "pysam_ex1.reheader", (pysam.reheader, "ex1.bam ex1.bam" ) ), ), "cat": ( ( "ex1.cat", "cat ex1.bam ex1.bam > ex1.cat"), ( "pysam_ex1.cat", (pysam.cat, "ex1.bam ex1.bam" ) ), ), "targetcut": ( ("ex1.targetcut", "targetcut ex1.bam > ex1.targetcut" ), ("pysam_ex1.targetcut", (pysam.targetcut, "pysam_ex1.bam") ), ), "phase": ( ("ex1.phase", "phase ex1.bam > ex1.phase" ), ("pysam_ex1.phase", (pysam.phase, "pysam_ex1.bam") ), ), "import" : ( ("ex1.bam", "import ex1.fa.fai ex1.sam.gz ex1.bam" ), ("pysam_ex1.bam", (pysam.samimport, "ex1.fa.fai ex1.sam.gz pysam_ex1.bam") ), ), "bam2fq": ( ("ex1.bam2fq", "bam2fq ex1.bam > ex1.bam2fq" ), ("pysam_ex1.bam2fq", (pysam.bam2fq, "pysam_ex1.bam") ), ), "pad2unpad": ( ("ex2.unpad", "pad2unpad -T ex1.fa ex2.bam > ex2.unpad" ), ("pysam_ex2.unpad", (pysam.pad2unpad, "-T ex1.fa ex2.bam") ), ), "bamshuf": ( ("ex1.bamshuf.bam", "bamshuf ex1.bam ex1.bamshuf" ), ("pysam_ex1.bamshuf.bam", (pysam.bamshuf, "ex1.bam pysam_ex1.bamshuf") ), ), "bedcov": ( ("ex1.bedcov", "bedcov ex1.bed ex1.bam > ex1.bedcov" ), ("pysam_ex1.bedcov", (pysam.bedcov, "ex1.bed ex1.bam") ), ), } # some tests depend on others. The order specifies in which order # the samtools commands are executed. # The first three (faidx, import, index) need to be in that order, # the rest is arbitrary. order = ('faidx', 'import', 'index', # 'pileup1', 'pileup2', deprecated # 'glfview', deprecated 'view', 'view2', 'sort', 'mpileup', 'depth', 'idxstats', 'fixmate', 'flagstat', ## 'calmd', 'merge', 'rmdup', 'reheader', 'cat', 'bedcov', 'targetcut', 'phase', 'bamshuf', 'bam2fq', 'pad2unpad', ) def setUp( self ): '''setup tests. For setup, all commands will be run before the first test is executed. Individual tests will then just compare the output files. ''' if BinaryTest.first_time: # remove previous files if os.path.exists( WORKDIR ): shutil.rmtree( WORKDIR ) pass # copy the source files to WORKDIR os.makedirs( WORKDIR ) shutil.copy( "ex1.fa", os.path.join( WORKDIR, "pysam_ex1.fa" ) ) shutil.copy( "ex1.fa", os.path.join( WORKDIR, "ex1.fa" ) ) shutil.copy( "ex1.sam.gz", os.path.join( WORKDIR, "ex1.sam.gz" ) ) shutil.copy( "ex1.sam", os.path.join( WORKDIR, "ex1.sam" ) ) shutil.copy( "ex2.bam", os.path.join( WORKDIR, "ex2.bam" ) ) # cd to workdir savedir = os.getcwd() os.chdir( WORKDIR ) for label in self.order: # print ("command=", label) command = self.commands[label] # build samtools command and target and run samtools_target, samtools_command = command[0] runSamtools( " ".join( (SAMTOOLS, samtools_command ))) # get pysam command and run try: pysam_target, pysam_command = command[1] except ValueError as msg: raise ValueError( "error while setting up %s=%s: %s" %\ (label, command, msg) ) pysam_method, pysam_options = pysam_command try: output = pysam_method( *pysam_options.split(" "), raw=True) except pysam.SamtoolsError as msg: raise pysam.SamtoolsError( "error while executing %s: options=%s: msg=%s" %\ (label, pysam_options, msg) ) if ">" in samtools_command: with open( pysam_target, "wb" ) as outfile: if type(output) == list: if IS_PYTHON3: for line in output: outfile.write( line.encode('ascii') ) else: for line in output: outfile.write( line ) else: outfile.write(output) os.chdir( savedir ) BinaryTest.first_time = False samtools_version = getSamtoolsVersion() def _r( s ): # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> 0.1.12 if s.count('-') > 0: s = s[0:s.find('-')] return re.sub( "[^0-9.]", "", s ) if _r(samtools_version) != _r( pysam.__samtools_version__): raise ValueError("versions of pysam/samtools and samtools differ: %s != %s" % \ (pysam.__samtools_version__, samtools_version )) def checkCommand( self, command ): if command: samtools_target, pysam_target = self.commands[command][0][0], self.commands[command][1][0] samtools_target = os.path.join( WORKDIR, samtools_target ) pysam_target = os.path.join( WORKDIR, pysam_target ) self.assertTrue( checkBinaryEqual( samtools_target, pysam_target ), "%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target) ) def testImport( self ): self.checkCommand( "import" ) def testIndex( self ): self.checkCommand( "index" ) def testSort( self ): self.checkCommand( "sort" ) def testMpileup( self ): self.checkCommand( "mpileup" ) def testDepth( self ): self.checkCommand( "depth" ) def testIdxstats( self ): self.checkCommand( "idxstats" ) def testFixmate( self ): self.checkCommand( "fixmate" ) def testFlagstat( self ): self.checkCommand( "flagstat" ) def testMerge( self ): self.checkCommand( "merge" ) def testRmdup( self ): self.checkCommand( "rmdup" ) def testReheader( self ): self.checkCommand( "reheader" ) def testCat( self ): self.checkCommand( "cat" ) def testTargetcut( self ): self.checkCommand( "targetcut" ) def testPhase( self ): self.checkCommand( "phase" ) def testBam2fq( self ): self.checkCommand( "bam2fq" ) def testBedcov( self ): self.checkCommand( "bedcov" ) def testBamshuf( self ): self.checkCommand( "bamshuf" ) def testPad2Unpad( self ): self.checkCommand( "pad2unpad" ) # def testPileup1( self ): # self.checkCommand( "pileup1" ) # def testPileup2( self ): # self.checkCommand( "pileup2" ) # deprecated # def testGLFView( self ): # self.checkCommand( "glfview" ) def testView( self ): self.checkCommand( "view" ) def testEmptyIndex( self ): self.assertRaises( IOError, pysam.index, "exdoesntexist.bam" ) def __del__(self): if os.path.exists( WORKDIR ): pass # shutil.rmtree( WORKDIR ) class IOTest(unittest.TestCase): '''check if reading samfile and writing a samfile are consistent.''' def checkEcho( self, input_filename, reference_filename, output_filename, input_mode, output_mode, use_template = True ): '''iterate through *input_filename* writing to *output_filename* and comparing the output to *reference_filename*. The files are opened according to the *input_mode* and *output_mode*. If *use_template* is set, the header is copied from infile using the template mechanism, otherwise target names and lengths are passed explicitely. ''' infile = pysam.Samfile( input_filename, input_mode ) if use_template: outfile = pysam.Samfile( output_filename, output_mode, template = infile ) else: outfile = pysam.Samfile( output_filename, output_mode, referencenames = infile.references, referencelengths = infile.lengths, add_sq_text = False ) iter = infile.fetch() for x in iter: outfile.write( x ) infile.close() outfile.close() self.assertTrue( checkBinaryEqual( reference_filename, output_filename), "files %s and %s are not the same" % (reference_filename, output_filename) ) def testReadWriteBam( self ): input_filename = "ex1.bam" output_filename = "pysam_ex1.bam" reference_filename = "ex1.bam" self.checkEcho( input_filename, reference_filename, output_filename, "rb", "wb" ) def testReadWriteBamWithTargetNames( self ): input_filename = "ex1.bam" output_filename = "pysam_ex1.bam" reference_filename = "ex1.bam" self.checkEcho( input_filename, reference_filename, output_filename, "rb", "wb", use_template = False ) def testReadWriteSamWithHeader( self ): input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex2.sam" self.checkEcho( input_filename, reference_filename, output_filename, "r", "wh" ) def testReadWriteSamWithoutHeader( self ): input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex1.sam" self.checkEcho( input_filename, reference_filename, output_filename, "r", "w" ) def testReadSamWithoutTargetNames( self ): '''see issue 104.''' input_filename = "example_unmapped_reads_no_sq.sam" # raise exception in default mode self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" ) # raise exception if no SQ files self.assertRaises( ValueError, pysam.Samfile, input_filename, "r", check_header = True) infile = pysam.Samfile( input_filename, check_header = False, check_sq = False ) result = list(infile.fetch()) def testReadBamWithoutTargetNames( self ): '''see issue 104.''' input_filename = "example_unmapped_reads_no_sq.bam" # raise exception in default mode self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" ) # raise exception if no SQ files self.assertRaises( ValueError, pysam.Samfile, input_filename, "r", check_header = True) infile = pysam.Samfile( input_filename, check_header = False, check_sq = False ) result = list(infile.fetch( until_eof = True)) def testReadSamWithoutHeader( self ): input_filename = "ex1.sam" output_filename = "pysam_ex1.sam" reference_filename = "ex1.sam" # reading from a samfile without header is not implemented. self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" ) self.assertRaises( ValueError, pysam.Samfile, input_filename, "r", check_header = False ) def testReadUnformattedFile( self ): '''test reading from a file that is not bam/sam formatted''' input_filename = "example.vcf40" # bam - file raise error self.assertRaises( ValueError, pysam.Samfile, input_filename, "rb" ) # sam - file error, but can't fetch self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" ) self.assertRaises( ValueError, pysam.Samfile, input_filename, "r", check_header = False) def testBAMWithoutAlignedReads( self ): '''see issue 117''' input_filename = "test_unaligned.bam" samfile = pysam.Samfile( input_filename, "rb", check_sq = False ) samfile.fetch( until_eof = True ) def testBAMWithShortBAI( self ): '''see issue 116''' input_filename = "example_bai.bam" samfile = pysam.Samfile( input_filename, "rb", check_sq = False ) samfile.fetch( 'chr2' ) def testFetchFromClosedFile( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) samfile.close() self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120) def testClosedFile( self ): '''test that access to a closed samfile raises ValueError.''' samfile = pysam.Samfile( "ex1.bam", "rb" ) samfile.close() self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120) self.assertRaises( ValueError, samfile.pileup, 'chr1', 100, 120) self.assertRaises( ValueError, samfile.getrname, 0 ) self.assertRaises( ValueError, samfile.tell ) self.assertRaises( ValueError, samfile.seek, 0 ) self.assertRaises( ValueError, getattr, samfile, "nreferences" ) self.assertRaises( ValueError, getattr, samfile, "references" ) self.assertRaises( ValueError, getattr, samfile, "lengths" ) self.assertRaises( ValueError, getattr, samfile, "text" ) self.assertRaises( ValueError, getattr, samfile, "header" ) # write on closed file self.assertEqual( 0, samfile.write(None) ) def testAutoDetection( self ): '''test if autodetection works.''' samfile = pysam.Samfile( "ex3.sam" ) self.assertRaises( ValueError, samfile.fetch, 'chr1' ) samfile.close() samfile = pysam.Samfile( "ex3.bam" ) samfile.fetch('chr1') samfile.close() def testReadingFromSamFileWithoutHeader( self ): '''read from samfile without header. ''' samfile = pysam.Samfile( "ex7.sam", check_header = False, check_sq = False ) self.assertRaises( NotImplementedError, samfile.__iter__ ) def testReadingFromFileWithoutIndex( self ): '''read from bam file without index.''' assert not os.path.exists( "ex2.bam.bai" ) samfile = pysam.Samfile( "ex2.bam", "rb" ) self.assertRaises( ValueError, samfile.fetch ) self.assertEqual( len(list( samfile.fetch(until_eof = True) )), 3270 ) def testReadingUniversalFileMode( self ): '''read from samfile without header. ''' input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex1.sam" self.checkEcho( input_filename, reference_filename, output_filename, "rU", "w" ) class TestFloatTagBug( unittest.TestCase ): '''see issue 71''' def testFloatTagBug( self ): '''a float tag before another exposed a parsing bug in bam_aux_get. Fixed in 0.1.19 ''' samfile = pysam.Samfile("tag_bug.bam") read = next(samfile.fetch(until_eof=True)) self.assertTrue( ('XC',1) in read.tags ) self.assertEqual(read.opt('XC'), 1) class TestLargeFieldBug( unittest.TestCase ): '''see issue 100''' def testLargeFileBug( self ): '''when creating a read with a large entry in the tag field causes an errror: NotImplementedError: tags field too large ''' samfile = pysam.Samfile("issue100.bam") read = next(samfile.fetch(until_eof=True)) new_read = pysam.AlignedRead() new_read.tags = read.tags self.assertEqual( new_read.tags, read.tags ) class TestTagParsing( unittest.TestCase ): '''tests checking the accuracy of tag setting and retrieval.''' def makeRead( self ): a = pysam.AlignedRead() a.qname = "read_12345" a.tid = 0 a.seq="ACGT" * 3 a.flag = 0 a.rname = 0 a.pos = 1 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,25) ) a.mrnm = 0 a.mpos=200 a.isize = 0 a.qual ="1234" * 3 # todo: create tags return a def testNegativeIntegers( self ): x = -2 aligned_read = self.makeRead() aligned_read.tags = [("XD", int(x) ) ] # print (aligned_read.tags) def testNegativeIntegers2( self ): x = -2 r = self.makeRead() r.tags = [("XD", int(x) ) ] outfile = pysam.Samfile( "test.bam", "wb", referencenames = ("chr1",), referencelengths = (1000,) ) outfile.write (r ) outfile.close() def testCigarString( self ): r = self.makeRead() self.assertEqual( r.cigarstring, "10M1D25M" ) r.cigarstring = "20M10D20M" self.assertEqual( r.cigar, [(0,20), (2,10), (0,20)]) def testLongTags( self ): '''see issue 115''' r = self.makeRead() rg = 'HS2000-899_199.L3' tags = [('XC', 85), ('XT', 'M'), ('NM', 5), ('SM', 29), ('AM', 29), ('XM', 1), ('XO', 1), ('XG', 4), ('MD', '37^ACCC29T18'), ('XA','5,+11707,36M1I48M,2;21,-48119779,46M1I38M,2;hs37d5,-10060835,40M1D45M,3;5,+11508,36M1I48M,3;hs37d5,+6743812,36M1I48M,3;19,-59118894,46M1I38M,3;4,-191044002,6M1I78M,3;')] r.tags = tags r.tags += [("RG",rg)] * 100 tags += [("RG",rg)] * 100 self.assertEqual( tags, r.tags ) class TestClipping(unittest.TestCase): def testClipping( self ): self.samfile = pysam.Samfile("softclip.bam", "rb" ) for read in self.samfile: if read.qname == "r001": self.assertEqual( read.seq, b'AAAAGATAAGGATA' ) self.assertEqual( read.query, b'AGATAAGGATA' ) self.assertEqual( read.qual, None ) self.assertEqual( read.qqual, None ) elif read.qname == "r002": self.assertEqual( read.seq, b'GCCTAAGCTAA' ) self.assertEqual( read.query, b'AGCTAA' ) self.assertEqual( read.qual, b'01234567890' ) self.assertEqual( read.qqual, b'567890' ) elif read.qname == "r003": self.assertEqual( read.seq, b'GCCTAAGCTAA' ) self.assertEqual( read.query, b'GCCTAA' ) self.assertEqual( read.qual, b'01234567890' ) self.assertEqual( read.qqual, b'012345' ) elif read.qname == "r004": self.assertEqual( read.seq, b'TAGGC' ) self.assertEqual( read.query, b'TAGGC' ) self.assertEqual( read.qual, b'01234' ) self.assertEqual( read.qqual, b'01234' ) class TestIteratorRow(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def checkRange( self, rnge ): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch(region=rnge)) sa = list(pysam.view( "ex1.bam", rnge, raw = True) ) self.assertEqual( len(ps), len(sa), "unequal number of results for range %s: %i != %i" % (rnge, len(ps), len(sa) )) # check if the same reads are returned and in the same order for line, (a, b) in enumerate( list(zip( ps, sa )) ): d = b.split("\t") self.assertEqual( a.qname, d[0], "line %i: read id mismatch: %s != %s" % (line, a.rname, d[0]) ) self.assertEqual( a.pos, int(d[3])-1, "line %i: read position mismatch: %s != %s, \n%s\n%s\n" % \ (line, a.pos, int(d[3])-1, str(a), str(d) ) ) if sys.version_info[0] < 3: qual = d[10] else: qual = d[10].encode('ascii') self.assertEqual( a.qual, qual, "line %i: quality mismatch: %s != %s, \n%s\n%s\n" % \ (line, a.qual, qual, str(a), str(d) ) ) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange( contig ) def testIterateRanges(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range( 1, length, 90): self.checkRange( "%s:%i-%i" % (contig, start, start + 90) ) # this includes empty ranges def tearDown(self): self.samfile.close() class TestIteratorRowAll(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testIterate(self): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch()) sa = list(pysam.view( "ex1.bam", raw = True) ) self.assertEqual( len(ps), len(sa), "unequal number of results: %i != %i" % (len(ps), len(sa) )) # check if the same reads are returned for line, pair in enumerate( list(zip( ps, sa )) ): data = pair[1].split("\t") self.assertEqual( pair[0].qname, data[0], "read id mismatch in line %i: %s != %s" % (line, pair[0].rname, data[0]) ) def tearDown(self): self.samfile.close() class TestIteratorColumn(unittest.TestCase): '''test iterator column against contents of ex4.bam.''' # note that samfile contains 1-based coordinates # 1D means deletion with respect to reference sequence # mCoverages = { 'chr1' : [ 0 ] * 20 + [1] * 36 + [0] * (100 - 20 -35 ), 'chr2' : [ 0 ] * 20 + [1] * 35 + [0] * (100 - 20 -35 ), } def setUp(self): self.samfile=pysam.Samfile( "ex4.bam","rb" ) def checkRange( self, contig, start = None, end = None, truncate = False ): '''compare results from iterator with those from samtools.''' # check if the same reads are returned and in the same order for column in self.samfile.pileup(contig, start, end, truncate = truncate): if truncate: self.assertGreaterEqual( column.pos, start ) self.assertLess( column.pos, end ) thiscov = len(column.pileups) refcov = self.mCoverages[self.samfile.getrname(column.tid)][column.pos] self.assertEqual( thiscov, refcov, "wrong coverage at pos %s:%i %i should be %i" % (self.samfile.getrname(column.tid), column.pos, thiscov, refcov)) def testIterateAll(self): '''check random access per contig''' self.checkRange( None ) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange( contig ) def testIterateRanges(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range( 1, length, 90): self.checkRange( contig, start, start + 90 ) # this includes empty ranges def testInverse( self ): '''test the inverse, is point-wise pileup accurate.''' for contig, refseq in list(self.mCoverages.items()): refcolumns = sum(refseq) for pos, refcov in enumerate( refseq ): columns = list(self.samfile.pileup( contig, pos, pos+1) ) if refcov == 0: # if no read, no coverage self.assertEqual( len(columns), refcov, "wrong number of pileup columns returned for position %s:%i, %i should be %i" %(contig,pos,len(columns), refcov) ) elif refcov == 1: # one read, all columns of the read are returned self.assertEqual( len(columns), refcolumns, "pileup incomplete at position %i: got %i, expected %i " %\ (pos, len(columns), refcolumns)) def testIterateTruncate( self ): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range( 1, length, 90): self.checkRange( contig, start, start + 90, truncate = True ) # this includes empty ranges def tearDown(self): self.samfile.close() class TestIteratorColumn2(unittest.TestCase): '''test iterator column against contents of ex1.bam.''' def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testStart( self ): #print self.samfile.fetch().next().pos #print self.samfile.pileup().next().pos pass def testTruncate( self ): '''see issue 107.''' # note that ranges in regions start from 1 p = self.samfile.pileup(region='chr1:170:172', truncate=True) columns = [ x.pos for x in p ] self.assertEqual( len(columns), 3) self.assertEqual( columns, [169,170,171] ) p = self.samfile.pileup( 'chr1', 169, 172, truncate=True) columns = [ x.pos for x in p ] self.assertEqual( len(columns), 3) self.assertEqual( columns, [169,170,171] ) def testAccessOnClosedIterator( self ): '''see issue 131 Accessing pileup data after iterator has closed. ''' pcolumn = self.samfile.pileup( 'chr1', 170, 180).__next__() self.assertRaises( ValueError, getattr, pcolumn, "pileups" ) class TestAlignedReadFromBam(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex3.bam","rb" ) self.reads=list(self.samfile.fetch()) def testARqname(self): self.assertEqual( self.reads[0].qname, "read_28833_29006_6945", "read name mismatch in read 1: %s != %s" % (self.reads[0].qname, "read_28833_29006_6945") ) self.assertEqual( self.reads[1].qname, "read_28701_28881_323b", "read name mismatch in read 2: %s != %s" % (self.reads[1].qname, "read_28701_28881_323b") ) def testARflag(self): self.assertEqual( self.reads[0].flag, 99, "flag mismatch in read 1: %s != %s" % (self.reads[0].flag, 99) ) self.assertEqual( self.reads[1].flag, 147, "flag mismatch in read 2: %s != %s" % (self.reads[1].flag, 147) ) def testARrname(self): self.assertEqual( self.reads[0].rname, 0, "chromosome/target id mismatch in read 1: %s != %s" % (self.reads[0].rname, 0) ) self.assertEqual( self.reads[1].rname, 1, "chromosome/target id mismatch in read 2: %s != %s" % (self.reads[1].rname, 1) ) def testARpos(self): self.assertEqual( self.reads[0].pos, 33-1, "mapping position mismatch in read 1: %s != %s" % (self.reads[0].pos, 33-1) ) self.assertEqual( self.reads[1].pos, 88-1, "mapping position mismatch in read 2: %s != %s" % (self.reads[1].pos, 88-1) ) def testARmapq(self): self.assertEqual( self.reads[0].mapq, 20, "mapping quality mismatch in read 1: %s != %s" % (self.reads[0].mapq, 20) ) self.assertEqual( self.reads[1].mapq, 30, "mapping quality mismatch in read 2: %s != %s" % (self.reads[1].mapq, 30) ) def testARcigar(self): self.assertEqual( self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)], "read name length mismatch in read 1: %s != %s" % (self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)]) ) self.assertEqual( self.reads[1].cigar, [(0, 35)], "read name length mismatch in read 2: %s != %s" % (self.reads[1].cigar, [(0, 35)]) ) def testARcigarstring(self): self.assertEqual( self.reads[0].cigarstring, '10M1D25M' ) self.assertEqual( self.reads[1].cigarstring, '35M' ) def testARmrnm(self): self.assertEqual( self.reads[0].mrnm, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].mrnm, 0) ) self.assertEqual( self.reads[1].mrnm, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].mrnm, 1) ) self.assertEqual( self.reads[0].rnext, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].rnext, 0) ) self.assertEqual( self.reads[1].rnext, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].rnext, 1) ) def testARmpos(self): self.assertEqual( self.reads[0].mpos, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].mpos, 200-1) ) self.assertEqual( self.reads[1].mpos, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].mpos, 500-1) ) self.assertEqual( self.reads[0].pnext, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].pnext, 200-1) ) self.assertEqual( self.reads[1].pnext, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].pnext, 500-1) ) def testARisize(self): self.assertEqual( self.reads[0].isize, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].isize, 167) ) self.assertEqual( self.reads[1].isize, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].isize, 412) ) self.assertEqual( self.reads[0].tlen, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].tlen, 167) ) self.assertEqual( self.reads[1].tlen, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].tlen, 412) ) def testARseq(self): self.assertEqual( self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 1: %s != %s" % (self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) self.assertEqual( self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "sequence size mismatch in read 2: %s != %s" % (self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") ) self.assertEqual( self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 4: %s != %s" % (self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) def testARqual(self): self.assertEqual( self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 1: %s != %s" % (self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) self.assertEqual( self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "quality string mismatch in read 2: %s != %s" % (self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") ) self.assertEqual( self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 3: %s != %s" % (self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) def testARquery(self): self.assertEqual( self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "query mismatch in read 1: %s != %s" % (self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) self.assertEqual( self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "query size mismatch in read 2: %s != %s" % (self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") ) self.assertEqual( self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT", "query mismatch in read 4: %s != %s" % (self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT") ) def testARqqual(self): self.assertEqual( self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "qquality string mismatch in read 1: %s != %s" % (self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) self.assertEqual( self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "qquality string mismatch in read 2: %s != %s" % (self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") ) self.assertEqual( self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22", "qquality string mismatch in read 3: %s != %s" % (self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22") ) def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 1, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 1) ) self.assertEqual( self.reads[0].opt('RG'), 'L1', "optional field mismatch in read 1, RG: %s != %s" % (self.reads[0].opt('RG'), 'L1') ) self.assertEqual( self.reads[1].opt('RG'), 'L2', "optional field mismatch in read 2, RG: %s != %s" % (self.reads[1].opt('RG'), 'L2') ) self.assertEqual( self.reads[1].opt('MF'), 18, "optional field mismatch in read 2, MF: %s != %s" % (self.reads[1].opt('MF'), 18) ) def testPairedBools(self): self.assertEqual( self.reads[0].is_paired, True, "is paired mismatch in read 1: %s != %s" % (self.reads[0].is_paired, True) ) self.assertEqual( self.reads[1].is_paired, True, "is paired mismatch in read 2: %s != %s" % (self.reads[1].is_paired, True) ) self.assertEqual( self.reads[0].is_proper_pair, True, "is proper pair mismatch in read 1: %s != %s" % (self.reads[0].is_proper_pair, True) ) self.assertEqual( self.reads[1].is_proper_pair, True, "is proper pair mismatch in read 2: %s != %s" % (self.reads[1].is_proper_pair, True) ) def testTags( self ): self.assertEqual( self.reads[0].tags, [('NM', 1), ('RG', 'L1'), ('PG', 'P1'), ('XT', 'U')] ) self.assertEqual( self.reads[1].tags, [('MF', 18), ('RG', 'L2'), ('PG', 'P2'),('XT', 'R') ] ) def testOpt( self ): self.assertEqual( self.reads[0].opt("XT"), "U" ) self.assertEqual( self.reads[1].opt("XT"), "R" ) def testMissingOpt( self ): self.assertRaises( KeyError, self.reads[0].opt, "XP" ) def testEmptyOpt( self ): self.assertRaises( KeyError, self.reads[2].opt, "XT" ) def tearDown(self): self.samfile.close() class TestAlignedReadFromSam(TestAlignedReadFromBam): def setUp(self): self.samfile=pysam.Samfile( "ex3.sam","r" ) self.reads=list(self.samfile.fetch()) # needs to be implemented # class TestAlignedReadFromSamWithoutHeader(TestAlignedReadFromBam): # # def setUp(self): # self.samfile=pysam.Samfile( "ex7.sam","r" ) # self.reads=list(self.samfile.fetch()) class TestHeaderSam(unittest.TestCase): header = {'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891', 'PU': 'SC_1_10', "CN":"name:with:colon"}, {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891', 'PU': 'SC_2_12', "CN":"name:with:colon"}], 'PG': [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}], 'HD': {'VN': '1.0'}, 'CO' : [ 'this is a comment', 'this is another comment'], } def compareHeaders( self, a, b ): '''compare two headers a and b.''' for ak,av in a.items(): self.assertTrue( ak in b, "key '%s' not in '%s' " % (ak,b) ) self.assertEqual( av, b[ak] ) def setUp(self): self.samfile=pysam.Samfile( "ex3.sam","r" ) def testHeaders(self): self.compareHeaders( self.header, self.samfile.header ) self.compareHeaders( self.samfile.header, self.header ) def testNameMapping( self ): for x, y in enumerate( ("chr1", "chr2")): tid = self.samfile.gettid( y ) ref = self.samfile.getrname( x ) self.assertEqual( tid, x ) self.assertEqual( ref, y ) self.assertEqual( self.samfile.gettid("chr?"), -1 ) self.assertRaises( ValueError, self.samfile.getrname, 2 ) def tearDown(self): self.samfile.close() class TestHeaderBam(TestHeaderSam): def setUp(self): self.samfile=pysam.Samfile( "ex3.bam","rb" ) class TestHeaderFromRefs( unittest.TestCase ): '''see issue 144 reference names need to be converted to string for python 3 ''' def testHeader( self ): refs = ['chr1', 'chr2'] tmpfile = "tmp_%i" % id(self) s = pysam.Samfile(tmpfile, 'wb', referencenames=refs, referencelengths=[100]*len(refs)) s.close() self.assertTrue( checkBinaryEqual( 'issue144.bam', tmpfile ), 'bam files differ') os.unlink( tmpfile ) class TestHeader1000Genomes( unittest.TestCase ): # bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam" bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase3_EX_or_LC_only_alignment/data/HG00104/alignment/HG00104.chrom11.ILLUMINA.bwa.GBR.low_coverage.20130415.bam" def testRead( self ): f = pysam.Samfile( self.bamfile, "rb" ) data = f.header.copy() self.assertTrue( data ) class TestUnmappedReads(unittest.TestCase): def testSAM(self): samfile=pysam.Samfile( "ex5.sam","r" ) self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 ) samfile.close() def testBAM(self): samfile=pysam.Samfile( "ex5.bam","rb" ) self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 ) samfile.close() class TestPileupObjects(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testPileupColumn(self): for pcolumn1 in self.samfile.pileup( region="chr1:105" ): if pcolumn1.pos == 104: self.assertEqual( pcolumn1.tid, 0, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn1.tid, 0) ) self.assertEqual( pcolumn1.pos, 105-1, "position mismatch in position 1: %s != %s" % (pcolumn1.pos, 105-1) ) self.assertEqual( pcolumn1.n, 2, "# reads mismatch in position 1: %s != %s" % (pcolumn1.n, 2) ) for pcolumn2 in self.samfile.pileup( region="chr2:1480" ): if pcolumn2.pos == 1479: self.assertEqual( pcolumn2.tid, 1, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn2.tid, 1) ) self.assertEqual( pcolumn2.pos, 1480-1, "position mismatch in position 1: %s != %s" % (pcolumn2.pos, 1480-1) ) self.assertEqual( pcolumn2.n, 12, "# reads mismatch in position 1: %s != %s" % (pcolumn2.n, 