cyvcf2-0.30.14/0000755000175000017500000000000014154107376012411 5ustar nileshnileshcyvcf2-0.30.14/htslib/0000755000175000017500000000000014154107376013676 5ustar nileshnileshcyvcf2-0.30.14/README.md0000644000175000017500000001077014154107376013675 0ustar nileshnileshcyvcf2 ====== Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10 The latest documentation for cyvcf2 can be found here: [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://brentp.github.io/cyvcf2/) If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2) Fast python **(2 and 3)** parsing of VCF and BCF including region-queries. [![Build Status](https://github.com/brentp/cyvcf2/workflows/Build/badge.svg)](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild) cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files. Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use. **note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense. To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`. Example ======= The example below shows much of the use of cyvcf2. ```Python from cyvcf2 import VCF for variant in VCF('some.vcf.gz'): # or VCF('some.bcf') variant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T'] variant.CHROM, variant.start, variant.end, variant.ID, \ variant.FILTER, variant.QUAL # numpy arrays of specific things we pull from the sample fields. # gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT variant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays variant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array ## INFO Field. ## extract from the info field by it's name: variant.INFO.get('DP') # int variant.INFO.get('FS') # float variant.INFO.get('AC') # float # convert back to a string. str(variant) ## sample info... # Get a numpy array of the depth per sample: dp = variant.format('DP') # or of any other format field: sb = variant.format('SB') assert sb.shape == (n_samples, 4) # 4-values per # to do a region-query: vcf = VCF('some.vcf.gz') for v in vcf('11:435345-556565'): if v.INFO["AF"] > 0.1: continue print(str(v)) ``` Installation ============ ## pip (assuming you have htslib < 1.10 installed) ``` pip install cyvcf2 ``` ## github (building htslib and cyvcf2 from source) ``` git clone --recursive https://github.com/brentp/cyvcf2 cd cyvcf2/htslib autoheader autoconf ./configure --enable-libcurl make cd .. pip install -r requirements.txt CYTHONIZE=1 pip install -e . ``` On **OSX**, using brew, you may have to set the following as indicated by the brew install: ``` For compilers to find openssl you may need to set: export LDFLAGS="-L/usr/local/opt/openssl/lib" export CPPFLAGS="-I/usr/local/opt/openssl/include" For pkg-config to find openssl you may need to set: export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig" ``` Testing ======= Install `pytest`, then tests can be run with: ``` pytest ``` CLI ======= Run with `cyvcf2 path_to_vcf` ``` $ cyvcf2 --help Usage: cyvcf2 [OPTIONS] or - fast vcf parsing with cython + htslib Options: -c, --chrom TEXT Specify what chromosome to include. -s, --start INTEGER Specify the start of region. -e, --end INTEGER Specify the end of the region. --include TEXT Specify what info field to include. --exclude TEXT Specify what info field to exclude. --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL] Set the level of log output. [default: INFO] --silent Skip printing of vcf. --help Show this message and exit. ``` See Also ======== Pysam also [has a cython wrapper to htslib](https://github.com/pysam-developers/pysam/blob/master/pysam/cbcf.pyx) and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project. Performance =========== For the performance comparison in the paper, we used [thousand genomes chromosome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz) With the full comparison runner [here](https://github.com/brentp/cyvcf2/blob/main/scripts/compare.sh). cyvcf2-0.30.14/requirements.txt0000644000175000017500000000004714154107376015676 0ustar nileshnileshcython>=0.23.3 numpy coloredlogs click cyvcf2-0.30.14/scripts/0000755000175000017500000000000014154107376014100 5ustar nileshnileshcyvcf2-0.30.14/scripts/filter-pysam.py0000644000175000017500000000054614154107376017073 0ustar nileshnileshimport sys from pysam import VariantFile vcf = VariantFile(sys.argv[1]) n = 0 for v in vcf: if len(v.alts) > 1: continue if v.qual < 20: continue gts = [s['GT'] for s in v.samples.values()] an = sum(len(gt) for gt in gts) ac = sum(sum(gt) for gt in gts) aaf = (float(ac) / float(an)) if aaf > 0.05: continue n += 1 print(n) cyvcf2-0.30.14/scripts/compare.sh0000644000175000017500000000226614154107376016070 0ustar nileshnilesh# This is a record of comparisons made in the cyvcf2 paper. These vcf filenames are now different and may not work to run the tests chrom=22 if [[ ! -e ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz ]]; then wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz fi if [[ ! -e ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi ]]; then wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi fi echo "#bcftools" time bcftools filter -e "N_ALT != 1 || QUAL < 20 || maf[0]>0.05" ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz | grep -cv ^# echo "#cyvcf2" time python filter-cyvcf2.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz echo "#pysam" time python filter-pysam.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz echo "#pyvcf" time python filter-pyvcf.py ALL.chr${chrom}.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz cyvcf2-0.30.14/scripts/table.py0000644000175000017500000000204414154107376015541 0ustar nileshnileshfrom tabulate import tabulate from collections import OrderedDict vals = """ #bcftools 986798 real 3m49.024s user 3m48.620s sys 0m7.848s #cyvcf2 984214 real 4m5.190s user 4m5.048s sys 0m0.112s #pysam 984214 real 33m12.417s user 33m11.920s sys 0m0.244s """.split("#") vals = [x.strip() for x in vals if x.strip()] key = 'time (seconds)' def parse_group(g): lines = g.split("\n") d = OrderedDict([ ('name', lines[0].strip()), ('time', next(x for x in lines if x.startswith('user')).split()[1].rstrip('s')) ]) minutes = float(d['time'].split('m')[0]) seconds = float(d['time'].split('m')[1]) d[key] = 60 * minutes + seconds del d['time'] return d tbl = [parse_group(g) for g in vals] base = next(d for d in tbl if d['name'] == 'cyvcf2')[key] for d in tbl: d['ratio'] = "%.2f" % (d[key] / base) d[key] = "%.1f" % d[key] print(r"\begin{table}[h]") print(r"\caption{Timing VCF filtering}") print(tabulate(tbl, headers="keys", tablefmt="latex")) print(r"\end{table}") cyvcf2-0.30.14/scripts/trio-denovo.py0000644000175000017500000000100214154107376016710 0ustar nileshnileshimport numpy as np import sys from scipy.stats import binom_test path = sys.argv[1] import cyvcf2 vcf = cyvcf2.VCF(path) PRO, MOM, DAD = range(3) for v in vcf: if v.QUAL < 10: continue if np.any(v.gt_depths < 10): continue refs, alts = v.gt_ref_depths, v.gt_alt_depths if not all(v.gt_types == [vcf.HET, vcf.HOM_REF, vcf.HOM_REF]): continue if alts[MOM] > 1 or alts[DAD] > 1: continue print("%s\t%d\t%s\t%s\t%s" % (v.CHROM, v.start, v.REF, ",".join(v.ALT), ",".join(v.gt_bases))) cyvcf2-0.30.14/scripts/filter-cyvcf2.py0000644000175000017500000000026014154107376017127 0ustar nileshnileshimport sys import cyvcf2 n = 0 for v in cyvcf2.VCF(sys.argv[1]): if len(v.ALT) > 1: continue if v.QUAL < 20: continue if v.aaf > 0.05: continue n += 1 print(n) cyvcf2-0.30.14/scripts/filter-pyvcf.py0000644000175000017500000000033414154107376017064 0ustar nileshnileshimport sys from vcf import Reader import gzip vcf = Reader(open(sys.argv[1], 'rb')) n = 0 for v in vcf: if len(v.ALT) > 1: continue if v.QUAL < 20: continue if v.aaf[0] > 0.05: continue n += 1 print(n) cyvcf2-0.30.14/setup.py0000644000175000017500000000667114154107376014135 0ustar nileshnileshimport os import glob import sys import subprocess import platform import pkg_resources from setuptools import setup, Extension, dist if sys.version_info.major == 2 and sys.version_info.minor != 7: sys.stderr.write("ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d\n", (sys.version_info.major, sys.version_info.minor)) sys.exit(1) # Install numpy right now dist.Distribution().fetch_build_eggs(['numpy']) import numpy as np def get_version(): """Get the version info from the mpld3 package without importing it""" import ast with open(os.path.join("cyvcf2", "__init__.py"), "r") as init_file: module = ast.parse(init_file.read()) version = (ast.literal_eval(node.value) for node in ast.walk(module) if isinstance(node, ast.Assign) and node.targets[0].id == "__version__") try: return next(version) except StopIteration: raise ValueError("version could not be located") def no_cythonize(extensions, **_ignore): for extension in extensions: sources = [] for sfile in extension.sources: path, ext = os.path.splitext(sfile) if ext in (".pyx", ".py"): sfile = path + ".c" sources.append(sfile) extension.sources[:] = sources return extensions # Build the Cython extension by statically linking to the bundled htslib sources = [ x for x in glob.glob('htslib/*.c') if not any(e in x for e in ['irods', 'plugin']) ] sources += glob.glob('htslib/cram/*.c') # Exclude the htslib sources containing main()'s sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))] sources.append('cyvcf2/helpers.c') extra_libs = [] if platform.system() != 'Darwin': extra_libs.append('crypt') if bool(int(os.getenv("LIBDEFLATE", 0))): extra_libs.append('deflate') extensions = [Extension("cyvcf2.cyvcf2", ["cyvcf2/cyvcf2.pyx"] + sources, libraries=['z', 'bz2', 'lzma', 'curl', 'ssl'] + extra_libs, extra_compile_args=["-Wno-sign-compare", "-Wno-unused-function", "-Wno-strict-prototypes", "-Wno-unused-result", "-Wno-discarded-qualifiers"], include_dirs=['htslib', 'cyvcf2', np.get_include()])] CYTHONIZE = bool(int(os.getenv("CYTHONIZE", 0))) if CYTHONIZE: try: from Cython.Build import cythonize except ImportError: sys.stderr.write( "Cannot find Cython. Have you installed all the requirements?\n" "Try pip install -r requirements.txt\n" ) sys.exit(1) compiler_directives = {"language_level": 2, "embedsignature": True} extensions = cythonize(extensions, compiler_directives=compiler_directives) else: extensions = no_cythonize(extensions) setup( name="cyvcf2", description="fast vcf parsing with cython + htslib", long_description_content_type="text/markdown", url="https://github.com/brentp/cyvcf2/", long_description=open("README.md").read(), license="MIT", author="Brent Pedersen", author_email="bpederse@gmail.com", version=get_version(), ext_modules=extensions, packages=['cyvcf2', 'cyvcf2.tests'], entry_points=dict( console_scripts=[ 'cyvcf2 = cyvcf2.__main__:cli', ], ), install_requires=['numpy', 'coloredlogs', 'click'], include_package_data=True, zip_safe=False, ) cyvcf2-0.30.14/CHANGES.md0000644000175000017500000000124114154107376014001 0ustar nileshnilesh# v0.30.14 + use warnings instead of sys.stderr (#229 from @grahamgower) + use libdeflate in wheel build (#231 from @grahamgower) + use pytest instead of nose and update numpy stuff (#232 from @grahamgower) # v0.30.13 + fixes for mixed ploidy samples affecting `variant.num_het`, `variant.num_hom_ref`, etc. Also affects `variant.genotypes` and `variant.genotype` (see #227. Thanks @davmlaw and @grahamgower for test-cases and insight.) # v0.30.12 + add variant.FILTERS (by @tomwhite, #149) # v0.30.11 + bump for CI # v0.30.10 + fix is_indel for (see #217) # 0.3.8 + just bumping for CI+wheels # 0.30.7 + fix gt_types for phased variants (see: #198) cyvcf2-0.30.14/setup.cfg0000644000175000017500000000004714154107376014233 0ustar nileshnilesh[tool:pytest] testpaths = cyvcf2/tests cyvcf2-0.30.14/.gitignore0000644000175000017500000000033114154107376014376 0ustar nileshnilesh*.pyc cyvcf2.egg-info/ build dist *.so cyvcf2/cyvcf2.c htslib/config.h.in~ *.so.1 *.swp htslib/test *.5 htslib/.gitignore *.o *.pico libhts.a _build _static _templates setup-requires/* .cache/v/cache/lastfailed .idea cyvcf2-0.30.14/LICENSE0000644000175000017500000000211314154107376013413 0ustar nileshnileshThe MIT License (MIT) Copyright (c) 2015 Brent Pedersen - Bioinformatics Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. cyvcf2-0.30.14/ci/0000755000175000017500000000000014154107376013004 5ustar nileshnileshcyvcf2-0.30.14/ci/osx-deps0000755000175000017500000000114314154107376014473 0ustar nileshnilesh#!/bin/bash set -e python -m pip install pip --upgrade git submodule init git submodule update # configure fails with autoconf 2.71, so downgrade # see https://github.com/asdf-vm/asdf-erlang/issues/195 brew install autoconf@2.69 && \ brew link --overwrite autoconf@2.69 && \ autoconf -V curl -L -o libdeflate-v1.8.tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.8.tar.gz tar xzf libdeflate-v1.8.tar.gz cd libdeflate-1.8 make make install cd .. cd htslib autoheader autoconf ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 make cd .. pip install -r requirements.txt cyvcf2-0.30.14/ci/linux-deps0000755000175000017500000000203014154107376015015 0ustar nileshnilesh#!/bin/bash set -e yum install -y openssl11-devel yum install -y libffi libffi-devel zlib-devel yum install -y bzip2-devel bzip2-libs xz-devel xz-libs python -m pip install pip --upgrade git submodule init git submodule update curl -O https://www.libssh2.org/download/libssh2-1.9.0.tar.gz tar xzf libssh2-1.9.0.tar.gz cd libssh2-1.9.0 ./configure --prefix=/root make make install cd .. rm -rf libssh2-1.9.0 curl -O https://curl.se/download/curl-7.73.0.tar.gz tar xzf curl-7.73.0.tar.gz cd curl-7.73.0 ./configure --with-libssh2 --prefix=/root make make install cd .. rm -rf curl-7.73.0 curl -L -o libdeflate-v1.8.tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.8.tar.gz tar xzf libdeflate-v1.8.tar.gz cd libdeflate-1.8 make make install PREFIX=/root cd .. cd htslib # configure fails with autoconf 2.71 (in /usr/local/bin), so use 2.69 (in /usr/bin) /usr/bin/autoconf -V /usr/bin/autoheader /usr/bin/autoconf ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 make cd .. pip install -r requirements.txt cyvcf2-0.30.14/ci/test0000755000175000017500000000042414154107376013711 0ustar nileshnilesh#!/bin/bash if (cd ~/ && cyvcf2 --help >/dev/null) then echo "cyvcf2 --help: OK" else exit 1 fi if (cd ~/ && python -c "from cyvcf2 import VCF; VCF('https://github.com/brentp/cyvcf2/raw/main/cyvcf2/tests/test.vcf.gz')") then echo "Remote reading: OK" else exit 1 fi cyvcf2-0.30.14/.github/0000755000175000017500000000000014154107376013751 5ustar nileshnileshcyvcf2-0.30.14/.github/workflows/0000755000175000017500000000000014154107376016006 5ustar nileshnileshcyvcf2-0.30.14/.github/workflows/wheels.yml0000644000175000017500000001002614154107376020017 0ustar nileshnileshname: Wheels on: push: branches: - main tags: - 'v*.*.*' workflow_dispatch: inputs: debug_enabled: description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' required: false default: false jobs: build_wheels: name: Build wheels on ${{ matrix.os }} runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-18.04, macos-latest] steps: - uses: actions/checkout@v2 with: submodules: true - uses: actions/setup-python@v2 name: Install Python with: python-version: "3.7" - name: Install cibuildwheel run: | python -m pip install -U cibuildwheel - name: Build wheels for Linux if: matrix.os == 'ubuntu-18.04' run: | python -m cibuildwheel --output-dir wheelhouse env: CIBW_SKIP: "pp* *i686* *musllinux*" CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 CIBW_BEFORE_BUILD_LINUX: "{project}/ci/linux-deps" CIBW_TEST_COMMAND: "{project}/ci/test" CIBW_ENVIRONMENT: "CYTHONIZE=1 LIBDEFLATE=1 LDFLAGS='-L/usr/lib64/openssl11' CPPFLAGS='-I/usr/include/openssl11' C_INCLUDE_PATH='/root/include' LIBRARY_PATH='/root/lib'" CIBW_REPAIR_WHEEL_COMMAND_LINUX: LD_LIBRARY_PATH='/root/lib' auditwheel repair -w {dest_dir} {wheel} - name: Build wheels for Mac OS if: matrix.os == 'macos-latest' run: | python -m cibuildwheel --output-dir wheelhouse env: CIBW_SKIP: "pp* cp310-* *i686*" CIBW_ARCHS_MACOS: "x86_64 arm64" CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 CIBW_BEFORE_BUILD_MACOS: "{project}/ci/osx-deps" CIBW_TEST_COMMAND: "{project}/ci/test" CIBW_TEST_SKIP: "*-macosx_arm64" CIBW_ENVIRONMENT: "CYTHONIZE=1 LIBDEFLATE=1 C_INCLUDE_PATH='/usr/local/include' LIBRARY_PATH='/usr/local/lib'" # https://cibuildwheel.readthedocs.io/en/stable/faq/#macos-passing-dyld_library_path-to-delocate CIBW_REPAIR_WHEEL_COMMAND_MACOS: > DYLD_LIBRARY_PATH=/usr/local/lib delocate-listdeps {wheel} && DYLD_LIBRARY_PATH=/usr/local/lib delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel} LDFLAGS: "-L/usr/local/opt/openssl@1.1/lib" CPPFLAGS: "-I/usr/local/opt/openssl@1.1/include" PKG_CONFIG_PATH: "/usr/local/opt/openssl@1.1/lib/pkgconfig" # Enable tmate debugging of manually-triggered workflows if the input option was provided - name: Setup tmate session if: ${{ always() && github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }} uses: mxschmitt/action-tmate@v3 - uses: actions/upload-artifact@v2 with: path: ./wheelhouse/*.whl build_sdist: name: Build source distribution runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v2 name: Install Python with: python-version: "3.7" - name: Install dependencies run: | sudo apt-get update sudo apt-get install libcurl4-openssl-dev libbz2-dev liblzma-dev libssl-dev git submodule init git submodule update cd htslib autoheader autoconf ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 make cd .. pip install -r requirements.txt - name: Build sdist run: CYTHONIZE=1 python setup.py sdist - uses: actions/upload-artifact@v2 with: path: dist/*.tar.gz upload_pypi: needs: [build_wheels, build_sdist] runs-on: ubuntu-latest # upload to PyPI on every tag starting with 'v' if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') steps: - uses: actions/download-artifact@v2 with: name: artifact path: dist - uses: pypa/gh-action-pypi-publish@master with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} cyvcf2-0.30.14/.github/workflows/build.yml0000644000175000017500000000162514154107376017634 0ustar nileshnileshname: Build on: [push, pull_request] jobs: build: name: Run tests on Python ${{ matrix.python-version }} runs-on: ubuntu-18.04 strategy: matrix: python-version: [3.6, 3.7, 3.8, 3.9, "3.10"] steps: - uses: actions/checkout@v2 with: submodules: true - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - name: Install run: | sudo apt-get update sudo apt-get install libcurl4-openssl-dev pip install -r requirements.txt pip install pytest pytest-cov cd htslib autoheader && autoconf ./configure --enable-s3 --disable-lzma --disable-bz2 make cd .. CYTHONIZE=1 python setup.py build_ext -i - name: Test run: | pytest --cov cyvcf2 --cov-report term-missing cyvcf2-0.30.14/MANIFEST.in0000644000175000017500000000036414154107376014152 0ustar nileshnileshinclude cyvcf2/tests/* include LICENSE include cyvcf2/*.pyx include cyvcf2/*.pxd include cyvcf2/*.c include cyvcf2/*.h include *.md include htslib/*.c include htslib/*.h include htslib/htslib/*.h include htslib/cram/*.c include htslib/cram/*.h cyvcf2-0.30.14/.gitmodules0000644000175000017500000000011614154107376014564 0ustar nileshnilesh[submodule "htslib"] path = htslib url = https://github.com/samtools/htslib cyvcf2-0.30.14/docs/0000755000175000017500000000000014154107376013341 5ustar nileshnileshcyvcf2-0.30.14/docs/source/0000755000175000017500000000000014154107376014641 5ustar nileshnileshcyvcf2-0.30.14/docs/source/index.rst0000644000175000017500000001177414154107376016514 0ustar nileshnilesh.. cyvcf2 documentation master file, created by sphinx-quickstart on Mon Nov 14 08:40:54 2016. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. cyvcf2 ====== cyvcf2 is a fast VCF parser for python (2 and 3) released under the MIT license. It is a `cython` wrapper for `htslib `_ developed in the `Quinlan lab `_. See the :ref:`api` for detailed documentation, but the most common usage is summarized in the snippet below: .. code-block:: python from cyvcf2 import VCF for variant in VCF('some.vcf.gz'): # or VCF('some.bcf') variant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T'] variant.CHROM, variant.start, variant.end, variant.ID, \ variant.FILTER, variant.QUAL # numpy arrays of specific things we pull from the sample fields. # gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT variant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays variant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array ## INFO Field. ## extract from the info field by it's name: variant.INFO.get('DP') # int variant.INFO.get('FS') # float variant.INFO.get('AC') # float # convert back to a string. str(variant) ## per-sample info... # Get a numpy array of the depth per sample: dp = variant.format('DP') # or of any other format field: sb = variant.format('SB') assert sb.shape == (n_samples, 4) # 4-values per # to do a region-query: vcf = VCF('some.vcf.gz') for v in vcf('11:435345-556565'): if v.INFO["AF"] > 0.1: continue print(str(v)) # single sample of 0|1 in vcf becomes [[0, 1, True]] # 2 samples of 0/0 and 1|1 would be [[0, 0, False], [1, 1, True]] print v.genotypes Modifying Existing Records ========================== .. this example is also in the writing.rst page `cyvcf2` is optimized for fast reading and extraction from existing files. However, it also offers some means of modifying existing VCFs. Here, we show an example of how to modify the INFO field at a locus to annotate variants with the genes that they overlap. .. code-block:: python from cyvcf2 import VCF, Writer vcf = VCF(VCF_PATH) # adjust the header to contain the new field # the keys 'ID', 'Description', 'Type', and 'Number' are required. vcf.add_info_to_header({'ID': 'gene', 'Description': 'overlapping gene', 'Type':'Character', 'Number': '1'}) # create a new vcf Writer using the input vcf as a template. fname = "out.vcf" w = Writer(fname, vcf) for v in vcf: # The get_gene_intersections function is not shown. # This could be any operation to find intersections # or any manipulation required by the user. genes = get_gene_intersections(v) if genes is not None: v.INFO["gene"] = ",".join(genes) w.write_record(v) w.close(); vcf.close() More info on writing vcfs can be found :doc:`here ` Setting Genotyping Strictness ============================= By default, genotypes containing a single missing allele (e.g. genotypes such as ``0/.``, ``./0``, ``1/.``, or ``./1``) are classified as heterozygous ("HET" or id: 1) instead of "UNKNOWN" (or id: 2). A case can be made for either classification on these partially missing genotypes depending on the situation. A better way to explicitly control the genotype classification for these cases, is to use the "strict genotype", or ``strict_gt``, feature. Here's an example usage: .. code-block:: python from cyvcf2 import VCF vcf = VCF("/path/to/vcf/file", strict_gt=True) for variant in vcf: # do something When the ``strict_gt`` flag is enabled, `cyvcf2` will treat any genotype containing a missing allele (containing a '.') as an UNKNOWN genotype; otherwise, genotypes like ``0/.``, ``./0``, ``1/.