12) ) def testPileupRead(self): for pcolumn1 in self.samfile.pileup( region="chr1:105" ): if pcolumn1.pos == 104: self.assertEqual( len(pcolumn1.pileups), 2, "# reads aligned to column mismatch in position 1: %s != %s" % (len(pcolumn1.pileups), 2) ) # self.assertEqual( pcolumn1.pileups[0] # need to test additional properties here def tearDown(self): self.samfile.close() def testIteratorOutOfScope( self ): '''test if exception is raised if pileup col is accessed after iterator is exhausted.''' for pileupcol in self.samfile.pileup(): pass self.assertRaises( ValueError, getattr, pileupcol, "pileups" ) class TestContextManager(unittest.TestCase): def testManager( self ): with pysam.Samfile('ex1.bam', 'rb') as samfile: samfile.fetch() self.assertEqual( samfile._isOpen(), False ) class TestExceptions(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testMissingFile(self): self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "rb" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "r" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "r" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "rb" ) def testBadContig(self): self.assertRaises( ValueError, self.samfile.fetch, "chr88" ) def testMeaninglessCrap(self): self.assertRaises( ValueError, self.samfile.fetch, "skljf" ) def testBackwardsOrderNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, 'chr1', 100, 10 ) def testBackwardsOrderOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, region="chr1:100-10") def testOutOfRangeNegativeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, -10 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, 0 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", -5, -10 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 5, -10 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 5, 0 ) self.assertRaises( ValueError, self.samfile.count, "chr1", -5, -10 ) def testOutOfRangeNegativeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-10" ) self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-0" ) self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5--10" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-10" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-0" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5--10" ) def testOutOfRangNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999, 99999999999 ) def testOutOfRangeLargeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 ) def testOutOfRangeLargeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" ) self.assertRaises( ValueError, self.samfile.count, "chr1:99999999999999999-999999999999999999" ) def testZeroToZero(self): '''see issue 44''' self.assertEqual( len(list(self.samfile.fetch('chr1', 0, 0))), 0) def tearDown(self): self.samfile.close() class TestWrongFormat(unittest.TestCase): '''test cases for opening files not in bam/sam format.''' def testOpenSamAsBam( self ): self.assertRaises( ValueError, pysam.Samfile, 'ex1.sam', 'rb' ) def testOpenBamAsSam( self ): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' ) pass def testOpenFastaAsSam( self ): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' ) pass def testOpenFastaAsBam( self ): self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'rb' ) class TestFastaFile(unittest.TestCase): mSequences = { 'chr1' : b"CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA", 'chr2' : b"TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT", } def setUp(self): self.file=pysam.Fastafile( "ex1.fa" ) def testFetch(self): for id, seq in list(self.mSequences.items()): self.assertEqual( seq, self.file.fetch( id ) ) for x in range( 0, len(seq), 10): self.assertEqual( seq[x:x+10], self.file.fetch( id, x, x+10) ) # test x:end self.assertEqual( seq[x:], self.file.fetch( id, x) ) # test 0:x self.assertEqual( seq[:x], self.file.fetch( id, None, x) ) # unknown sequence returns "" # change: should be an IndexError self.assertEqual( b"", self.file.fetch("chr12") ) def testOutOfRangeAccess( self ): '''test out of range access.''' # out of range access returns an empty string for contig, s in self.mSequences.items(): self.assertEqual( self.file.fetch( contig, len(s), len(s)+1), b"" ) self.assertEqual( self.file.fetch( "chr3", 0 , 100), b"" ) def testFetchErrors( self ): self.assertRaises( ValueError, self.file.fetch ) self.assertRaises( IndexError, self.file.fetch, "chr1", -1, 10 ) self.assertRaises( ValueError, self.file.fetch, "chr1", 20, 10 ) # does not work yet # self.assertRaises( KeyError, self.file.fetch, "chrX" ) def testLength( self ): self.assertEqual( len(self.file), 2 ) def testSequenceLengths( self ): self.assertEqual( 1575, self.file.getReferenceLength( "chr1" ) ) self.assertEqual( 1584, self.file.getReferenceLength( "chr2" ) ) def tearDown(self): self.file.close() class TestFastqFile(unittest.TestCase): def setUp(self): self.file=pysam.Fastqfile( "ex1.fq" ) def testCounts( self ): self.assertEqual( len( [ x for x in self.file ] ), 3270 ) def testMissingFile( self ): self.assertRaises( IOError, pysam.Fastqfile, "nothere.fq" ) def testSequence( self ): s = self.file.__next__() # test first entry self.assertEqual( s.sequence, b"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC") self.assertEqual( s.quality, b"<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;") self.assertEqual( s.name, b"B7_589:1:101:825:28" ) for s in self.file: pass # test last entry self.assertEqual( s.sequence, b"TAATTGAAAAATTCATTTAAGAAATTACAAAATAT") self.assertEqual( s.quality, b"<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<") self.assertEqual( s.name, b"EAS56_65:8:64:507:478" ) class TestAlignedRead(unittest.TestCase): '''tests to check if aligned read can be constructed and manipulated. ''' def checkFieldEqual( self, read1, read2, exclude = []): '''check if two reads are equal by comparing each field.''' for x in ("qname", "seq", "flag", "rname", "pos", "mapq", "cigar", "mrnm", "mpos", "isize", "qual", "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate", "bin"): if x in exclude: continue self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" % (x, getattr(read1, x), getattr(read2,x))) def testEmpty( self ): a = pysam.AlignedRead() self.assertEqual( a.qname, None ) self.assertEqual( a.seq, None ) self.assertEqual( a.qual, None ) self.assertEqual( a.flag, 0 ) self.assertEqual( a.rname, 0 ) self.assertEqual( a.mapq, 0 ) self.assertEqual( a.cigar, None ) self.assertEqual( a.tags, [] ) self.assertEqual( a.mrnm, 0 ) self.assertEqual( a.mpos, 0 ) self.assertEqual( a.isize, 0 ) def buildRead( self ): '''build an example read.''' a = pysam.AlignedRead() a.qname = "read_12345" a.seq="ACGT" * 10 a.flag = 0 a.rname = 0 a.pos = 20 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) ) a.mrnm = 0 a.mpos=200 a.isize=167 a.qual="1234" * 10 # todo: create tags return a def testUpdate( self ): '''check if updating fields affects other variable length data ''' a = self.buildRead() b = self.buildRead() # check qname b.qname = "read_123" self.checkFieldEqual( a, b, "qname" ) b.qname = "read_12345678" self.checkFieldEqual( a, b, "qname" ) b.qname = "read_12345" self.checkFieldEqual( a, b) # check cigar b.cigar = ( (0,10), ) self.checkFieldEqual( a, b, "cigar" ) b.cigar = ( (0,10), (2,1), (0,10) ) self.checkFieldEqual( a, b, "cigar" ) b.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) ) self.checkFieldEqual( a, b) # check seq b.seq = "ACGT" self.checkFieldEqual( a, b, ("seq", "qual") ) b.seq = "ACGT" * 3 self.checkFieldEqual( a, b, ("seq", "qual") ) b.seq = "ACGT" * 10 self.checkFieldEqual( a, b, ("qual",)) # reset qual b = self.buildRead() # check flags: for x in ( "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate"): setattr( b, x, True ) self.assertEqual( getattr(b, x), True ) self.checkFieldEqual( a, b, ("flag", x,) ) setattr( b, x, False ) self.assertEqual( getattr(b, x), False ) self.checkFieldEqual( a, b ) def testUpdate( self ): '''issue 135: inplace update of sequence and quality score. This does not work as setting the sequence will erase the quality scores. ''' a = self.buildRead() a.seq = a.seq[5:10] self.assertEqual( a.qual, None ) a = self.buildRead() s = a.qual a.seq = a.seq[5:10] a.qual = s[5:10] self.assertEqual( a.qual, s[5:10]) def testLargeRead( self ): '''build an example read.''' a = pysam.AlignedRead() a.qname = "read_12345" a.seq="ACGT" * 200 a.flag = 0 a.rname = 0 a.pos = 20 a.mapq = 20 a.cigar = ( (0, 4 * 200), ) a.mrnm = 0 a.mpos=200 a.isize=167 a.qual="1234" * 200 return a def testTagParsing( self ): '''test for tag parsing see http://groups.google.com/group/pysam-user-group/browse_thread/thread/67ca204059ea465a ''' samfile=pysam.Samfile( "ex8.bam","rb" ) for entry in samfile: before = entry.tags entry.tags = entry.tags after = entry.tags self.assertEqual( after, before ) def testUpdateTlen( self ): '''check if updating tlen works''' a = self.buildRead() oldlen = a.tlen oldlen *= 2 a.tlen = oldlen self.assertEqual( a.tlen, oldlen ) def testPositions( self ): a = self.buildRead() self.assertEqual( a.positions, [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59] ) self.assertEqual( a.aligned_pairs, [(0, 20), (1, 21), (2, 22), (3, 23), (4, 24), (5, 25), (6, 26), (7, 27), (8, 28), (9, 29), (None, 30), (10, 31), (11, 32), (12, 33), (13, 34), (14, 35), (15, 36), (16, 37), (17, 38), (18, 39), (19, None), (20, 40), (21, 41), (22, 42), (23, 43), (24, 44), (25, 45), (26, 46), (27, 47), (28, 48), (29, 49), (30, 50), (31, 51), (32, 52), (33, 53), (34, 54), (35, 55), (36, 56), (37, 57), (38, 58), (39, 59)] ) self.assertEqual( a.positions, [x[1] for x in a.aligned_pairs if x[0] != None and x[1] != None] ) # alen is the length of the aligned read in genome self.assertEqual( a.alen, a.aligned_pairs[-1][0] + 1 ) # aend points to one beyond last aligned base in ref self.assertEqual( a.positions[-1], a.aend - 1 ) class TestDeNovoConstruction(unittest.TestCase): '''check BAM/SAM file construction using ex6.sam (note these are +1 coordinates): read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 ''' header = { 'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], } bamfile = "ex6.bam" samfile = "ex6.sam" def checkFieldEqual( self, read1, read2, exclude = []): '''check if two reads are equal by comparing each field.''' for x in ("qname", "seq", "flag", "rname", "pos", "mapq", "cigar", "mrnm", "mpos", "isize", "qual", "bin", "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate"): if x in exclude: continue self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" % (x, getattr(read1, x), getattr(read2,x))) def setUp( self ): a = pysam.AlignedRead() a.qname = "read_28833_29006_6945" a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG" a.flag = 99 a.rname = 0 a.pos = 32 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,25) ) a.mrnm = 0 a.mpos=199 a.isize=167 a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<" a.tags = ( ("NM", 1), ("RG", "L1") ) b = pysam.AlignedRead() b.qname = "read_28701_28881_323b" b.seq="ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA" b.flag = 147 b.rname = 1 b.pos = 87 b.mapq = 30 b.cigar = ( (0,35), ) b.mrnm = 1 b.mpos=499 b.isize=412 b.qual="<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<" b.tags = ( ("MF", 18), ("RG", "L2") ) self.reads = (a,b) def testSAMWholeFile( self ): tmpfilename = "tmp_%i.sam" % id(self) outfile = pysam.Samfile( tmpfilename, "wh", header = self.header ) for x in self.reads: outfile.write( x ) outfile.close() self.assertTrue( checkBinaryEqual( tmpfilename, self.samfile ), "mismatch when construction SAM file, see %s %s" % (tmpfilename, self.samfile)) os.unlink( tmpfilename ) def testBAMPerRead( self ): '''check if individual reads are binary equal.''' infile = pysam.Samfile( self.bamfile, "rb") others = list(infile) for denovo, other in zip( others, self.reads): self.checkFieldEqual( other, denovo ) self.assertEqual( other.compare( denovo ), 0 ) def testSAMPerRead( self ): '''check if individual reads are binary equal.''' infile = pysam.Samfile( self.samfile, "r") others = list(infile) for denovo, other in zip( others, self.reads): self.checkFieldEqual( other, denovo ) self.assertEqual( other.compare( denovo), 0 ) def testBAMWholeFile( self ): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.Samfile( tmpfilename, "wb", header = self.header ) for x in self.reads: outfile.write( x ) outfile.close() self.assertTrue( checkBinaryEqual( tmpfilename, self.bamfile ), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) os.unlink( tmpfilename ) class TestDeNovoConstructionUserTags(TestDeNovoConstruction): '''test de novo construction with a header that contains lower-case tags.''' header = { 'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'x1': {'A': 2, 'B': 5 }, 'x3': {'A': 6, 'B': 5 }, 'x2': {'A': 4, 'B': 5 } } bamfile = "example_user_header.bam" samfile = "example_user_header.sam" class TestEmptyHeader( unittest.TestCase ): '''see issue 84.''' def testEmptyHeader( self ): s = pysam.Samfile('example_empty_header.bam') self.assertEqual( s.header, {'SQ': [{'LN': 1000, 'SN': 'chr1'}]} ) class TestBTagSam( unittest.TestCase ): '''see issue 81.''' compare = [ [100, 1, 91, 0, 7, 101, 0, 201, 96, 204, 0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78, 197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1, 186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195, 101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0, 212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2, 197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194, 0, 180, 0, 108, 0, 203, 104, 16, 5, 205, 0, 0, 0, 1, 1, 100, 98, 0, 0, 204, 6, 0, 79, 0, 0, 101, 7, 109, 90, 265, 1, 27, 10, 109, 102, 9, 0, 292, 0, 110, 0, 0, 102, 112, 0, 0, 84, 100, 103, 2, 81, 126, 0, 2, 90, 0, 15, 96, 15, 1, 0, 2, 0, 107, 92, 0, 0, 101, 3, 98, 15, 102, 13, 116, 116, 90, 93, 198, 0, 0, 0, 199, 92, 26, 495, 100, 5, 0, 100, 5, 209, 0, 92, 107, 90, 0, 0, 0, 0, 109, 194, 7, 94, 200, 0, 40, 197, 0, 11, 0, 0, 112, 110, 6, 4, 200, 28, 0, 196, 0, 203, 1, 129, 0, 0, 1, 0, 94, 0, 1, 0, 107, 5, 201, 3, 3, 100, 0, 121, 0, 7, 0, 1, 105, 306, 3, 86, 8, 183, 0, 12, 163, 17, 83, 22, 0, 0, 1, 8, 109, 103, 0, 0, 295, 0, 200, 16, 172, 3, 16, 182, 3, 11, 0, 0, 223, 111, 103, 0, 5, 225, 0, 95], [-100,200,-300,-400], [-100,12], [12,15], [-1.0,5.0,2.5] ] filename = 'example_btag.sam' def testRead( self ): s = pysam.Samfile(self.filename) for x, read in enumerate(s): if x == 0: self.assertEqual( read.tags, [('RG', 'QW85I'), ('PG', 'tmap'), ('MD', '140'), ('NM', 0), ('AS', 140), ('FZ', [100, 1, 91, 0, 7, 101, 0, 201, 96, 204, 0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78, 197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1, 186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195, 101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0, 212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2, 197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194, 0, 180, 0, 108, 0, 203, 104, 16, 5, 205, 0, 0, 0, 1, 1, 100, 98, 0, 0, 204, 6, 0, 79, 0, 