``, or ``./1`` will be classified as heterozygous ("HET"). The "strict genotype" feature is not enabled by default (i.e. ``strict_gt`` is set to `False` by default) to preserve backwards compatibility. Installation ============ .. code-block:: bash pip install cyvcf2 or via bioconda. Testing ======= Install `pytest`, then tests can be run with: .. code-block:: bash pytest Known Limitations ================= * `cyvcf2` currently does not support reading VCFs encoded with UTF-8 with non-ASCII characters in the contents of string-typed FORMAT fields. For limitations on writing VCFs, see :ref:`here ` See Also ======== Pysam also `has a cython wrapper to htslib `_ and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project. .. toctree:: :maxdepth: 1 docstrings writing cyvcf2-0.30.14/docs/source/writing.rst0000644000175000017500000000660114154107376017061 0ustar nileshnileshModifying Existing VCFs ======================= `cyvcf2` is optimized for fast reading and extraction from existing files. However, it also offers some means of modifying existing VCFs. Modifying the INFO field ------------------------ .. this is the same example as on the index.rst page Here, we show an example of how to modify the INFO field at a locus to annotate variants with the genes that they overlap. .. code-block:: python from cyvcf2 import VCF, Writer vcf = VCF(VCF_PATH) # adjust the header to contain the new field # the keys 'ID', 'Description', 'Type', and 'Number' are required. vcf.add_info_to_header({'ID': 'gene', 'Description': 'overlapping gene', 'Type':'Character', 'Number': '1'}) # create a new vcf Writer using the input vcf as a template. fname = "out.vcf" w = Writer(fname, vcf) for v in vcf: # The get_gene_intersections function is not shown. # This could be any operation to find intersections # or any manipulation required by the user. genes = get_gene_intersections(v) if genes is not None: v.INFO["gene"] = ",".join(genes) w.write_record(v) w.close(); vcf.close() Modifying genotypes and the FORMAT field ---------------------------------------- Here is an example where we filter some calls from records in a VCF. This demonstrates how to add to the FORMAT field and how to modify genotypes at a locus. .. code-block:: python from cyvcf2 import VCF, Writer vcf = VCF(VCF_PATH) # adjust the header to contain the new field # the keys 'ID', 'Description', 'Type', and 'Number' are required. vcf.add_format_to_header({ 'ID': 'FILTER_CODE', 'Description': 'Numeric code for filtering reason', 'Type': 'Integer', 'Number': '1' }) # create a new vcf Writer using the input vcf as a template. fname = "out.vcf" w = Writer(fname, vcf) for v in vcf: # The filter_samples function is not shown. # This could be any manipulation required by the user. # Since we specified the FILTER_CODE format field is an Integer # with Number=1, reasons must be an n x 1 numpy array of integers # where n is the number of samples. indicies, reasons = filter_samples(v) if indicies: # add the reasons array to the format dictionary at this locus v.set_format('FILTER_CODE', reasons) for index in indicies: # overwrite the genotypes of each filtered locus to be nocalls # Note: until the reassignment to v.genotypes below, this # leaves the v Variant object in an inconsistent state v.genotypes[index] = [-1]*v.ploidy + [False] # it is necessary to reassign the genotypes field # so that the v Variant object reprocess it and future calls # to functions like v.genotype.array() properly reflect # the changed genotypes v.genotypes = v.genotypes w.write_record(v) w.close(); vcf.close() .. _Limitations with writing: Known Limitations with Writing VCFs ----------------------------------- * `cyvcf2` currently does not support writing VCFs encoded with UTF-8 with non-ASCII characters in the contents of string-typed FORMAT fields. * `cyvcf2` currently does not support writing string type format fields with number>1. cyvcf2-0.30.14/docs/source/docstrings.rst0000644000175000017500000000064314154107376017555 0ustar nileshnilesh.. _api: cyvcf2 API ========== .. autoclass:: cyvcf2.cyvcf2.VCF :members: :no-undoc-members: :exclude-members: het_check,ibd,next,plot_relatedness,set_threads,site_relatedness,update .. autoclass:: cyvcf2.cyvcf2.Variant :members: :exclude-members: relatedness .. autoclass:: cyvcf2.cyvcf2.Writer :members: :no-undoc-members: .. autoclass:: cyvcf2.cyvcf2.INFO :no-undoc-members: cyvcf2-0.30.14/docs/source/conf.py0000644000175000017500000002315014154107376016141 0ustar nileshnilesh# -*- coding: utf-8 -*- # # cyvcf2 documentation build configuration file, created by # sphinx-quickstart on Mon Nov 14 08:40:54 2016. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. import sys import os import re # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.insert(0, os.path.abspath('.')) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. #needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.imgmath', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages', 'sphinx.ext.napoleon', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'cyvcf2' copyright = u'2016..2020, Brent Pedersen' author = u'Brent Pedersen' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # init_file = os.path.abspath( os.path.join(os.path.dirname(__file__), "../../cyvcf2/__init__.py") ) with open(init_file, 'r') as f: version_file = f.read() version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M) if version_match: pkg_version = version_match.group(1) # The short X.Y version. version = pkg_version # The full version, including alpha/beta/rc tags. release = pkg_version # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all # documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. #keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = False # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = 'alabaster' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. #html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. # " v documentation" by default. #html_title = u'cyvcf2 v0.6.5' # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. #html_logo = None # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. #html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. 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These files are copied # directly to the root of the documentation. #html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. #html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. #html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' #html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. #html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. #html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'cyvcf2doc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). #'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. #'preamble': '', # Latex figure (float) alignment #'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'cyvcf2.tex', u'cyvcf2 Documentation', u'Brent Pedersen', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'cyvcf2', u'cyvcf2 Documentation', [author], 1) ] # If true, show URL addresses after external links. #man_show_urls = False # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'cyvcf2', u'cyvcf2 Documentation', author, 'cyvcf2', 'One line description of project.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. #texinfo_appendices = [] # If false, no module index is generated. #texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. #texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. #texinfo_no_detailmenu = False cyvcf2-0.30.14/docs/Makefile0000644000175000017500000001761114154107376015007 0ustar nileshnilesh# Makefile for Sphinx documentation # # You can set these variables from the command line. 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The XML files are in $(BUILDDIR)/xml." .PHONY: pseudoxml pseudoxml: $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml @echo @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." .PHONY: dummy dummy: $(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy @echo @echo "Build finished. Dummy builder generates no files." cyvcf2-0.30.14/cyvcf2/0000755000175000017500000000000014154107376013605 5ustar nileshnileshcyvcf2-0.30.14/cyvcf2/cli.py0000644000175000017500000001177214154107376014736 0ustar nileshnileshimport logging from datetime import datetime import coloredlogs import click from . import VCF from . import __version__ log = logging.getLogger(__name__) LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] def print_header(vcf_obj, include, exclude, samples=None): """Print the header of a vcf obj Parameters ---------- vcf_obj: cyvcf2.VCF include: tuple set of strings with info fields that should be included exclude: tuple set of strings with info fields that should be excluded samples: list list of samples to extract. """ if not samples is None: vcf_obj.set_samples(samples) for header_line in vcf_obj.raw_header.split('\n'): if len(header_line) == 0: continue print_line = True if 'INFO' not in header_line: pass elif include: print_line = any('ID='+inc+','for inc in include) elif exclude: print_line = not any('ID='+exc+','for exc in exclude) if print_line: click.echo(header_line) def print_variant(variant, include, exclude): """Print a vcf variant Parameters ---------- variant: cyvcf2.Variant include: tuple set of strings with info fields that should be included include: tuple set of strings with info fields that should be included """ if include: for info in variant.INFO: key = info[0] if not key in include: del variant.INFO[key] if exclude: for exc in exclude: if variant.INFO.get(exc): del variant.INFO[exc] print_string = str(variant).rstrip() click.echo(print_string) @click.command() @click.argument('vcf', metavar=' or -', ) @click.option('-c', '--chrom', help="Specify what chromosome to include.", ) @click.option('-s', '--start', type=int, help="Specify the start of region.", ) @click.option('-e', '--end', type=int, help="Specify the end of the region.", ) @click.option('--include', help="Specify what info field to include.", multiple=True, ) @click.option('--exclude', help="Specify what info field to exclude.", multiple=True, ) @click.option('--individual', '-i', help="Only print genotype call for individual.", multiple=True, ) @click.option('--no-inds', help="Do not print genotypes.", is_flag=True, ) @click.option('--loglevel', default='INFO', type=click.Choice(LOG_LEVELS), help="Set the level of log output.", show_default=True, ) @click.option('--silent', is_flag=True, help='Skip printing of vcf.' ) @click.pass_context def cyvcf2(context, vcf, include, exclude, chrom, start, end, loglevel, silent, individual, no_inds): """fast vcf parsing with cython + htslib""" coloredlogs.install(log_level=loglevel) start_parsing = datetime.now() log.info("Running cyvcf2 version %s", __version__) if include and exclude: log.warning("Can not use include and exclude at the same time") context.abort() region = '' if (chrom or start or end): if not (chrom and start and end): log.warning("Please specify chromosome, start and end for region") context.abort() else: region = "{0}:{1}-{2}".format(chrom, start, end) vcf_obj = VCF(vcf) for inclusion in include: if vcf_obj.contains(inclusion): log.info("Including %s in output", inclusion) else: log.warning("%s does not exist in header", inclusion) context.abort() for exclusion in exclude: if vcf_obj.contains(exclusion): log.info("Excluding %s in output", exclusion) else: log.warning("%s does not exist in header", exclusion) context.abort() if individual: # Check if the choosen individuals exists in vcf test = True for ind_id in individual: if ind_id not in vcf_obj.samples: log.warning("Individual '%s' does not exist in vcf", ind_id) test = False if not test: context.abort() # Convert individuals to list for VCF.set_individuals individual = list(individual) else: individual = None # Set individual to be empty list to skip all genotypes if no_inds: individual = [] if not silent: print_header(vcf_obj, include, exclude, individual) nr_variants = None try: for nr_variants, variant in enumerate(vcf_obj(region)): if not silent: print_variant(variant, include, exclude) except Exception as err: log.warning(err) context.abort() if nr_variants is None: log.info("No variants in vcf") return log.info("{0} variants parsed".format(nr_variants+1)) log.info("Time to parse variants: {0}".format(datetime.now() - start_parsing)) cyvcf2-0.30.14/cyvcf2/cyvcf2.pyx0000644000175000017500000025105214154107376015550 0ustar nileshnilesh#cython: profile=False #cython:language_level=3 #cython: embedsignature=True from __future__ import print_function import os import sys from collections import defaultdict import atexit import tempfile import numpy as np from array import array import math import ctypes import warnings try: from pathlib import Path except ImportError: from pathlib2 import Path # python 2 backport from libc cimport stdlib cimport numpy as np np.seterr(invalid='ignore') np.import_array() import locale ENC = locale.getpreferredencoding() from cython cimport view from cpython.version cimport PY_MAJOR_VERSION # overcome lack of __file__ in cython import inspect if not hasattr(sys.modules[__name__], '__file__'): __file__ = inspect.getfile(inspect.currentframe()) def par_relatedness(vcf_path, samples, ncpus, sites, min_depth=5, each=1): from multiprocessing import Pool p = Pool(ncpus) cdef np.ndarray aibs, an, ahets for i, fname in enumerate(p.imap_unordered(_par_relatedness, [ (vcf_path, samples, min_depth, i, ncpus, each, sites) for i in range(ncpus)])): arrays = np.load(fname) os.unlink(fname) if i == 0: aibs, an, ahets = arrays['ibs'], arrays['n'], arrays['hets'] else: aibs += arrays['ibs'] an += arrays['n'] ahets += arrays['hets'] return VCF(vcf_path, samples=samples)._relatedness_finish(aibs, an, ahets) def par_het(vcf_path, samples, ncpus, qsites, min_depth=8, percentiles=(10, 90), int each=1, int offset=0): from multiprocessing import Pool p = Pool(ncpus) any_counts, sum_counts, het_counts = 0, 0, 0 all_gt_types, mean_depths, sites = [], [], [] maf_lists = defaultdict(list) for ret in p.imap_unordered(_par_het, [(vcf_path, samples, qsites, min_depth, i, ncpus, each) for i in range(ncpus)]): (mean_depths_, maf_lists_, het_counts_, sum_counts_, all_gt_types_, sites_, any_counts_) = ret mean_depths.extend(mean_depths_) any_counts += any_counts_ sites.extend(sites_) all_gt_types.extend(all_gt_types_) sum_counts += sum_counts_ # an array het_counts += het_counts_ # an array for k in maf_lists_: li = maf_lists_[k] maf_lists[k].extend(li) mean_depths = np.array(mean_depths, dtype=np.int32).T vcf = VCF(vcf_path, samples=samples, gts012=True) return vcf._finish_het(mean_depths, maf_lists, percentiles, het_counts, sum_counts, all_gt_types, sites, any_counts) def _par_het(args): vcf_path, samples, sites, min_depth, offset, ncpus, each = args each *= ncpus vcf = VCF(vcf_path, samples=samples, gts012=True) return vcf.het_check(min_depth=min_depth, sites=sites, each=each, offset=offset, _finish=False) def _par_relatedness(args): vcf_path, samples, min_depth, offset, ncpus, each, sites = args vcf = VCF(vcf_path, samples=samples, gts012=True) each = each * ncpus vibs, vn, vhet = vcf._site_relatedness(min_depth=min_depth, offset=offset, each=each, sites=sites) # to get around limits of multiprocessing size of transmitted data, we save # the arrays to disk and return the file fname = tempfile.mktemp(suffix=".npz") atexit.register(os.unlink, fname) np.savez_compressed(fname, ibs=np.asarray(vibs), hets=np.asarray(vhet), n=np.asarray(vn)) return fname cdef unicode xstr(s): if type(s) is unicode: # fast path for most common case(s) return s elif PY_MAJOR_VERSION < 3 and isinstance(s, bytes): # only accept byte strings in Python 2.x, not in Py3 return (s).decode('ascii') elif isinstance(s, unicode): # an evil cast to might work here in some(!) cases, # depending on what the further processing does. to be safe, # we can always create a copy instead return unicode(s) else: raise TypeError(...) def r_(int32_t[::view.contiguous] a_gts, int32_t[::view.contiguous] b_gts, float f, int32_t n_samples): return r_unphased(&a_gts[0], &b_gts[0], f, n_samples) cdef set_constants(VCF v): v.HOM_REF = 0 v.HET = 1 if v.gts012: v.HOM_ALT = 2 v.UNKNOWN = 3 else: v.UNKNOWN = 2 v.HOM_ALT = 3 cdef class HTSFile: cdef htsFile *hts cdef bytes fname cdef bytes mode cdef bint from_path cdef _open_htsfile(self, fname, mode): """Opens an htsfile for reading or writing. Parameters ---------- fname: str filename (str or Path), file descriptor (int), or file-like object (has fileno method). mode: str the mode to pass to hts_open. """ cdef hFILE *hf self.mode = to_bytes(mode) reading = b"r" in self.mode writing = b"w" in self.mode if not reading and not writing: raise IOError("No 'r' or 'w' in mode %s" % str(self.mode)) self.from_path = isinstance(fname, (basestring, Path)) if self.from_path: self.fname = to_bytes(str(fname)) if self.fname == b"-": self.fname = to_bytes(b"/dev/stdin") if reading else to_bytes(b"/dev/stdout") self.hts = hts_open(self.fname, self.mode) # from a file descriptor elif isinstance(fname, int): hf = hdopen(int(fname), self.mode) self.hts = hts_hopen(hf, "", self.mode) self.fname = None # reading