0, 101, 7, 109, 90, 265, 1, 27, 10, 109, 102, 9, 0, 292, 0, 110, 0, 0, 102, 112, 0, 0, 84, 100, 103, 2, 81, 126, 0, 2, 90, 0, 15, 96, 15, 1, 0, 2, 0, 107, 92, 0, 0, 101, 3, 98, 15, 102, 13, 116, 116, 90, 93, 198, 0, 0, 0, 199, 92, 26, 495, 100, 5, 0, 100, 5, 209, 0, 92, 107, 90, 0, 0, 0, 0, 109, 194, 7, 94, 200, 0, 40, 197, 0, 11, 0, 0, 112, 110, 6, 4, 200, 28, 0, 196, 0, 203, 1, 129, 0, 0, 1, 0, 94, 0, 1, 0, 107, 5, 201, 3, 3, 100, 0, 121, 0, 7, 0, 1, 105, 306, 3, 86, 8, 183, 0, 12, 163, 17, 83, 22, 0, 0, 1, 8, 109, 103, 0, 0, 295, 0, 200, 16, 172, 3, 16, 182, 3, 11, 0, 0, 223, 111, 103, 0, 5, 225, 0, 95]), ('XA', 'map2-1'), ('XS', 53), ('XT', 38), ('XF', 1), ('XE', 0)] ) fz = dict(read.tags)["FZ"] self.assertEqual( fz, self.compare[x] ) self.assertEqual( read.opt("FZ"), self.compare[x]) def testWrite( self ): s = pysam.Samfile(self.filename) for read in s: before = read.tags read.tags = read.tags after = read.tags self.assertEqual( after, before ) class TestBTagBam( TestBTagSam ): filename = 'example_btag.bam' class TestDoubleFetch(unittest.TestCase): '''check if two iterators on the same bamfile are independent.''' def testDoubleFetch( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') for a,b in zip(samfile1.fetch(), samfile1.fetch()): self.assertEqual( a.compare( b ), 0 ) def testDoubleFetchWithRegion( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') chr, start, stop = 'chr1', 200, 3000000 self.assertTrue(len(list(samfile1.fetch ( chr, start, stop))) > 0) #just making sure the test has something to catch for a,b in zip(samfile1.fetch( chr, start, stop), samfile1.fetch( chr, start, stop)): self.assertEqual( a.compare( b ), 0 ) def testDoubleFetchUntilEOF( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') for a,b in zip(samfile1.fetch( until_eof = True), samfile1.fetch( until_eof = True )): self.assertEqual( a.compare( b), 0 ) class TestRemoteFileFTP(unittest.TestCase): '''test remote access. ''' # Need to find an ftp server without password on standard # port. url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam" region = "1:1-1000" def testFTPView( self ): return result = pysam.view( self.url, self.region ) self.assertEqual( len(result), 36 ) def testFTPFetch( self ): return samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch( region = self.region )) self.assertEqual( len(result), 36 ) class TestRemoteFileHTTP( unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam" region = "chr1:1-1000" local = "ex1.bam" def testView( self ): samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch( region = self.region )) result = pysam.view( self.url, self.region ) self.assertEqual( len(result), len(ref) ) def testFetch( self ): samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch( region = self.region )) samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch( region = self.region )) self.assertEqual( len(ref), len(result) ) for x, y in zip(result, ref): self.assertEqual( x.compare( y ), 0 ) def testFetchAll( self ): samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch()) samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch() ) self.assertEqual( len(ref), len(result) ) for x, y in zip(result, ref): self.assertEqual( x.compare( y ), 0 ) class TestLargeOptValues( unittest.TestCase ): ints = ( 65536, 214748, 2147484, 2147483647 ) floats = ( 65536.0, 214748.0, 2147484.0 ) def check( self, samfile ): i = samfile.fetch() for exp in self.ints: rr = next(i) obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [ -x for x in self.ints ]: rr = next(i) obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in self.floats: rr = next(i) obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [ -x for x in self.floats ]: rr = next(i) obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) def testSAM( self ): samfile = pysam.Samfile("ex10.sam", "r") self.check( samfile ) def testBAM( self ): samfile = pysam.Samfile("ex10.bam", "rb") self.check( samfile ) # class TestSNPCalls( unittest.TestCase ): # '''test pysam SNP calling ability.''' # def checkEqual( self, a, b ): # for x in ("reference_base", # "pos", # "genotype", # "consensus_quality", # "snp_quality", # "mapping_quality", # "coverage" ): # self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" % # (x, getattr(a, x), getattr(b,x), str(a), str(b))) # def testAllPositionsViaIterator( self ): # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # try: # refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base != "*"] # except pysam.SamtoolsError: # pass # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # calls = list(pysam.IteratorSNPCalls(i)) # for x,y in zip( refs, calls ): # self.checkEqual( x, y ) # def testPerPositionViaIterator( self ): # # test pileup for each position. This is a slow operation # # so this test is disabled # return # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base == "*": continue # i = samfile.pileup( x.chromosome, x.pos, x.pos+1, # fastafile = fastafile, # stepper = "samtools" ) # z = [ zz for zz in pysam.IteratorSamtools(i) if zz.pos == x.pos ] # self.assertEqual( len(z), 1 ) # self.checkEqual( x, z[0] ) # def testPerPositionViaCaller( self ): # # test pileup for each position. This is a fast operation # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # caller = pysam.SNPCaller( i ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base == "*": continue # call = caller.call( x.chromosome, x.pos ) # self.checkEqual( x, call ) # class TestIndelCalls( unittest.TestCase ): # '''test pysam indel calling.''' # def checkEqual( self, a, b ): # for x in ("pos", # "genotype", # "consensus_quality", # "snp_quality", # "mapping_quality", # "coverage", # "first_allele", # "second_allele", # "reads_first", # "reads_second", # "reads_diff"): # if b.genotype == "*/*" and x == "second_allele": # # ignore test for second allele (positions chr2:439 and chr2:1512) # continue # self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" % # (x, getattr(a, x), getattr(b,x), str(a), str(b))) # def testAllPositionsViaIterator( self ): # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # try: # refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base == "*"] # except pysam.SamtoolsError: # pass # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # calls = [ x for x in list(pysam.IteratorIndelCalls(i)) if x != None ] # for x,y in zip( refs, calls ): # self.checkEqual( x, y ) # def testPerPositionViaCaller( self ): # # test pileup for each position. This is a fast operation # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # caller = pysam.IndelCaller( i ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base != "*": continue # call = caller.call( x.chromosome, x.pos ) # self.checkEqual( x, call ) class TestLogging( unittest.TestCase ): '''test around bug issue 42, failed in versions < 0.4 ''' def check( self, bamfile, log ): if log: logger = logging.getLogger('franklin') logger.setLevel(logging.INFO) formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s') log_hand = logging.FileHandler('log.txt') log_hand.setFormatter(formatter) logger.addHandler(log_hand) bam = pysam.Samfile(bamfile, 'rb') cols = bam.pileup() self.assertTrue( True ) def testFail1( self ): self.check( "ex9_fail.bam", False ) self.check( "ex9_fail.bam", True ) def testNoFail1( self ): self.check( "ex9_nofail.bam", False ) self.check( "ex9_nofail.bam", True ) def testNoFail2( self ): self.check( "ex9_nofail.bam", True ) self.check( "ex9_nofail.bam", True ) # TODOS # 1. finish testing all properties within pileup objects # 2. check exceptions and bad input problems (missing files, optional fields that aren't present, etc...) # 3. check: presence of sequence class TestSamfileUtilityFunctions( unittest.TestCase ): def testCount( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) for contig in ("chr1", "chr2" ): for start in range( 0, 2000, 100 ): end = start + 1 self.assertEqual( len( list( samfile.fetch( contig, start, end ) ) ), samfile.count( contig, start, end ) ) # test empty intervals self.assertEqual( len( list( samfile.fetch( contig, start, start ) ) ), samfile.count( contig, start, start ) ) # test half empty intervals self.assertEqual( len( list( samfile.fetch( contig, start ) ) ), samfile.count( contig, start ) ) def testMate( self ): '''test mate access.''' with open( "ex1.sam", "rb" ) as inf: readnames = [ x.split(b"\t")[0] for x in inf.readlines() ] if sys.version_info[0] >= 3: readnames = [ name.decode('ascii') for name in readnames ] counts = collections.defaultdict( int ) for x in readnames: counts[x] += 1 samfile = pysam.Samfile( "ex1.bam", "rb" ) for read in samfile.fetch(): if not read.is_paired: self.assertRaises( ValueError, samfile.mate, read ) elif read.mate_is_unmapped: self.assertRaises( ValueError, samfile.mate, read ) else: if counts[read.qname] == 1: self.assertRaises( ValueError, samfile.mate, read ) else: mate = samfile.mate( read ) self.assertEqual( read.qname, mate.qname ) self.assertEqual( read.is_read1, mate.is_read2 ) self.assertEqual( read.is_read2, mate.is_read1 ) self.assertEqual( read.pos, mate.mpos ) self.assertEqual( read.mpos, mate.pos ) def testIndexStats( self ): '''test if total number of mapped/unmapped reads is correct.''' samfile = pysam.Samfile( "ex1.bam", "rb" ) self.assertEqual( samfile.mapped, 3235 ) self.assertEqual( samfile.unmapped, 35 ) class TestSamtoolsProxy( unittest.TestCase ): '''tests for sanity checking access to samtools functions.''' def testIndex( self ): self.assertRaises( IOError, pysam.index, "missing_file" ) def testView( self ): # note that view still echos "open: No such file or directory" self.assertRaises( pysam.SamtoolsError, pysam.view, "missing_file" ) def testSort( self ): self.assertRaises( pysam.SamtoolsError, pysam.sort, "missing_file" ) class TestSamfileIndex( unittest.TestCase): def testIndex( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) index = pysam.IndexedReads( samfile ) index.build() reads = collections.defaultdict( int ) for read in samfile: reads[read.qname] += 1 for qname, counts in reads.items(): found = list(index.find( qname )) self.assertEqual( len(found), counts ) for x in found: self.assertEqual( x.qname, qname ) if __name__ == "__main__": # build data files print ("building data files") subprocess.call( "make", shell=True) print ("starting tests") unittest.main() print ("completed tests") pysam-0.7.7/tests/example.bed.gz.tbi0000664000076400007650000000036511700526652017162 0ustar andreasandreasBC;0 DN!8ƎvɌ[q6omE30 ֯hd~0F)OZ'n UỤU'S=tu]OC7f5ޕ^?Qm&|;zgh>`m9QΗ}]ז*Z*k|VBCpysam-0.7.7/tests/ex10.sam0000664000076400007650000000337311700526652015140 0ustar andreasandreas@HD VN:1.0 @SQ SN:1 LN:249250621 read1 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:65536 ZL:i:25 read2 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:214748 ZL:i:25 read3 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:2147484 ZL:i:25 read4 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:2147483647 ZL:i:25 read5 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-65536 ZL:i:25 read6 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-214748 ZL:i:25 read7 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-2147484 ZL:i:25 read8 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:i:-2147483647 ZL:i:25 read1 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:65536 ZL:i:25 read2 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:214748 ZL:i:25 read3 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:2147484 ZL:i:25 read5 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-65536 ZL:i:25 read6 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-214748 ZL:i:25 read7 115 1 142618765 255 25M = 142618765 25 CGACCCACTCCGCCATTTTCATCCG IIGIIIHIGIIFIIIIIIIGIGIII NM:i:0 ZP:f:-2147484 ZL:i:25 pysam-0.7.7/tests/tabix_test.py0000664000076400007650000006745312241537230016405 0ustar andreasandreas#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import sys, os, shutil, gzip import pysam import unittest import itertools import subprocess import glob import re IS_PYTHON3 = sys.version_info[0] >= 3 def myzip_open( infile, mode = "r" ): '''open compressed file and decode.''' def _convert(f): for l in f: yield l.decode("ascii") if IS_PYTHON3: if mode == "r": return _convert(gzip.open(infile,"r")) else: return gzip.open( mode ) def loadAndConvert( infile, encode = True ): '''load data from infile and convert all fields to bytes. infile can be either plain or compressed (ending in .gz). ''' data = [] if infile.endswith(".gz"): for line in gzip.open( infile ): line = line.decode("ascii") if line.startswith("#"): continue d = line.strip().split("\t") if encode: data.append( [x.encode("ascii") for x in d ] ) else: data.append( d ) else: with open(infile) as f: for line in f: if line.startswith("#"): continue d = line.strip().split("\t") if encode: data.append( [x.encode("ascii") for x in d ] ) else: data.append( d ) return data def splitToBytes( s ): '''split string and return list of bytes.''' return [x.encode("ascii") for x in s.split("\t")] def checkBinaryEqual( filename1, filename2 ): '''return true if the two files are binary equal.''' if os.path.getsize( filename1 ) != os.path.getsize( filename2 ): return False infile1 = open(filename1, "rb") infile2 = open(filename2, "rb") d1, d2 = infile1.read(), infile2.read() found = False for c1,c2 in zip( d1, d2 ): if c1 != c2: break else: found = True infile1.close() infile2.close() return found class TestIndexing(unittest.TestCase): filename = "example.gtf.gz" filename_idx = "example.gtf.gz.tbi" def setUp( self ): self.tmpfilename = "tmp_%i.gtf.gz" % id(self) shutil.copyfile( self.filename, self.tmpfilename ) def testIndexPreset( self ): '''test indexing via preset.''' pysam.tabix_index( self.tmpfilename, preset = "gff" ) checkBinaryEqual( self.tmpfilename + ".tbi", self.filename_idx ) def tearDown( self ): os.unlink( self.tmpfilename ) os.unlink( self.tmpfilename + ".tbi" ) class TestCompression(unittest.TestCase): filename = "example.gtf.gz" filename_idx = "example.gtf.gz.tbi" preset = "gff" def setUp( self ): self.tmpfilename = "tmp_%i" % id(self) infile = gzip.open( self.filename, "rb") outfile = open( self.tmpfilename, "wb" ) outfile.write( infile.read() ) outfile.close() infile.close() def testCompression( self ): '''see also issue 106''' pysam.tabix_compress( self.tmpfilename, self.tmpfilename + ".gz" ) checkBinaryEqual( self.tmpfilename, self.tmpfilename + ".gz" ) def testIndexPresetUncompressed( self ): '''test indexing via preset.''' pysam.tabix_index( self.tmpfilename, preset = self.preset ) # check if uncompressed file has been removed self.assertEqual( os.path.exists( self.tmpfilename ), False ) checkBinaryEqual( self.tmpfilename + ".gz", self.filename ) checkBinaryEqual( self.tmpfilename + ".gz.tbi", self.filename_idx ) def testIndexPresetCompressed( self ): '''test indexing via preset.''' pysam.tabix_compress( self.tmpfilename, self.tmpfilename + ".gz" ) pysam.tabix_index( self.tmpfilename + ".gz", preset = self.preset ) checkBinaryEqual( self.tmpfilename + ".gz", self.filename ) checkBinaryEqual( self.tmpfilename + ".gz.tbi", self.filename_idx ) def tearDown( self ): try: os.unlink( self.tmpfilename ) os.unlink( self.tmpfilename + ".gz" ) os.unlink( self.tmpfilename + ".gz.tbi" ) except OSError: pass class TestCompressionSam( TestCompression ): filename = "example.sam.gz" filename_index = "example.sam.gz.tbi" preset = "sam" class TestCompressionBed( TestCompression ): filename = "example.bed.gz" filename_index = "example.bed.gz.tbi" preset = "bed" class TestCompressionVCF( TestCompression ): filename = "example.vcf.gz" filename_index = "example.vcf.gz.tbi" preset = "vcf" class TestIteration( unittest.TestCase ): filename = "example.gtf.gz" def setUp( self ): self.tabix = pysam.Tabixfile( self.filename ) lines = [] inf = gzip.open( self.filename, "rb") for line in inf: line = line.decode('ascii') if line.startswith("#"): continue lines.append( line ) inf.close() # creates index of contig, start, end, adds content without newline. self.compare = [ (x[0][0], int(x[0][3]), int(x[0][4]), x[1]) for x in [ (y.split("\t"), y[:-1]) for y in lines ] ] def getSubset( self, contig = None, start = None, end = None): if contig == None: # all lines subset = [ x[3] for x in self.compare ] else: if start != None and end == None: # until end of contig subset = [ x[3] for x in self.compare if x[0] == contig and x[2] > start ] elif start == None and end != None: # from start of contig subset = [ x[3] for x in self.compare if x[0] == contig and x[1] <= end ] elif start == None and end == None: subset = [ x[3] for x in self.compare if x[0] == contig ] else: # all within interval subset = [ x[3] for x in self.compare if x[0] == contig and \ min( x[2], end) - max(x[1], start) > 0 ] return subset def checkPairwise( self, result, ref ): '''check pairwise results. ''' result.sort() ref.sort() a = set(result) b = set(ref) self.assertEqual( len(result), len(ref), "unexpected number of results: result=%i, expected ref=%i, differences are %s: %s" \ % (len(result), len(ref), a.difference(b), b.difference(a) )) for x, d in enumerate( list(zip( result, ref ))): self.assertEqual( d[0], d[1], "unexpected results in pair %i:\n'%s', expected\n'%s'" % \ (x, d[0], d[1]) ) def testAll( self ): result = list(self.tabix.fetch()) ref = self.getSubset( ) self.checkPairwise( result, ref ) def testPerContig( self ): for contig in ("chr1", "chr2", "chr1", "chr2" ): result = list(self.tabix.fetch( contig )) ref = self.getSubset( contig ) self.checkPairwise( result, ref ) def testPerContigToEnd( self ): end = None for contig in ("chr1", "chr2", "chr1", "chr2" ): for start in range( 0, 200000, 1000): result = list(self.tabix.fetch( contig, start, end )) ref = self.getSubset( contig, start, end ) self.checkPairwise( result, ref ) def testPerContigFromStart( self ): start = None for contig in ("chr1", "chr2", "chr1", "chr2" ): for end in range( 0, 200000, 1000): result = list(self.tabix.fetch( contig, start, end )) ref = self.getSubset( contig, start, end ) self.checkPairwise( result, ref ) def testPerContig( self ): start, end = None, None for contig in ("chr1", "chr2", "chr1", "chr2" ): result = list(self.tabix.fetch( contig, start, end )) ref = self.getSubset( contig, start, end ) self.checkPairwise( result, ref ) def testPerInterval( self ): start, end = None, None for contig in ("chr1", "chr2", "chr1", "chr2" ): for start in range( 0, 200000, 2000): for end in range( start, start + 2000, 500): result = list(self.tabix.fetch( contig, start, end )) ref = self.getSubset( contig, start, end ) self.checkPairwise( result, ref ) def testInvalidIntervals( self ): # invalid intervals (start > end) self.assertRaises( ValueError, self.tabix.fetch, "chr1", 0, -10) self.assertRaises( ValueError, self.tabix.fetch, "chr1", 200, 0) # out of range intervals self.assertRaises( IndexError, self.tabix.fetch, "chr1", -10, 200) self.assertRaises( IndexError, self.tabix.fetch, "chr1", -10, -20) # unknown chromosome self.assertRaises( KeyError, self.tabix.fetch, "chrUn" ) # out of range access # to be implemented # self.assertRaises( IndexError, self.tabix.fetch, "chr1", 1000000, 2000000 ) # raise no error for invalid intervals self.tabix.fetch( "chr1", 100,100) def testGetContigs( self ): self.assertEqual( sorted(self.tabix.contigs), [b"chr1", b"chr2"] ) # check that contigs is read-only self.assertRaises( AttributeError, setattr, self.tabix, "contigs", ["chr1", "chr2"] ) def testHeader( self ): ref = [] inf = gzip.open( self.filename ) for x in inf: x = x.decode("ascii") if not x.startswith("#"): break ref.append( x[:-1].encode('ascii') ) inf.close() header = list( self.tabix.header ) self.assertEqual( ref, header ) def testReopening( self ): '''test repeated opening of the same file.''' def func1(): # opens any tabix file inf = pysam.Tabixfile(self.filename) return for i in range(10000): func1() class TestParser( unittest.TestCase ): filename = "example.gtf.gz" def setUp( self ): self.tabix = pysam.Tabixfile( self.filename ) self.compare = loadAndConvert( self.filename ) def testRead( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )): self.assertEqual( self.compare[x], list(r) ) self.assertEqual( len(self.compare[x]), len(r) ) # test indexing for c in range(0,len(r)): self.assertEqual( self.compare[x][c], r[c] ) # test slicing access for c in range(0, len(r)-1): for cc in range(c+1, len(r)): self.assertEqual( self.compare[x][c:cc], r[c:cc] ) def testWrite( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )): self.assertEqual( self.compare[x], list(r) ) c = list(r) for y in range(len(r)): r[y] = "test_%05i" % y c[y] = "test_%05i" % y self.assertEqual( [x.encode("ascii") for x in c], list(r) ) self.assertEqual( "\t".join( c ), str(r) ) # check second assignment for y in range(len(r)): r[y] = "test_%05i" % y self.assertEqual( [x.encode("ascii") for x in c], list(r) ) self.assertEqual( "\t".join( c ), str(r) ) def testUnset( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asTuple() )): self.assertEqual( self.compare[x], list(r) ) c = list(r) e = [ x.decode('ascii') for x in r ] for y in range(len(r)): r[y] = None c[y] = None e[y] = "" self.assertEqual( c, list(r) ) self.assertEqual( "\t".join(e), str(r) ) def testIteratorCompressed( self ): '''test iteration from compressed file.''' with gzip.open( self.filename ) as infile: for x, r in enumerate(pysam.tabix_iterator( infile, pysam.asTuple() )): self.assertEqual( self.compare[x], list(r) ) self.assertEqual( len(self.compare[x]), len(r) ) # test indexing for c in range(0,len(r)): self.assertEqual( self.compare[x][c], r[c] ) # test slicing access for c in range(0, len(r)-1): for cc in range(c+1, len(r)): self.assertEqual( self.compare[x][c:cc], r[c:cc] ) def testIteratorUncompressed( self ): '''test iteration from uncompressed file.''' tmpfilename = 'tmp_testIteratorUncompressed' infile = gzip.open( self.filename, "rb") outfile = open( tmpfilename, "wb" ) outfile.write( infile.read() ) outfile.close() infile.close() with open( tmpfilename ) as infile: for x, r in enumerate(pysam.tabix_iterator( infile, pysam.asTuple() )): self.assertEqual( self.compare[x], list(r) ) self.assertEqual( len(self.compare[x]), len(r) ) # test indexing for c in range(0,len(r)): self.assertEqual( self.compare[x][c], r[c] ) # test slicing access for c in range(0, len(r)-1): for cc in range(c+1, len(r)): self.assertEqual( self.compare[x][c:cc], r[c:cc] ) os.unlink( tmpfilename ) class TestIterators( unittest.TestCase ): filename = "example.gtf.gz" iterator = pysam.tabix_generic_iterator parser = pysam.asTuple is_compressed = False def setUp( self ): self.tabix = pysam.Tabixfile( self.filename ) self.compare = loadAndConvert( self.filename ) self.tmpfilename_uncompressed = 'tmp_TestIterators' infile = gzip.open( self.filename, "rb") outfile = open( self.tmpfilename_uncompressed, "wb" ) outfile.write( infile.read() ) outfile.close() infile.close() def open( self ): if self.is_compressed: infile = gzip.open( self.filename ) else: infile = open( self.tmpfilename_uncompressed ) return infile def testIteration( self ): infile = self.open() for x, r in enumerate(self.iterator( infile, self.parser())): self.assertEqual( self.compare[x], list(r) ) self.assertEqual( len(self.compare[x]), len(r) ) # test indexing for c in range(0,len(r)): self.assertEqual( self.compare[x][c], r[c] ) # test slicing access for c in range(0, len(r)-1): for cc in range(c+1, len(r)): self.assertEqual( self.compare[x][c:cc], r[c:cc] ) def testClosedFile( self ): '''test for error when iterating from closed file.''' infile = self.open() infile.close() # iterating from a closed file should raise a value error self.assertRaises( ValueError, self.iterator, infile, self.parser()) def testClosedFileIteration( self ): '''test for error when iterating from file that has been closed''' infile = self.open() i = self.iterator( infile, self.parser()) x = i.next() infile.close() # Not implemented #self.assertRaises( ValueError, i.next ) def tearUp( self ): os.unlink( self.tmpfilename_uncompressed ) class TestIteratorsGenericCompressed( TestIterators ): is_compressed = True class TestIteratorsFileCompressed( TestIterators ): iterator = pysam.tabix_file_iterator is_compressed = True class TestIteratorsFileUncompressed( TestIterators ): iterator = pysam.tabix_file_iterator is_compressed = False class TestGTF( TestParser ): def testRead( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asGTF() )): c = self.compare[x] self.assertEqual( len(c), len(r) ) self.assertEqual( list(c), list(r) ) self.assertEqual( c, splitToBytes( str(r) ) ) self.assertTrue( r.gene_id.startswith("ENSG") ) if r.feature != b'gene': self.assertTrue( r.transcript_id.startswith("ENST") ) self.assertEqual( c[0], r.contig ) class TestBed( unittest.TestCase ): filename = "example.bed.gz" def setUp( self ): self.tabix = pysam.Tabixfile( self.filename) self.compare = loadAndConvert( self.filename ) def testRead( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asBed() )): c = self.compare[x] self.assertEqual( len(c), len(r) ) self.assertEqual( c, splitToBytes( str(r) ) ) self.assertEqual( list(c), list(r) ) self.assertEqual( c[0], r.contig) self.assertEqual( int(c[1]), r.start) self.assertEqual( int(c[2]), r.end) def testWrite( self ): for x, r in enumerate(self.tabix.fetch( parser = pysam.asBed() )): c = self.compare[x] self.assertEqual( c, splitToBytes(str(r) )) self.assertEqual( list(c), list(r) ) r.contig = "test" self.assertEqual( b"test", r.contig) self.assertEqual( b"test", r[0]) r.start += 1 self.assertEqual( int(c[1]) + 1, r.start ) self.assertEqual( str(int(c[1]) + 1), r[1].decode("ascii" )) r.end += 1 self.assertEqual( int(c[2]) + 1, r.end ) self.assertEqual( str(int(c[2]) + 1), r[2].decode("ascii") ) class TestVCF( unittest.TestCase ): filename = "example.vcf40" def setUp( self ): self.tmpfilename = "tmp_%s.vcf" % id(self) shutil.copyfile( self.filename, self.tmpfilename ) pysam.tabix_index( self.tmpfilename, preset = "vcf" ) def tearDown( self ): os.unlink( self.tmpfilename + ".gz" ) if os.path.exists( self.tmpfilename + ".gz.tbi" ): os.unlink( self.tmpfilename + ".gz.tbi" ) class TestVCFFromTabix( TestVCF ): columns = ("contig", "pos", "id", "ref", "alt", "qual", "filter", "info", "format" ) def setUp( self ): TestVCF.setUp( self ) self.tabix = pysam.Tabixfile( self.tmpfilename + ".gz" ) self.compare = loadAndConvert( self.filename ) def testRead( self ): ncolumns = len(self.columns) for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )): c = self.compare[x] for y, field in enumerate( self.columns ): # it is ok to have a missing format column if y == 8 and y == len(c): continue if field == "pos": self.assertEqual( int(c[y]) - 1, getattr( r, field ) ) self.assertEqual( int(c[y]) - 1, r.pos ) else: self.assertEqual( c[y], getattr( r, field ), "mismatch in field %s: %s != %s" %\ ( field,c[y], getattr( r, field ) ) ) if len(c) == 8: self.assertEqual( 0, len(r) ) else: self.assertEqual( len(c), len( r ) + ncolumns ) for y in range(len(c) - ncolumns): self.assertEqual( c[ncolumns+y], r[y] ) def testWrite( self ): ncolumns = len(self.columns) for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )): c = self.compare[x] # check unmodified string cmp_string = str(r) ref_string = "\t".join( [x.decode() for x in c] ) self.assertEqual( ref_string, cmp_string ) # set fields and compare field-wise for y, field in enumerate( self.columns ): # it is ok to have a missing format column if y == 8 and y == len(c): continue if field == "pos": rpos = getattr( r, field ) self.assertEqual( int(c[y]) - 1, rpos ) self.assertEqual( int(c[y]) - 1, r.pos ) # increment pos by 1 setattr( r, field, rpos + 1 ) self.assertEqual( getattr( r, field ), rpos + 1 ) c[y] = str(int(c[y]) + 1 ) else: setattr( r, field, "test_%i" % y) c[y] = ("test_%i" % y).encode('ascii') self.assertEqual( c[y], getattr( r, field ), "mismatch in field %s: %s != %s" %\ ( field,c[y], getattr( r, field ) ) ) if len(c) == 8: self.assertEqual( 0, len(r) ) else: self.assertEqual( len(c), len( r ) + ncolumns ) for y in range(len(c) - ncolumns): c[ncolumns+y] = ("test_%i" % y).encode('ascii') r[y] = ("test_%i" % y).encode('ascii') self.assertEqual( c[ncolumns+y], r[y] ) class TestVCFFromVCF( TestVCF ): columns = ("chrom", "pos", "id", "ref", "alt", "qual", "filter", "info", "format" ) # tests failing while parsing fail_on_parsing = ( (5, "Flag fields should not have a value"), (9, "aouao" ), (13, "aoeu" ), (18, "Error BAD_NUMBER_OF_PARAMETERS" ), (24, "Error HEADING_NOT_SEPARATED_BY_TABS" ) ) # tests failing on opening fail_on_opening = ( (24, "Error HEADING_NOT_SEPARATED_BY_TABS" ), ) def setUp( self ): TestVCF.setUp( self ) self.vcf = pysam.VCF() self.compare = loadAndConvert( self.filename, encode = False ) def testParsing( self ): # self.vcf.connect( self.tmpfilename + ".gz" ) ncolumns = len(self.columns) fn = os.path.basename( self.filename ) with open(self.filename) as f: for x, msg in self.fail_on_opening: if "%i.vcf" % x == fn: self.assertRaises( ValueError, self.vcf.parse, f ) return else: iter = self.vcf.parse(f) for x, msg in self.fail_on_parsing: if "%i.vcf" % x == fn: self.assertRaises( ValueError, list, iter ) break # python 2.7 # self.assertRaisesRegexp( ValueError, re.compile(msg), self.vcf.parse, f ) else: # do the actual parsing for x, r in enumerate(iter): c = self.compare[x] for y, field in enumerate( self.columns ): # it is ok to have a missing format column if y == 8 and y == len(c): continue val = r[field] if field == "pos": self.assertEqual( int(c[y]) - 1, val ) elif field == "alt": if c[y] == ".": # convert . to empty list self.assertEqual( [], val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) else: # convert to list self.assertEqual( c[y].split(","), val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) elif field == "filter": if c[y] == "PASS" or c[y] == ".": # convert PASS to empty list self.assertEqual( [], val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) else: # convert to list self.assertEqual( c[y].split(";"), val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) elif field == "info": # tests for info field not implemented pass elif field == "qual" and c[y] == ".": self.assertEqual( -1, val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) elif field == "format": # format field converted to list self.assertEqual( c[y].split(":"), val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) elif type(val) in (int, float): if c[y] == ".": self.assertEqual( None, val, "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) else: self.assertEqual( float( c[y]), float(val), "mismatch in field %s: expected %s, got %s" %\ ( field,c[y], val ) ) else: self.assertEqual( c[y], val, "mismatch in field %s: expected %s, got %s" %\ ( field, c[y], val ) ) ############################################################################ # create a test class for each example vcf file. # Two samples are created - # 1. Testing pysam/tabix access # 2. Testing the VCF class vcf_files = glob.glob( "vcf-examples/*.vcf" ) for vcf_file in vcf_files: n = "VCFFromTabixTest_%s" % os.path.basename( vcf_file[:-4] ) globals()[n] = type( n, (TestVCFFromTabix,), dict( filename=vcf_file,) ) n = "VCFFromVCFTest_%s" % os.path.basename( vcf_file[:-4] ) globals()[n] = type( n, (TestVCFFromVCF,), dict( filename=vcf_file,) ) ############################################################################ class TestRemoteFileHTTP( unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz" region = "chr1:1-1000" local = "example.gtf.gz" def testFetchAll( self ): remote_file = pysam.Tabixfile(self.url, "r") remote_result = list(remote_file.fetch()) local_file = pysam.Tabixfile(self.local, "r") local_result = list(local_file.fetch()) self.assertEqual( len(remote_result), len(local_result) ) for x, y in zip(remote_result, local_result): self.assertEqual( x, y ) if __name__ == "__main__": unittest.main() pysam-0.7.7/tests/tag_bug.bam0000664000076400007650000000057711700526652015755 0ustar andreasandreasBCsred~ fb# l`Gj Ë 5N N=#kcX#D"AJXsg°q6J()Jd($ bt238 7$?9#?/(3?/>=5/?7ևBCk=UPuu 621242242752445V6`p`b`PpjriqhPttRUQPPQVTQQUQVSVSSWr%A"Ҫ~ ~LΎi'z{x:3D8;3>`BCpysam-0.7.7/tests/test_unaligned.bam0000664000076400007650000000100212162643754017340 0ustar andreasandreasBCsre,e``pp 23 *,M-KMrrtʭL )K  042615q2]B u u B HhU0To^1SBCVN0AӺ$ii<6'"%<6fі,R_ L)*jZ#_ݣ;O!S,Fh͢E]}=_,WYֳ7f 1#h4t>!$(s`@roU%~η[g[TJ-z9"x?hǘm{րNфX%%:N|4ť!fpxs6`=8 BL܁ !lCcj(-#uEYP$X}0V*|FCf,#8lf%%EQO4BCpysam-0.7.7/tests/ex9_nofail.bam0000664000076400007650000002403611700526652016376 0ustar andreasandreasBCr&]{X9D %6|blebN%L2 2:9 0X!j!Ix0y>pu]=Sw]N>qO;[tGsywcG?q^.g^gu/?=,qC!їB·QC"6:jcSǠa+}tA6]/Dæ=rfl_6}w%ЗM[ᲒWO}\ئueY+1nzy!M{a|SMlgza߲=qGlo1vjot˶7GFZ+:}y ![c/w^y6hMhʦx=o}i,}vͪ+Jz,v5LQ{bۗ] +[F[CTjZQպY[抦چg=X^I[L,}[tE]i>4,v|Ѭf5 "n>li>PFx w|}mYM;n;~֬w[<ݴ]cYQ#WvH8ZxrpuǛkab[M8glW0r7HqvZ*]H_pZPgwa;DJ;^]ʍݵ?A k9GAyubK9UҜ]/^v ]%  "]\cvsme^q#v&9+#v׏2h]c i#vx]\_c ɂ>v#v݈]T:࢜pSo1A )-簳 o┖H$NX|s{hnla}'1 B0VW+ pN*Ubn&uO0Z7lgu<%궨&#uиĪ:UCguzd/ZC ]:VBXݶ1-zcu[h>#uH " Xh~5RƚH"&-acuxѺFT78TѺ-h]Eﴮ hݖ;rM өVqH]!'>.a;`G9S%..~i2.CYGguX]SZ#|4Vii.n6VeB[頛G(F]`cIssv:a8<ݲݲsp>:[ʑ݂G8{G JUuRy9sߍ?n#^w(ІAwT~vòA8kFvG',o!Hn#Lv^4h^#ꛓzZc1=.,OGZ''?q=^ncŅ|٩^%@&g`% [qgz Q7O\\Td6ld0)vS\VN80HQ,P;of'{deZ}ò^/շ>] b\)N ibT5Kq{G*骥7-Dk~zZ{e:kq`'\ܞIq+ݵĂ=6jD-9 zDA=eޱ.7Q-qZsi\E"\-]&ݣIMz呌>dC)NXJ\bl X+/pQ~ǂsϧsY;K3.NhTÑK^B,n#_LDyGy 鼒}s3蘳b17H9MzdA)6MţX9#OqWxVqT) x7cXǖhC4_`Xqy;kd-F:E|kh$zwyVZX*8}qm YqG̿QorǾ2YB<ŭzd/[<$TN[#zjn+,x;DRf<a$ e<*=DՋs#w2Ixnt~_:\Դg; ZY{v\Z7SKX،HZ-nؕ&Lܵ-3hloôѪhɤ׌% ]hF29[Xs>q&6@M)f6g|ziHڢvhƌ799mzpa>/d'|NEơa=^ d@j%5 26'| 񤖦3o܅Z9勤H ֣Z9&S|E 3 ǖ?qіv_㲼ؑ:~Ƥ/c>a~睚kiǻ?B̬xD_~мY/ˋlNjܶCʻ=:ۤ͡Ish<\XXEydhe͸1a߀ɻ1X\^4uɁpVFbzMLbcZ64m!m}DypY'p #hl$I.׭z 1q>B]t.됃>\nצXpJ/M1Tؘqk4`c%Lwz 4|781pZT>l[(_ z1,f%^ ӗȉŻք|A~aZ ܪaA{ȪE(x: tE/o_k"wϓĉu~%?p8 3O=1R۟' 4uo.rG(Qk,DQ[ߣŘj EA(MPPcz F"4مw8(+. c yL嫘*ɍ(*r6f$5I(c؈!s(-3* JQn$AQțQT؈&ߏ\3Q(r)Ԙ<Se"}.r LUJL0hHeOQ'd/r3,c1U-ZT y%d| R@kF%R 5WNrjO0˱!_"x@+c$ 5,OEEIk9j/r|EQՓ<Se'W/r\#w<Dc1)i1$_Y"gPԨC˧Q4]6U\~|nEs̘䖘Q=!gH( r?h;`$EQ1cQGQn+"9APb0UK0UToHVA<5u% )>ڥXzȨXG(Jey*7FQCk!BSk k3,LZ_zXwb,BQ *b&DQ?ƌC^k < Rb{1U!XOY(B,~C`k 5*EQ>$n+>XJUNҽ X@F(ț bE(J 0UۡMPXV'P04U[( kߍKWbY(x( ACEQOP2ba{@ r *MQX|?=Dr0ՐH(_$g`,e9SUBZlb/H(Rg(^1UOTm0\ cXfhbNX X{SHX{X{;L(ҠSU9EM~ZX{GL52enbQTIA/+־3VOD Q(BXqE.fLzڛc"TUbcP4d7*{C#kOIX2LUmX|okS R<jT}0/Y5*^˪r΍rkHk? ;Yb.ey!+t[JX{lĐAXjȨX{[XkEYN⋼ ZX(jF,KOX֐W*J 7T(vO`"碨_`M^:\R/QJPb{@$QF͔kwaUe54%ڷbƁ.)֞ }T.tQƓtR}-369qۊ`ULa$)־EE"fkDMIaJPb-bo(!-H?)֞hJI( l$ϠX|EBR'tHQjY!ڿTAQgC#koee%ڣ0cEWVR2rwbG`wlPbm]/ŌIjT=*vUy .?)RRUhb`a*>3fyK+rOHXuhb0 3CΊR=Suy>8͐J[Y5b-bcYY^l Y*L5>kkq})^P9̘e/kLzX|+1? 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VN:1.0 @SQ SN:chr1 LN:1575 @SQ SN:chr2 LN:1584 @RG ID:L1 PU:SC_1_10 LB:SC_1 SM:NA12891 CN:name:with:colon @RG ID:L2 PU:SC_2_12 LB:SC_2 SM:NA12891 CN:name:with:colon @PG ID:P1 VN:1.0 @PG ID:P2 VN:1.1 @CO this is a comment @CO this is another comment read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 PG:Z:P1 XT:A:U read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 PG:Z:P2 XT:A:R read_28701_28881_323c 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< test_clipped1 99 chr2 997 20 4S6M1D20M5S = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 PG:Z:P1 XT:A:U pysam-0.7.7/tests/example.gtf.gz0000664000076400007650000000736111700526652016436 0ustar andreasandreasBC [o7ǟBp _'o&&8aBb K)v3#irjNP<i~Xj}g<{{}aI 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contains some example code ## illustrating ways to to use the pysam ## interface to samtools. ## ## The unit tests in the script pysam_test.py ## contain more examples. ## import pysam samfile = pysam.Samfile( "ex1.bam", "rb" ) print "###################" # check different ways to iterate print len(list(samfile.fetch())) print len(list(samfile.fetch( "chr1", 10, 200 ))) print len(list(samfile.fetch( region="chr1:10-200" ))) print len(list(samfile.fetch( "chr1" ))) print len(list(samfile.fetch( region="chr1"))) print len(list(samfile.fetch( "chr2" ))) print len(list(samfile.fetch( region="chr2"))) print len(list(samfile.fetch())) print len(list(samfile.fetch( "chr1" ))) print len(list(samfile.fetch( region="chr1"))) print len(list(samfile.fetch())) print len(list(samfile.pileup( "chr1", 10, 200 ))) print len(list(samfile.pileup( region="chr1:10-200" ))) print len(list(samfile.pileup( "chr1" ))) print len(list(samfile.pileup( region="chr1"))) print len(list(samfile.pileup( "chr2" ))) print len(list(samfile.pileup( region="chr2"))) print len(list(samfile.pileup())) print len(list(samfile.pileup())) print "########### fetch with callback ################" def my_fetch_callback( alignment ): print str(alignment) samfile.fetch( region="chr1:10-200", callback=my_fetch_callback ) print "########## pileup with callback ################" def my_pileup_callback( column ): print str(column) samfile.pileup( region="chr1:10-200", callback=my_pileup_callback ) print "########### Using a callback object ###### " class Counter: mCounts = 0 def __call__(self, alignment): self.mCounts += 1 c = Counter() samfile.fetch( region = "chr1:10-200", callback = c ) print "counts=", c.mCounts print "########### Calling a samtools command line function ############" for p in pysam.mpileup( "-c", "ex1.bam" ): print str(p) print pysam.mpileup.getMessages() print "########### Investigating headers #######################" # playing arount with headers samfile = pysam.Samfile( "ex3.sam", "r" ) print samfile.references print samfile.lengths print samfile.text print samfile.header header = samfile.header samfile.close() header["HD"]["SO"] = "unsorted" outfile = pysam.Samfile( "out.sam", "wh", header = header ) outfile.close() pysam-0.7.7/tests/example.vcf400000664000076400007650000000273412241537037016160 0ustar andreasandreas##fileformat=VCFv4.0 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=1000GenomesPilot-NCBI36 ##phasing=partial ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 M 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 17 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 20 1234567 microsat1 GTCT G,GTACT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 pysam-0.7.7/tests/ex6.sam0000664000076400007650000000051411700526652015057 0ustar andreasandreas@HD VN:1.0 @SQ SN:chr1 LN:1575 @SQ SN:chr2 LN:1584 read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 pysam-0.7.7/tests/example_empty_header.bam0000664000076400007650000001660212075070776020531 0ustar andreasandreasBC.sred E /<BC~mUǟ +lBw&,E̾~ѻ5MHcLh4x5&~t׍&&F([AښZKiRm{iPlPzs0S|ޝ9g?iH!g9L)Nn?A[vFͤzlJfS7:\nuF]i4r]=iZM62n&kd;i4MFvZLw褶nXs]~N>2A \674sF*ֲMCtөTm#]K7SuC74#MUOm͚+LEgȱBS, CI8{"~^d'e $H|#$^KdK[V)ɆTO$-((dIVdR~I M`pJuHu(WMP䕎]e*L)0>xeW:%2! 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[.q & PƒYx`Sx`ӔnjՒ \^A2K'5,,`0yt/5ǠBo -t(*CQ͙CQ576m&^;κt_'N"7]5Z9?n[yCqOSi\TF6\&+e4*^YkU .rKv@n)9H`5ͅxd|eշX'ʈ¼AkDwH7HW/s L{wp?np?)t,J}LLf:daTϹs9b: }N<}9//5e&{VMo2}0 c8k`=DrְqW^,a9Zj.jYtV?rvebVg HN'EQA['֟;&L tN˿ͧn̨[!ZqYFb|\WG+?~\뢣 qSKo=j>&VGzi,WY,GqL$C'Ӽ83ރT?cbpJ/l^#epXQzۉHtsR'KYɶVֆNzIvڶ& H6 cAz4Opqo1=mTTOuNl,X-PVNbټZW]+kB{UU[.3EIБ6{;uM͟ ɦS!T?ms}ePΨ*f;m->EgVr&(RGK,.  ~tAOgQ8qZq;r_0iax6 'vB?Q5i~֛jq;7զ(՛jx)< x{ fCF%Jc/"vFELU"泜[HJ#g(' }8MWgA$>BCZFm&`xwǣQ}h!2X4̷ŨY40Zgz[MWRCy|V72XBN fG]J/&ccXwN]ѝVcC}v8>GaD)XSL]6H%å49 ex2.sam.gz %.bam: %.sam ex1.fa.fai samtools import ex1.fa.fai $< $@ %.sam: %.sam.gz gunzip < $< > $@ ex1.fa.fai:ex1.fa samtools faidx ex1.fa ex1.bam:ex1.sam.gz ex1.fa.fai samtools import ex1.fa.fai ex1.sam.gz ex1.bam %.bam.bai:%.bam samtools index $< ex1.pileup.gz:ex1.bam ex1.fa samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam touch tmp.list samtools import tmp.list $< $@ rm -f tmp.list example_bai.bam: ex1.bam cp ex1.bam $@ samtools index $@ mv $@.bai example_bai.bai softclip.bam: softclip.sam samtools view -bS $< > $@ clean: rm -fr *.bam *.bai *.fai *.pileup* \ *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam pysam-0.7.7/tests/segfault_tests.py0000775000076400007650000000227511700526652017272 0ustar andreasandreas#!/usr/bin/env python '''unit testing code for pysam.''' import pysam import unittest import os import itertools import subprocess import shutil class TestExceptions(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testOutOfRangeNegativeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, -10 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, 0 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", -5, -10 ) def testOutOfRangeNegativeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1:-5-10" ) self.assertRaises( ValueError, self.samfile.fetch, "chr1:-5-0" ) self.assertRaises( ValueError, self.samfile.fetch, "chr1:-5--10" ) def testOutOfRangeLargeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 99999999999999999, 999999999999999999 ) def testOutOfRangeLargeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" ) def tearDown(self): self.samfile.close() if __name__ == "__main__": unittest.main() pysam-0.7.7/doc/0000775000076400007650000000000012241575073013260 5ustar andreasandreaspysam-0.7.7/doc/release.rst0000664000076400007650000000437612241575047015445 0ustar andreasandreas============= Release notes ============= Release 0.7.7 ============= * added Fastafile.references, .nreferences and .lengths * tabix_iterator now uses kseq.h for python 2.7 Release 0.7.6 ============= * added inferred_length property * issue 122: MACOSX getline missing, now it works? * seq and qual can be set None * added Fastqfile Release 0.7.5 ============= * switch to samtools 0.1.19 * issue 122: MACOSX getline missing * issue 130: clean up tempfiles * various other bugfixes Release 0.7.4 ============= * further bugfixes to setup.py and package layout Release 0.7.3 ============= * further bugfixes to setup.py * upgraded distribute_setup.py to 0.6.34 Release 0.7.2 ============= * bugfix in installer - failed when cython not present * changed installation locations of shared libraries Release 0.7.1 ============= * bugfix: missing PP tag PG records in header * added pre-built .c files to distribution Release 0.7 =========== * switch to tabix 0.2.6 * added cigarstring field * python3 compatibility * added B tag handling * added check_sq and check_header options to Samfile.__init__ * added lazy GTF parsing to tabix * reworked support for VCF format parsing * bugfixes Release 0.6 =========== * switch to samtools 0.1.18 * various bugfixes * removed references to deprecated 'samtools pileup' functionality * AlignedRead.tags now returns an empty list if there are no tags. * added pnext, rnext and tlen Release 0.5 =========== * switch to samtools 0.1.16 and tabix 0.2.5 * improved tabix parsing, added vcf support * re-organized code to permit linking againts pysam * various bugfixes * added Samfile.positions and Samfile.overlap Release 0.4 =========== * switch to samtools 0.1.12a and tabix 0.2.3 * added snp and indel calling. * switch from pyrex to cython * changed handling of samtools stderr * various bugfixes * added Samfile.count and Samfile.mate * deprecated AlignedRead.rname, added AlignedRead.tid Release 0.3 =========== * switch to samtools 0.1.8 * added support for tabix files * numerous bugfixes including * permit simultaneous iterators on the same file * working access to remote files pysam-0.7.7/doc/make.bat0000664000076400007650000000562311700526652014671 0ustar andreasandreas@ECHO OFF REM Command file for Sphinx documentation set SPHINXBUILD=sphinx-build set ALLSPHINXOPTS=-d _build/doctrees %SPHINXOPTS% . if NOT "%PAPER%" == "" ( set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% ) if "%1" == "" goto help if "%1" == "help" ( :help echo.Please use `make ^` where ^ is one of echo. html to make standalone HTML files echo. dirhtml to make HTML files named index.html in directories echo. pickle to make pickle files echo. json to make JSON files echo. htmlhelp to make HTML files and a HTML help project echo. qthelp to make HTML files and a qthelp project echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter echo. changes to make an overview over all changed/added/deprecated items echo. linkcheck to check all external links for integrity echo. doctest to run all doctests embedded in the documentation if enabled goto end ) if "%1" == "clean" ( for /d %%i in (_build\*) do rmdir /q /s %%i del /q /s _build\* goto end ) if "%1" == "html" ( %SPHINXBUILD% -b html %ALLSPHINXOPTS% _build/html echo. echo.Build finished. The HTML pages are in _build/html. goto end ) if "%1" == "dirhtml" ( %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% _build/dirhtml echo. echo.Build finished. The HTML pages are in _build/dirhtml. goto end ) if "%1" == "pickle" ( %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% _build/pickle echo. echo.Build finished; now you can process the pickle files. goto end ) if "%1" == "json" ( %SPHINXBUILD% -b json %ALLSPHINXOPTS% _build/json echo. echo.Build finished; now you can process the JSON files. goto end ) if "%1" == "htmlhelp" ( %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% _build/htmlhelp echo. echo.Build finished; now you can run HTML Help Workshop with the ^ .hhp project file in _build/htmlhelp. goto end ) if "%1" == "qthelp" ( %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% _build/qthelp echo. echo.Build finished; now you can run "qcollectiongenerator" with the ^ .qhcp project file in _build/qthelp, like this: echo.