from a File object or other object with fileno elif hasattr(fname, "fileno"): if fname.closed: raise IOError('I/O operation on closed file') hf = hdopen(fname.fileno(), self.mode) self.hts = hts_hopen(hf, "", self.mode) # .name can be TextIOWrapper try: self.fname = to_bytes(fname.name) except AttributeError: self.fname = None else: raise IOError("Cannot open '%s' for writing." % str(type(fname))) if self.hts == NULL: raise IOError("Error opening %s" % str(fname)) if reading: if self.hts.format.format != vcf and self.hts.format.format != bcf: raise IOError( "%s is not valid bcf or vcf (format: %s mode: %s)" % (fname, self.hts.format.format, mode) ) else: if self.hts.format.format != text_format and self.hts.format.format != binary_format: raise IOError( "%s is not valid text_format or binary_format (format: %s mode: %s)" % (fname, self.hts.format.format, mode) ) def close(self): if self.hts != NULL: if self.from_path: hts_close(self.hts) self.hts = NULL cdef class VCF(HTSFile): """ VCF class holds methods to iterate over and query a VCF. Parameters ---------- fname: str path to file gts012: bool if True, then gt_types will be 0=HOM_REF, 1=HET, 2=HOM_ALT, 3=UNKNOWN. If False, 3, 2 are flipped. lazy: bool if True, then don't unpack (parse) the underlying record until needed. strict_gt: bool if True, then any '.' present in a genotype will classify the corresponding element in the gt_types array as UNKNOWN. samples: list list of samples to extract from full set in file. threads: int the number of threads to use including this reader. Returns ------- VCF object for iterating and querying. """ cdef const bcf_hdr_t *hdr cdef tbx_t *idx cdef hts_idx_t *hidx cdef int n_samples cdef int PASS cdef bint gts012 cdef bint lazy cdef bint strict_gt cdef list _seqnames cdef list _seqlens # holds a lookup of format field -> type. cdef dict format_types #: The constant used to indicate the the genotype is HOM_REF. cdef readonly int HOM_REF #: The constant used to indicate the the genotype is HET. cdef readonly int HET #: The constant used to indicate the the genotype is HOM_ALT. cdef readonly int HOM_ALT #: The constant used to indicate the the genotype is UNKNOWN. cdef readonly int UNKNOWN def __init__(self, fname, mode="r", gts012=False, lazy=False, strict_gt=False, samples=None, threads=None): cdef bcf_hdr_t *hdr self._open_htsfile(fname, mode) hdr = self.hdr = bcf_hdr_read(self.hts) if hdr == NULL: raise Exception("cannot parse VCF header") if samples is not None: self.set_samples(samples) self.n_samples = bcf_hdr_nsamples(self.hdr) self.PASS = -1 self.gts012 = gts012 self.lazy = lazy self.strict_gt = strict_gt self._seqnames = [] self._seqlens = [] set_constants(self) self.format_types = {} if threads is not None: self.set_threads(threads) def set_threads(self, int n): v = hts_set_threads(self.hts, n) if v < 0: raise Exception("error setting number of threads: %d" % v) cdef get_type(self, fmt): fmt = from_bytes(fmt) if not fmt in self.format_types: s = self.get_header_type(fmt, order=[BCF_HL_FMT]) self.format_types[fmt] = s["Type"] return from_bytes(self.format_types[fmt]) def add_to_header(self, line): """Add a new line to the VCF header. Parameters ---------- line: str full vcf header line. """ ret = bcf_hdr_append(self.hdr, to_bytes(line)) if ret != 0: raise Exception("couldn't add '%s' to header") ret = bcf_hdr_sync(self.hdr) if ret != 0: raise Exception("couldn't add '%s' to header") if line.startswith("##contig"): # need to trigger a refresh of seqnames self._seqnames = [] return ret def add_info_to_header(self, adict): """Add a INFO line to the VCF header. Parameters ---------- adict: dict dict containing keys for ID, Number, Type, Description. """ return self.add_to_header("##INFO=".format(**adict)) def add_format_to_header(self, adict): """Add a FORMAT line to the VCF header. Parameters ---------- adict: dict dict containing keys for ID, Number, Type, Description. """ return self.add_to_header("##FORMAT=".format(**adict)) def add_filter_to_header(self, adict): """Add a FILTER line to the VCF header. Parameters ---------- adict: dict dict containing keys for ID, Description. """ return self.add_to_header("##FILTER=".format(**adict)) def set_samples(self, samples): """Set the samples to be pulled from the VCF; this must be called before any iteration. Parameters ---------- samples: list list of samples to extract. """ if samples is None: samples = "-".encode() if isinstance(samples, list): samples = to_bytes(",".join(samples)) else: samples = to_bytes(samples) ret = bcf_hdr_set_samples(self.hdr, samples, 0) assert ret >= 0, ("error setting samples", ret) self.n_samples = bcf_hdr_nsamples(self.hdr) if ret != 0 and samples != "-": s = from_bytes(samples).split(",") if self.n_samples < len(s): warnings.warn("not all requested samples found in VCF") def update(self, id, type, number, description): """Update the header with an INFO field of the given parameters. Parameters ---------- id: str ID type: str valid VCF type number: str valid VCF number description: str description of added line. """ ret = bcf_hdr_append(self.hdr, "##INFO=".format(id=id, type=type, number=number, description=description)) if ret != 0: raise Exception("unable to update to header: %d", ret) ret = bcf_hdr_sync(self.hdr) if ret != 0: raise Exception("unable to update to header") def set_index(self, index_path=""): if index_path.endswith(".tbi"): self.idx = tbx_index_load2(to_bytes(self.fname), to_bytes(index_path)) if self.idx != NULL: return self.hidx = hts_idx_load2(to_bytes(self.fname), to_bytes(index_path)) if self.hidx == NULL: self.idx = tbx_index_load2(to_bytes(self.fname), to_bytes(index_path)) if self.hidx == NULL and self.idx == NULL: raise OSError("unable to open index:'%s' for '%s'" % (index_path, self.fname)) def _bcf_region(VCF self, region): if self.hidx == NULL: self.hidx = bcf_index_load(self.fname) assert self.hidx != NULL, ("error loading .csi index for %s" % self.fname) cdef bcf1_t *b cdef int ret cdef hts_itr_t *itr itr = bcf_itr_querys(self.hidx, self.hdr, to_bytes(region)) if itr == NULL: warnings.warn("no intervals found for %s at %s" % (self.fname, region)) raise StopIteration try: while True: b = bcf_init() ret = bcf_itr_next(self.hts, itr, b) if ret < 0: bcf_destroy(b) break ret = bcf_subset_format(self.hdr, b) assert ret == 0, ("could not subset variant", self.fname, region) yield newVariant(b, self) finally: if itr != NULL: hts_itr_destroy(itr) def __call__(VCF self, region=None): """ Extract the region from the VCF. Parameters ---------- region: str region string like chr1:1234-34566 or 'chr7 Returns ------- An Iterator over the requested region. """ if not region: yield from self raise StopIteration if self.fname.decode(ENC).endswith(('.bcf', '.bcf.gz')): yield from self._bcf_region(region) raise StopIteration if self.idx == NULL: self.idx = tbx_index_load(to_bytes(self.fname)) assert self.idx != NULL, "error loading tabix index for %s" % self.fname cdef hts_itr_t *itr cdef kstring_t s cdef bcf1_t *b cdef int slen = 1, ret = 0 cdef bytes bregion = to_bytes(region) cdef char *cregion = bregion with nogil: itr = tbx_itr_querys(self.idx, cregion) if itr == NULL: warnings.warn("no intervals found for %s at %s" % (self.fname, region)) raise StopIteration try: while 1: with nogil: slen = tbx_itr_next(self.hts, self.idx, itr, &s) if slen > 0: b = bcf_init() ret = vcf_parse(&s, self.hdr, b) if slen <= 0: break if ret > 0: bcf_destroy(b) stdlib.free(s.s) hts_itr_destroy(itr) raise Exception("error parsing") yield newVariant(b, self) finally: stdlib.free(s.s) hts_itr_destroy(itr) def header_iter(self): """ Iterate over fields in the HEADER """ cdef int i for i in range(self.hdr.nhrec): yield newHREC(self.hdr.hrec[i], self.hdr) def ibd(self, int nmax=-1): assert self.gts012 import itertools cdef int i, rl, n_bins = 16 samples = self.samples sample_to_idx = {s: samples.index(s) for s in samples} sample_pairs = list(itertools.combinations(samples, 2)) # values of bins, run_length cdef int n = 0 cdef float pi cdef int[:] b cdef int[:] gts