^> qcollectiongenerator _build\qthelp\samtools.qhcp echo.To view the help file: echo.^> assistant -collectionFile _build\qthelp\samtools.ghc goto end ) if "%1" == "latex" ( %SPHINXBUILD% -b latex %ALLSPHINXOPTS% _build/latex echo. echo.Build finished; the LaTeX files are in _build/latex. goto end ) if "%1" == "changes" ( %SPHINXBUILD% -b changes %ALLSPHINXOPTS% _build/changes echo. echo.The overview file is in _build/changes. goto end ) if "%1" == "linkcheck" ( %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% _build/linkcheck echo. echo.Link check complete; look for any errors in the above output ^ or in _build/linkcheck/output.txt. goto end ) if "%1" == "doctest" ( %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% _build/doctest echo. echo.Testing of doctests in the sources finished, look at the ^ results in _build/doctest/output.txt. goto end ) :end pysam-0.7.7/doc/faq.rst0000664000076400007650000000744512216133345014565 0ustar andreasandreaspysam coordinates are wrong =========================== pysam uses 0-based coordinates and the half-open notation for ranges as does python. Coordinates and intervals reported from pysam always follow that convention. Confusion might arise as different file formats might have different conventions. For example, the SAM format is 1-based while the BAM format is 0-based. It is important to remember that pysam will always conform to the python convention and translate to/from the file format automatically. The only exception is the :term:`region string` in the :meth:`Samfile.fetch` and :meth:`Samfile.pileup` methods. This string follows the convention of the samtools command line utilities. The same is true for any coordinates passed to the samtools command utilities directly, such as :meth:`pysam.mpileup`. BAM files with a large number of reference sequences is slow ============================================================ If you have many reference sequences in a bam file, the following might be slow:: track = pysam.Samfile(fname, "rb") for aln in track.fetch(): pass The reason is that track.fetch() will iterate through the bam file for each reference sequence in the order as it is defined in the header. This might require a lot of jumping around in the file. To avoid this, use:: track = pysam.Samfile(fname, "rb") for aln in track.fetch( until_eof = True ): pass This will iterate through reads as they appear in the file. Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file =============================================================================================================== Spliced reads are reported within samfile.pileup. To ignore these in your analysis, test the flags ``is_del == True and indel=0`` in the :class:`~.PileupRead` object. I can't edit quality scores in place ==================================== Editing reads in-place generally works, though there is some quirk to be aware of. Assigning to AlignedRead.seq will invalidate any quality scores in AlignedRead.qual. The reason is that samtools manages the memory of the sequence and quality scores together and thus requires them to always be of the same length or 0. Thus, to in-place edit the sequence and quality scores, copies of the quality scores need to be taken. Consider trimming for example:: q = read.qual read.seq = read.seq[5:10] read.qual = q[5:10] Why is there no SNPCaller class anymore? ========================================= SNP calling is highly complex and heavily parameterized. There was a danger that the pysam implementations might show different behaviour from the samtools implementation, which would have caused a lot of confusion. The best way to use samtools SNP calling from python is to use the :meth:`pysam.mpileup` command and parse the output directly. I get an error 'PileupProxy accessed after iterator finished' ============================================================= Pysam works by providing proxy objects to objects defined within the C-samtools package. Thus, some attention must be paid at the lifetime of objects. The following to code snippets will cause an error:: s = Samfile( 'ex1.bam' ) for p in s.pileup('chr1', 1000,1010): pass for pp in p.pileups: print pp The iteration has finished, thus the contents of p are invalid. A variation of this:: p = Samfile( 'ex1.bam' ).pileup( 'chr1', 1000, 1010).next() for pp in p.pileups: print pp Again, the iteration finishes as the temporary iterator created by pileup goes out of scope. The solution is to keep a handle to the iterator that remains alive:: i = Samfile( 'ex1.bam' ).pileup( 'chr1', 1000, 1010) p = i.next() for pp in p.pileups: print pp pysam-0.7.7/doc/usage.rst0000664000076400007650000002256412216376103015122 0ustar andreasandreas.. _Usage: ************************************* Working with BAM/SAM-formatted files ************************************* In order to follow the examples below, execute make in the :file:`test` directory. Opening a sampfile ------------------ The first operation is to import the pysam module and open a :class:`pysam.Samfile`:: import pysam samfile = pysam.Samfile( "ex1.bam", "rb" ) The above command opens the file :file:`ex1.bam` for reading. The ``b`` qualifier indicates that this is a :term:`BAM` file. To open a :term:`SAM` file, type:: import pysam samfile = pysam.Samfile( "ex1.bam", "r" ) Fetching reads mapped to a :term:`region` ----------------------------------------- There are two ways to obtain the reads mapped to a genomic region. The first method follows the :term:`csamtools` API and works via a callback function. The callback will be executed for each alignment in a :term:`region`:: def my_fetch_callback( alignment ): print str(alignment) samfile.fetch( 'seq1', 10, 20, callback = my_fetch_callback ) Using a function object, work can be done on the alignments. The code below simply counts aligned reads:: class Counter: cCounts = 0 def __call__(self, alignment): self.counts += 1 c = Counter() samfile.fetch( 'seq1', 10, 20, callback = c ) print "counts=", c.counts The second method uses python iterators. If you call :meth:`pysam.Samfile.fetch` without a callback, an iterator of the type :class:`pysam.IteratorRow` is returned. It will iterate through mapped reads and return a :class:`pysam.AlignedRead` object for each:: iter = samfile.fetch( 'seq1', 10, 20) for x in iter: print str(x) Note that both methods iterate through a :term:`BAM` file on a read-by-read basis. :meth:`pysam.Samfile.fetch` returns all reads overlapping a region sorted by the first aligned base in the :term:`reference` sequence. Note that it will also return reads that are only partially overlapping with the :term:`region`. Thus the reads returned might span a region that is larger than the one queried. Using the pileup-engine ----------------------- The :term:`pileup` engine of :term:`csamtools` iterates over all reads that are aligned to a :term:`region`. In contrast to :term:`fetching`, the :term:`pileup` engine returns for each base in the :term:`reference` sequence the reads that map to that particular position. Again, there are two principal methods to iterate. The first works via a callback function:: def my_pileup_callback( pileups ): print str(pileups) samfile.pileup( 'seq1', 10, 20, callback = my_pileup_callback ) The second method uses python iterators. The iterator :class:`pysam.IteratorColumn` will iterate through each :term:`column` (reference bases) and return a list of aligned reads:: iter = samfile.pileup( 'seq1', 10, 20 ) for x in iter: print str(x) Aligned reads are returned as a :class:`pysam.PileupColumn`. Using samtools commands within python ------------------------------------- Commands available in :term:`csamtools` are available as simple function calls. For example:: pysam.sort( "ex1.bam", "output" ) corresponds to the command line:: samtools sort ex1.bam output Command line options can be provided as arguments:: pysam.sort( "-n", "ex1.bam", "output" ) or:: pysam.sort( "-m", "1000000", "ex1.bam", "output" ) In order to get usage information, try:: print pysam.sort.usage() Argument errors raise a :class:`pysam.SamtoolsError`:: pysam.sort() Traceback (most recent call last): File "x.py", line 12, in pysam.sort() File "/home/andreas/pysam/build/lib.linux-x86_64-2.6/pysam/__init__.py", line 37, in __call__ if retval: raise SamtoolsError( "\n".join( stderr ) ) pysam.SamtoolsError: 'Usage: samtools sort [-n] [-m ] \n' Messages from :term:`csamtools` on stderr are captured and are available using the :meth:`getMessages` method:: pysam.sort.getMessage() Note that only the output from the last invocation of a command is stored. Creating SAM/BAM files from scratch ----------------------------------- The following example shows how a new BAM file is constructed from scratch. The important part here is that the :class:`pysam.Samfile` class needs to receive the sequence identifiers. These can be given either as a dictionary in a header structure, as lists of names and sizes, or from a template file. Here, we use a header dictionary:: header = { 'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}] } outfile = pysam.Samfile( tmpfilename, "wh", header = header ) a = pysam.AlignedRead() a.qname = "read_28833_29006_6945" a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG" a.flag = 99 a.rname = 0 a.pos = 32 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,25) ) a.mrnm = 0 a.mpos=199 a.isize=167 a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<" a.tags = ( ("NM", 1), ("RG", "L1") ) outfile.write(a) outfile.close() Using streams ------------- Pysam does not support reading and writing from true python file objects, but it does support reading and writing from stdin and stdout. The following example reads from stdin and writes to stdout:: infile = pysam.Samfile( "-", "r" ) outfile = pysam.Samfile( "-", "w", template = infile ) for s in infile: outfile.write(s) It will also work with :term:`BAM` files. The following script converts a :term:`BAM` formatted file on stdin to a :term:`SAM` formatted file on stdout:: infile = pysam.Samfile( "-", "rb" ) outfile = pysam.Samfile( "-", "w", template = infile ) for s in infile: outfile.write(s) Note, only the file open mode needs to changed from ``r`` to ``rb``. .. Currently inactivated as pileup deprecated .. Using the samtools SNP caller .. ----------------------------- .. There are two ways to access the samtools SNP caller. The :class:`pysam.IteratorSNPCalls` .. is appropriate when calling many consecutive SNPs, while :class:`pysam.SNPCaller` is .. best when calling SNPs at non-consecutive genomic positions. Each snp caller returns objects of .. type :class:`pysam.SNPCall`. .. To use :class:`pysam.IteratorSNPCalls`, associate it with a :class:`pysam.IteratorColumn`:: .. samfile = pysam.Samfile( "ex1.bam", "rb") .. fastafile = pysam.Fastafile( "ex1.fa" ) .. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile ) .. sncpall_iter = pysam.IteratorSNPCalls(pileup_iter) .. for call in snpcall_iter: .. print str(call) .. Usage of :class:`pysam.SNPCaller` is similar:: .. samfile = pysam.Samfile( "ex1.bam", "rb") .. fastafile = pysam.Fastafile( "ex1.fa" ) .. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile ) .. snpcaller = pysam.SNPCaller.call(pileup_iter) .. print snpcaller( "chr1", 100 ) .. Note the use of the option *stepper* to control which reads are included in the .. in the :term:`pileup`. The ``samtools`` stepper implements the same read selection .. and processing as in the samtools pileup command. .. Calling indels works along the same lines, using the :class:`pysam.IteratorIndelCalls` .. and :class:`pysam.IteratorIndelCaller`. Extending pysam --------------- Using pyximport_, it is (relatively) straight-forward to access pysam internals and the underlying samtools library. An example is provided in the :file:`test` directory. The example emulates the samtools flagstat command and consists of three files: 1. The main script :file:`pysam_flagstat.py`. The important lines in this script are:: import pyximport pyximport.install() import _pysam_flagstat ... flag_counts = _pysam_flagstat.count( pysam_in ) The first part imports, sets up pyximport_ and imports the cython module :file:`_pysam_flagstat`. The second part calls the ``count`` method in :file:`_pysam_flagstat`. 2. The cython implementation :file:`_pysam_flagstat.pyx`. This script imports the pysam API via:: from csamtools cimport * This statement imports, amongst others, :class:`AlignedRead` into the namespace. Speed can be gained from declaring variables. For example, to efficiently iterate over a file, an :class:`AlignedRead` object is declared:: # loop over samfile cdef AlignedRead read for read in samfile: ... 3. A :file:`pyxbld` providing pyximport_ with build information. Required are the locations of the samtools and pysam header libraries of a source installation of pysam plus the :file:`csamtools.so` shared library. For example:: def make_ext(modname, pyxfilename): from distutils.extension import Extension import pysam, os dirname = os.path.dirname( pysam.__file__ )[:-len("pysam")] return Extension(name = modname, sources=[pyxfilename], extra_link_args=[ os.path.join( dirname, "csamtools.so")], include_dirs = pysam.get_include(), define_macros = pysam.get_defines() ) If the script :file:`pysam_flagstat.py` is called the first time, pyximport_ will compile the cython_ extension :file:`_pysam_flagstat.pyx` and make it available to the script. Compilation requires a working compiler and cython_ installation. Each time :file:`_pysam_flagstat.pyx` is modified, a new compilation will take place. pyximport_ comes with cython_. .. _cython: http://cython.org/ .. _pyximport: http://www.prescod.net/pyximport/ pysam-0.7.7/doc/developer.rst0000664000076400007650000000341611700526652016001 0ustar andreasandreas***************** Developer's guide ***************** Code organization ***************** The top level directory is organized in the following directories: pysam Code specific to pysam samtools Original and unmodified source code from :term:`csamtools`. Use :file:`setup.py` to obtain the latest code. tests Examples and data for testing Importing :term:`csamtools` *************************** Running :file:`setup.py` will import the csamtools source code. The command:: python setup.py import PATH where ``PATH`` points to a :term:`csamtools` source directory. For example:: python setup.py import ~/samtools-0.1.6 Note that files will not be overwritten. To import all anew, delete all :file:`*.c` and :file:`*.h` files in the :file:`samtools` directory first. Unit testing ************ Unit tests are currently in the script :file:`pysam_test.py`. Unit tests for the python methods --------------------------------- Few implemented yet. This will require also writing functionality, hence postponed Unit tests for the command line interface ----------------------------------------- The current suite of tests compare the binary files of selected samtools commands against running the same commands from within the pysam module. The general expectation is that the files are binary identical given that most of the code is from :term:`csamtools` anyway. However, differences might be found if the installed :term:`csamtools` version is different from the one wrapped with pysam. The tests create files in the current test directory. They are modeled on the example given within the :term:`csamtools` distribution. Two files are required in the working directory of the test script: 1. :file:`ex1.fa`: a fasta file 2. :file:`ex1.sam.gz`: a sam file pysam-0.7.7/doc/api.rst0000664000076400007650000001013011700526652014554 0ustar andreasandreaspysam - An interface for reading and writing SAM files ====================================================== Pysam is a python module that makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files. It is a lightweight wrapper of the samtools_ C-API. This page provides a quick introduction in using pysam followed by the API. See :ref:`usage` for more detailed usage instructions. To use the module to read a file in BAM format, create a :class:`~pysam.Samfile` object:: import pysam samfile = pysam.Samfile( "ex1.bam", "rb" ) Once a file is opened you can iterate over all of the read mapping to a specified region using :meth:`~pysam.Samfile.fetch`. Each iteration returns a :class:`~pysam.AlignedRead` object which represents a single read along with its fields and optional tags:: for alignedread in samfile.fetch('chr1', 100, 120): print alignedread samfile.close() To give:: EAS56_57:6:190:289:82 0 99 <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<; 69 CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA 0 192 1 EAS56_57:6:190:289:82 0 99 <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2; 137 AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC 73 64 1 EAS51_64:3:190:727:308 0 102 <<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844 99 GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG 99 18 1 ... You can also write to a :class:`~pysam.Samfile`:: import pysam samfile = pysam.Samfile("ex1.bam", "rb") pairedreads = pysam.Samfile("allpaired.bam", "wb", template=samfile) for read in samfile.fetch(): if read.is_paired: pairedreads.write(read) pairedreads.close() samfile.close() An alternative way of accessing the data in a SAM file is by iterating over each base of a specified region using the :meth:`~pysam.Samfile.pileup` method. Each iteration returns a :class:`~pysam.PileupColumn` which represents all the reads in the SAM file that map to a single base in the reference sequence. The list of reads are represented as :class:`~pysam.PileupRead` objects in the :attr:`PileupColumn.pileups ` property:: import pysam samfile = pysam.Samfile("ex1.bam", "rb" ) for pileupcolumn in samfile.pileup( 'chr1', 100, 120): print print 'coverage at base %s = %s' % (pileupcolumn.pos , pileupcolumn.n) for pileupread in pileupcolumn.pileups: print '\tbase in read %s = %s' % (pileupread.alignment.qname, pileupread.alignment.seq[pileupread.qpos]) samfile.close() The above code outputs:: coverage at base 99 = 1 base in read EAS56_57:6:190:289:82 = A coverage at base 100 = 1 base in read EAS56_57:6:190:289:82 = G coverage at base 101 = 1 base in read EAS56_57:6:190:289:82 = G coverage at base 102 = 2 base in read EAS56_57:6:190:289:82 = G base in read EAS51_64:3:190:727:308 = G ... Commands available in :term:`csamtools` are available as simple function calls. For example:: pysam.sort( "ex1.bam", "output" ) corresponds to the command line:: samtools sort ex1.bam output Analogous to :class:`~pysam.Samfile`, a :class:`~pysam.Tabixfile` allows fast random access to compressed and tabix indexed tab-separated file formats with genomic data:: import pysam tabixfile = pysam.Tabixfile( "example.gtf.gz" ) for gtf in tabixfile.fetch('chr1', 1000, 2000): print gtf.contig, gtf.start, gtf.end, gtf.gene_id :class:`~pysam.Tabixfile` implements lazy parsing in order to iterate over large tables efficiently. More detailed usage instructions is at :ref:`usage`. .. note:: Coordinates in pysam are always 0-based (following the python convention). SAM text files use 1-based coordinates. .. note:: The above examples can be run in the :file:`tests` directory of the installation directory. Type 'make' before running them. .. seealso:: http://code.google.com/p/pysam/ The pysam Google code page, containing source code and download instructions http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/contents.html The pysam website containing documentation .. _samtools: http://samtools.sourceforge.net/ API ***** .. automodule:: pysam :members: :undoc-members: pysam-0.7.7/doc/conf.py0000664000076400007650000001520411700526652014557 0ustar andreasandreas# -*- coding: utf-8 -*- # # samtools documentation build configuration file, created by # sphinx-quickstart on Wed Aug 12 14:43:42 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys, os, glob # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. _libdir = "../build/lib.%s-%s-%s.%s" % (os.uname()[0].lower(), os.uname()[4],sys.version_info[0], sys.version_info[1] ) if os.path.exists( _libdir ): sys.path.append( os.path.abspath( _libdir ) ) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.ifconfig', 'sphinx.ext.intersphinx'] intersphinx_mapping = {'python': ('http://docs.python.org/3.2', None)} # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'contents' # General information about the project. project = u'pysam' copyright = u'2009, Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Kevin Jacobs' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # sys.path.insert( 0, "../pysam") import version # The short X.Y version. version = version.__version__ # The full version, including alpha/beta/rc tags. release = version # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. #html_logo = None # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'samtoolsdoc' # -- Options for LaTeX output -------------------------------------------------- # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('contents', 'samtools.tex', ur'samtools Documentation', ur'Andreas Heger, Tildon Grant Belgrad, Martin Goodson', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True pysam-0.7.7/doc/glossary.rst0000664000076400007650000000423711700526652015661 0ustar andreasandreas********* Glossary ********* .. glossary:: :sorted: cigar An alignment format string. In the python API, the cigar alignment is presented as a list of tuples ``(operation,length)``. For example, the tuple ``[ (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5 insertions and another 2 matches. region A genomic region, stated relative to a reference sequence. A region consists of reference name ('chr1'), start (100000), and end (200000). 0-based coordinates. Can be expressed as a string ('chr1:10000:20000') column Reads that are aligned to a base in the :term:`reference` sequence. tid The :term:`target` id. The target id is 0 or a positive integer mapping to entries within the sequence dictionary in the header section of a :term:`TAM` file or :term:`BAM` file. Reference The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``. SAM A textual format for storing genomic alignment information. BAM Binary SAM format. BAM files are binary formatted, indexed and allow random access. TAM Text SAM file. TAM files are human readable files of tab-separated fields. TAM files do not allow random access. sam file A file containing aligned reads. The :term:`sam file` can either be a :term:`BAM` file or a :term:`TAM` file. pileup Pileup samtools The samtools_ package. csamtools The samtools_ C-API. fetching Retrieving all mapped reads mapped to a :term:`region`. target The sequence that a read has been aligned to. Target sequences have bot a numerical identifier (:term:`tid`) and an alphanumeric name (:term:`Reference`). tabix file A sorted, compressed and indexed tab-separated file created by the command line tool :file:`tabix` or the commands :meth:`tabix_compress` and :meth:`tabix_index`. The file is indexed by chromosomal coordinates. tabix row A row in a :term:`tabix file`. Fields within a row are tab-separated. .. _samtools: http://samtools.sourceforge.net pysam-0.7.7/doc/contents.rst0000664000076400007650000000356212075070776015662 0ustar andreasandreas.. samtools documentation master file, created by sphinx-quickstart on Wed Aug 12 14:43:42 2009. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. pysam: samtools interface for python ==================================== :Author: Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Leo Goodstad, Kevin Jacobs :Date: |today| :Version: |version| The *SAM/BAM* format is a way to store efficiently large numbers of alignments [Li2009]_, such as those routinely are created by next-generation sequencing methods. This module provides a low-level wrapper around the samtools_ C-API using `cython`_ and a high-level API for convenient access to the data in *SAM/BAM* formatted files. Also included is an interface to the tabix_ C-API for reading compressed and indexed tabular data. The current version wraps *samtools-0.1.18* and *tabix-0.2.6*. Contents -------- .. toctree:: :maxdepth: 2 api.rst usage.rst tabix.rst faq.rst glossary.rst developer.rst release.rst Indices and tables ------------------ Contents: * :ref:`genindex` * :ref:`modindex` * :ref:`search` References ---------- .. [Li2009] The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8. `PMID: 19505943 `_ .. seealso:: The samtools homepage http://samtools.sourceforge.net The cython C-extensions for python http://cython.org/ The python language http://www.python.org .. _samtools: http://samtools.sourceforge.net .. _tabix: http://samtools.sourceforge.net/tabix.shtml .. _cython: http://cython.org/ .. _python: http://www.python.org pysam-0.7.7/doc/Makefile0000664000076400007650000000622512031346464014722 0ustar andreasandreas# Makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build PAPER = # Internal variables. PAPEROPT_a4 = -D latex_paper_size=a4 PAPEROPT_letter = -D latex_paper_size=letter ALLSPHINXOPTS = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . DIR_PUBLISH=/ifs/home/andreas/public_html/documentation/pysam .PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest help: @echo "Please use \`make ' where is one of" @echo " html to make standalone HTML files" @echo " dirhtml to make HTML files named index.html in directories" @echo " pickle to make pickle files" @echo " json to make JSON files" @echo " htmlhelp to make HTML files and a HTML help project" @echo " qthelp to make HTML files and a qthelp project" @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" @echo " changes to make an overview of all changed/added/deprecated items" @echo " linkcheck to check all external links for integrity" @echo " doctest to run all doctests embedded in the documentation (if enabled)" @echo " publish to copy the HTML documentation to the server." clean: -rm -rf _build/* html: $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html @echo @echo "Build finished. The HTML pages are in _build/html." dirhtml: $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml @echo @echo "Build finished. The HTML pages are in _build/dirhtml." pickle: $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle @echo @echo "Build finished; now you can process the pickle files." json: $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json @echo @echo "Build finished; now you can process the JSON files." htmlhelp: $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp @echo @echo "Build finished; now you can run HTML Help Workshop with the" \ ".hhp project file in _build/htmlhelp." qthelp: $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp @echo @echo "Build finished; now you can run "qcollectiongenerator" with the" \ ".qhcp project file in _build/qthelp, like this:" @echo "# qcollectiongenerator _build/qthelp/samtools.qhcp" @echo "To view the help file:" @echo "# assistant -collectionFile _build/qthelp/samtools.qhc" latex: $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex @echo @echo "Build finished; the LaTeX files are in _build/latex." @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ "run these through (pdf)latex." changes: $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes @echo @echo "The overview file is in _build/changes." linkcheck: $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck @echo @echo "Link check complete; look for any errors in the above output " \ "or in _build/linkcheck/output.txt." doctest: $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest @echo "Testing of doctests in the sources finished, look at the " \ "results in _build/doctest/output.txt." publish: rm -rf $(DIR_PUBLISH) mkdir -p $(DIR_PUBLISH) cp -r _build/html/* $(DIR_PUBLISH) pysam-0.7.7/COPYING0000664000076400007650000000207511700526652013550 0ustar andreasandreasThe MIT License Copyright (c) 2008-2009 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.pysam-0.7.7/pysam.py0000664000076400007650000000020712147510164014210 0ustar andreasandreasraise ImportError( '''calling "import pysam" from the source directory is not supported - please import pysam from somewhere else.''') pysam-0.7.7/INSTALL0000664000076400007650000000252111700526652013542 0ustar andreasandreasSystem Requirements =================== SAMtools depends on the zlib library . The latest version 1.2.3 is preferred and with the latest version you can compile razip and use it to compress a FASTA file. SAMtools' faidx is able to index a razip-compressed FASTA file to save diskspace. Older zlib also works with SAMtools, but razip cannot be compiled. The text-based viewer (tview) requires the GNU ncurses library , which comes with Mac OS X and most of the modern Linux/Unix distributions. If you do not have this library installed, you can still compile the rest of SAMtools by manually modifying one line in Makefile. Pysam requires pyrex (0.9.8 or greater) and python (2.6 or greater). It has not been tested on many other platforms. Compilation =========== Unpack the distribution and enter the pysam directory. Type python setup.py build to compile. Installation ============ Type python setup.py install to install it within the site-packages directory of your python distribution. Type python setup.py install --help for more options. Architecture specific options ============================= Pysam has been compiled on various linux systems and works with python 2.6 and python 2.5. Python 2.7 and Python 3 have not been tested. Windows support does not work yet