cdef int idx0, idx1 bins = np.zeros((len(sample_pairs), n_bins), dtype=np.int32) rls = np.zeros(len(sample_pairs), dtype=np.int32) for v in self: if n == nmax: break n += 1 gts = v.gt_types pi = v.aaf for i, (s0, s1) in enumerate(sample_pairs): b = bins[i, :] idx0, idx1 = sample_to_idx[s0], sample_to_idx[s1] rls[i] = ibd(gts[idx0], gts[idx1], rls[i], pi, &b[0], n_bins) return {sample_pairs[i]: bins[i, :] for i in range(len(sample_pairs))} # pull something out of the HEADER, e.g. CSQ cpdef get_header_type(self, key, order=[BCF_HL_INFO, BCF_HL_FMT]): """Extract a field from the VCF header by id. Parameters ---------- key: str ID to pull from the header. Returns ------- rec: dict dictionary containing header information. """ key = to_bytes(key) cdef bcf_hrec_t *b cdef int i for typ in order: b = bcf_hdr_get_hrec(self.hdr, typ, b"ID", key, NULL); if b != NULL: break if b == NULL: b = bcf_hdr_get_hrec(self.hdr, BCF_HL_GEN, key, NULL, NULL); if b == NULL: raise KeyError(key) d = {from_bytes(b.key): from_bytes(b.value)} else: d = {from_bytes(b.keys[i]): from_bytes(b.vals[i]) for i in range(b.nkeys)} #bcf_hrec_destroy(b) return d def __getitem__(self, key): return self.get_header_type(key) def __contains__(self, key): """Check if the given ID is in the header.""" try: self[key] return True except KeyError: return False contains = __contains__ def __dealloc__(self): if self.hts != NULL and self.hdr != NULL: bcf_hdr_destroy(self.hdr) self.hdr = NULL self.close() if self.idx != NULL: tbx_destroy(self.idx) if self.hidx != NULL: hts_idx_destroy(self.hidx) def __iter__(self): return self def __next__(self): cdef bcf1_t *b cdef int ret if self.hts == NULL: raise Exception("attempt to iterate over closed/invalid VCF") with nogil: b = bcf_init() ret = bcf_read(self.hts, self.hdr, b) if ret >= 0 or b.errcode == BCF_ERR_CTG_UNDEF: return newVariant(b, self) else: bcf_destroy(b) if ret == -1: # end-of-file raise StopIteration else: raise Exception("error parsing variant with `htslib::bcf_read` error-code: %d and ret: %d" % ( b.errcode, ret)) property samples: "list of samples pulled from the VCF." def __get__(self): cdef int i return [str(self.hdr.samples[i].decode('utf-8')) for i in range(self.n_samples)] property raw_header: "string of the raw header from the VCF" def __get__(self): cdef kstring_t s s.s, s.l, s.m = NULL, 0, 0 bcf_hdr_format(self.hdr, 0, &s) return from_bytes(s.s) property seqlens: def __get__(self): if len(self._seqlens) > 0: return self._seqlens cdef int32_t nseq; cdef int32_t* sls = bcf_hdr_seqlen(self.hdr, &nseq) if sls == NULL or nseq <= 0: raise AttributeError("no sequence lengths found in header") self._seqlens = [sls[i] for i in range(nseq)] stdlib.free(sls) return self._seqlens property seqnames: "list of chromosomes in the VCF" def __get__(self): if len(self._seqnames) > 0: return self._seqnames cdef char **cnames cdef int i, n = 0 cnames = bcf_hdr_seqnames(self.hdr, &n) if n == 0 and self.fname.decode(ENC).endswith(('.bcf', '.bcf.gz')): if self.hidx == NULL: self.hidx = bcf_index_load(self.fname) if self.hidx != NULL: cnames = bcf_index_seqnames(self.hidx, self.hdr, &n) elif n == 0: if self.idx == NULL: self.idx = tbx_index_load(to_bytes(self.fname)) if self.idx !=NULL: cnames = tbx_seqnames(self.idx, &n) self._seqnames = [cnames[i].decode() for i in range(n)] stdlib.free(cnames) return self._seqnames def plot_relatedness(self, riter): import pandas as pd from matplotlib import pyplot as plt from matplotlib import gridspec import seaborn as sns sns.set_style("ticks") df = [] for row in riter: row['jtags'] = '|'.join(row['tags']) df.append(row) df = pd.DataFrame(df) fig = plt.figure(figsize=(9, 9)) gs = gridspec.GridSpec(2, 1, height_ratios=[3.5, 1]) ax0, ax1 = plt.subplot(gs[0]), plt.subplot(gs[1]) if "error" in df.columns: # plot all gray except points that don't match our expectation. import matplotlib matplotlib.rcParams['pdf.fonttype'] = 42 import matplotlib.colors as mc colors = [mc.hex2color(h) for h in ('#b6b6b6', '#ff3333')] for i, err in enumerate(("ok", "error")): subset = df[df.error == err] subset.plot(kind='scatter', x='rel', y='ibs0', c=colors[i], edgecolor=colors[0], label=err, ax=ax0, s=17 if i == 0 else 35) sub = df[df.error == "error"] for i, row in sub.iterrows(): ax0.annotate(row['sample_a'] + "\n" + row['sample_b'], (row['rel'], row['ibs0']), fontsize=8) else: # color by the relation derived from the genotypes. colors = sns.color_palette("Set1", len(set(df.jtags))) for i, tag in enumerate(set(df.jtags)): subset = df[df.jtags == tag] subset.plot(kind='scatter', x='rel', y='ibs0', c=colors[i], label=tag, ax=ax0) ax0.legend() ax0.set_ylim(ymin=0) ax0.set_xlim(xmin=df.rel.min()) ax1.set_xlim(*ax0.get_xlim()) ax1.hist(df.rel, 40) ax1.set_yscale('log', nonposy='clip') return fig def gen_variants(self, sites, offset=0, each=1, call_rate=0.8): seqnames = set(self.seqnames) if sites is not None: if isinstance(sites, basestring): isites = [] for i in (x.strip().split(":") for x in open(sites)): if not i[0] in seqnames and 'chr' + i[0] in seqnames: i[0] = 'chr' + i[0] i[1] = int(i[1]) isites.append(i) else: isites = sites for i in isites: if not i[0] in seqnames and 'chr' + i[0] in seqnames: i[0] = 'chr' + i[0] cdef Variant v cdef int k, last_pos if sites: isites = isites[offset::each] ref, alt = None, None j = 0 for i, osite in enumerate(isites): if len(osite) >= 4: chrom, pos, ref, alt = osite[:4] else: chrom, pos = osite[:2] for v in self("%s:%s-%s" % (chrom, pos, pos)): if len(v.ALT) != 1: continue if ref is not None and v.REF != ref: continue if alt is not None and v.ALT[0] != alt: continue if v.call_rate < call_rate: continue yield i, v j += 1 break else: last_pos, k = -10000, 0 for v in self: if abs(v.POS - last_pos) < 5000: continue if len(v.REF) != 1: continue if len(v.ALT) != 1: continue if v.call_rate < 0.5: continue if not 0.03 < v.aaf < 0.6: continue if np.mean(v.gt_depths > 7) < 0.5: continue last_pos = v.POS if k >= offset and k % each == 0: yield k, v k += 1 if k > 20000: break def het_check(self, min_depth=8, percentiles=(10, 90), _finish=True, int each=1, int offset=0, sites=None): cdef int i, k, n_samples = len(self.samples) cdef Variant v cdef np.ndarray het_counts = np.zeros((n_samples,), dtype=np.int32) cdef np.ndarray sum_depths = np.zeros((n_samples,), dtype=np.int32) cdef np.ndarray sum_counts = np.zeros((n_samples,), dtype=np.int32) cdef int any_counts = 0 # keep the sites and gts that we used for PCA used_sites, all_gt_types = [], [] mean_depths = [] maf_lists = defaultdict(list) idxs = np.arange(n_samples) for i, v in self.gen_variants(sites, each=each, offset=offset): if v.CHROM in ('X', 'chrX'): break if v.aaf < 0.01: continue if v.call_rate < 0.5: continue used_sites.append("%s:%d:%s:%s" % (v.CHROM, v.start + 1, v.REF, v.ALT[0])) alts = v.gt_alt_depths assert len(alts) == n_samples depths = (alts + v.gt_ref_depths).astype(np.int32) sum_depths += depths sum_counts += (depths > min_depth) any_counts += 1 mean_depths.append(depths) mafs = alts / depths.astype(float) gt_types = v.gt_types hets = gt_types == 1 het_counts[hets] += 1 for k in idxs[hets]: if depths[k] <= min_depth: continue maf_lists[k].append(mafs[k]) all_gt_types.append(np.array(gt_types, dtype=np.uint8)) if _finish: mean_depths = np.array(mean_depths, dtype=np.int32).T return self._finish_het(mean_depths, maf_lists, percentiles, het_counts, sum_counts, all_gt_types, used_sites, any_counts) return (mean_depths, maf_lists, het_counts, sum_counts, all_gt_types, used_sites, any_counts) def _finish_het(self, mean_depths, maf_lists, percentiles, het_counts, sum_counts, all_gt_types, sites, any_counts): sample_ranges = {} for i, sample in enumerate(self.samples): qs = np.asarray(np.percentile(maf_lists[i] or [0], percentiles)) sample_ranges[sample] = dict(zip(['p' + str(p) for p in percentiles], qs)) sample_ranges[sample]['range'] = qs.max() - qs.min() sample_ranges[sample]['het_ratio'] = het_counts[i] / float(any_counts) sample_ranges[sample]['het_count'] = het_counts[i] sample_ranges[sample]['sampled_sites'] = sum_counts[i] sample_ranges[sample]['mean_depth'] = np.mean(mean_depths[i]) sample_ranges[sample]['median_depth'] = np.median(mean_depths[i]) # used for the peddy paper. if os.environ.get('PEDDY_MAF_DUMP'): path = os.environ['PEDDY_MAF_DUMP'] import cPickle cPickle.dump({s: maf_lists[i] for i, s in enumerate(self.samples)}, open(path, 'wb', -1)) return sample_ranges, sites, np.transpose(all_gt_types) def site_relatedness(self, sites=None, min_depth=5, each=1): vibs, vn, vhet = self._site_relatedness(sites=sites, min_depth=min_depth, each=each) return self._relatedness_finish(vibs, vn, vhet) cdef _site_relatedness(self, sites=None, int min_depth=5, int each=1, int offset=0): """ sites must be an file of format: chrom:pos1:ref:alt where we match on all parts. it must have a matching file with a suffix of .bin.gz that is the binary genotype data. with 0 == hom_ref, 1 == het, 2 == hom_alt, 3 == unknown. min_depth applies per-sample """ cdef int n_samples = len(self.samples) cdef int k, i assert each >= 0 cdef int32_t[:, ::view.contiguous] ibs = np.zeros((n_samples, n_samples), np.int32) cdef int32_t[:, ::view.contiguous] n = np.zeros((n_samples, n_samples), np.int32) cdef int32_t[:] hets = np.zeros((n_samples, ), np.int32) cdef int32_t[:] gt_types = np.zeros((n_samples, ), np.int32) cdef int32_t[:] depths = np.zeros((n_samples, ), np.int32) cdef double[:] alt_freqs = np.zeros((n_samples,), np.double) cdef Variant v for j, (i, v) in enumerate(self.gen_variants(sites, offset=offset, each=each)): gt_types = v.gt_types alt_freqs = v.gt_alt_freqs krelated(>_types[0], &ibs[0, 0], &n[0, 0], &hets[0], n_samples, &alt_freqs[0]) return ibs, n, hets def relatedness(self, int n_variants=35000, int gap=30000, float min_af=0.04, float max_af=0.8, float linkage_max=0.2, min_depth=8): cdef Variant v cdef int last = -gap, nv = 0, nvt=0 cdef int32_t *last_gts = NULL samples = self.samples cdef int n_samples = len(samples) cdef float aaf = 0.0 cdef int n_unlinked = 0 cdef int32_t[:, ::view.contiguous] ibs = np.zeros((n_samples, n_samples), np.int32) cdef int32_t[:, ::view.contiguous] n = np.zeros((n_samples, n_samples), np.int32) cdef int32_t[:] hets = np.zeros((n_samples, ), np.int32) cdef int32_t[:] gt_types = np.zeros((n_samples, ), np.int32) for v in self: nvt += 1 if last_gts == NULL: if v._gt_types == NULL: v.gt_types last_gts = v._gt_types if v.POS - last < gap and v.POS > last: continue if v.call_rate < 0.5: continue # require half of the samples to meet the min depth if np.mean(v.gt_depths > min_depth) < 0.5: continue aaf = v.aaf if aaf < min_af: continue if aaf > max_af: continue if linkage_max < 1 and v.POS - last < 40000: if v._gt_types == NULL: v.gt_types # require 5 unlinked variants if r_unphased(last_gts, v._gt_types, 1e-5, n_samples) > linkage_max: continue n_unlinked += 1 if n_unlinked < 5: continue n_unlinked = 0 if v._gt_types == NULL: gt_types = v.gt_types last, last_gts = v.POS, v._gt_types v.relatedness(ibs, n, hets) nv += 1 if nv == n_variants: break warnings.warn("tested: %d variants out of %d" % (nv, nvt)) return self._relatedness_finish(ibs, n, hets) cdef dict _relatedness_finish(self, int32_t[:, ::view.contiguous] _ibs, int32_t[:, ::view.contiguous] _n, int32_t[:] _hets): samples = self.samples cdef int sj, sk, ns = len(samples) res = {'sample_a': [], 'sample_b': [], 'rel': array('f'), 'hets_a': array('I'), 'hets_b': array('I'), 'shared_hets': array('I'), 'ibs0': array('I'), 'ibs2': array('I'), 'n': array('I')} cdef float bot for sj in range(ns): sample_j = samples[sj] if _hets[sj] == 0: warnings.warn("peddy: no hets found for sample %s" % sample_j) for sk in range(sj, ns): if sj == sk: continue sample_k = samples[sk] # calculate relatedness. we use the geometric mean. #bot = math.exp(0.5 * (math.log(1 + _hets[sk]) + math.log(1 + _hets[sj]))) #bot = (_hets[sk] + _hets[sj])/2.0 bot = min(_hets[sk], _hets[sj]) if bot == 0: bot = max(_hets[sk], _hets[sj]) if bot == 0: # set to negative value if we are unable to calculate it. bot = -1 phi = (_ibs[sk, sj] - 2.0 * _ibs[sj, sk]) / (bot) res['sample_a'].append(sample_j) res['sample_b'].append(sample_k) res['hets_a'].append(_hets[sj]) res['hets_b'].append(_hets[sk]) res['rel'].append(phi) # rel is 2*kinship res['ibs0'].append(_ibs[sj, sk]) res['shared_hets'].append(_ibs[sk, sj]) res['ibs2'].append(_n[sk, sj]) res['n'].append(_n[sj, sk]) return res cdef class Allele(object): cdef int32_t *_raw cdef int i cdef int _value(self): if self._raw[self.i] < 0: return self._raw[self.i] return (self._raw[self.i] >> 1) - 1 @property def phased(self): return self._raw[self.i] & 1 == 1 @phased.setter def phased(self, bint ph): if ph: self._raw[self.i] = (self._value() + 1)<<1|1 else: self._raw[self.i] = (self._value() + 1)<<1 @property def value(self): if self._raw[self.i] < 0: return self._raw[self.i] return (self._raw[self.i] >> 1) - 1 @value.setter def value(self, int value): if value < 0: self._raw[self.i] = value return if self.phased: self._raw[self.i] = (value + 1)<<1|1 else: self._raw[self.i] = (value + 1)<<1 def __repr__(self): if self.value < 0: return "." return str(self.value) + ("|" if self.phased else "/") cdef inline Allele newAllele(int32_t *raw, int i): cdef Allele a = Allele.__new__(Allele) a._raw = raw a.i = i return a cdef class Genotypes(object): cdef int32_t *_raw cdef readonly int n_samples cdef readonly int ploidy def __cinit__(self): self.ploidy = 0 self.n_samples = 0 self._raw = NULL def __dealloc__(self): if self._raw != NULL: stdlib.free(self._raw) def phased(self, int i): """ a boolean indicating that the ith sample is phased. """ return (self._raw[i * self.ploidy + 1] & 1) == 1 def alleles(self, int i): cdef list result = [] cdef int32_t v for j in range(self.ploidy): v = self._raw[i * self.ploidy + j] if v != bcf_int32_vector_end: result.append((v >> 1) - 1) return result def __repr__(self): return str(self.array()) def array(Genotypes self, int fill=-2): """ array returns an int16 numpy array of shape n_samples, (ploidy + 1). The last column indicates phased (1 is phased, 0 is unphased). The other columns indicate the alleles, e.g. [0, 1, 1] is 0|1. Unknown alleles are represented by -1. If a mixture of ploidy levels are present then the array is padded with the `fill` value (default = -2) to indicate non-alleles. """ cdef np.ndarray[np.int16_t, ndim=2] to_return = np.zeros((self.n_samples, self.ploidy + 1), dtype=np.int16) cdef int raw cdef int ind cdef int allele cdef int p = self.ploidy + 1 for ind in range(self.n_samples): for allele in range(self.ploidy): raw = self._raw[ind * self.ploidy + allele] if raw == bcf_int32_vector_end: to_return[ind, allele] = fill else: to_return[ind, allele] = (raw >> 1) - 1 to_return[ind, self.ploidy] = (self._raw[ind * self.ploidy + 1] & 1) == 1 return to_return def __getitem__(self, int i): ## return the Allele objects for the i'th sample. cdef int k return [newAllele(self._raw, k) for k in range(i*self.ploidy,(i+1)*self.ploidy)] cdef inline Genotypes newGenotypes(int32_t *raw, int ploidy, int n_samples): cdef Genotypes gs = Genotypes.__new__(Genotypes) gs._raw = raw gs.ploidy = ploidy gs.n_samples = n_samples return gs cdef class Variant(object): """ Variant represents a single VCF Record. It is created internally by iterating over a VCF. Attributes ---------- INFO: `INFO` a dictionary-like field that provides access to the VCF INFO field. """ cdef bcf1_t *b cdef VCF vcf cdef int32_t *_gt_types cdef int *_gt_ref_depths cdef int *_gt_alt_depths cdef float *_gt_alt_freqs cdef void *fmt_buffer cdef int *_gt_phased cdef float *_gt_quals cdef int *_int_gt_quals cdef int *_gt_idxs cdef int _gt_nper cdef int *_gt_pls cdef float *_gt_gls cdef readonly INFO INFO cdef int _ploidy cdef list _genotypes cdef readonly int POS def __init__(self, *args, **kwargs): raise TypeError("Variant object cannot be instantiated directly.") def __cinit__(self): self.b = NULL self._gt_types = NULL self._gt_phased = NULL self._gt_pls = NULL self._ploidy = -1 def __repr__(self): return "Variant(%s:%d %s/%s)" % (self.CHROM, self.POS, self.REF, ",".join(self.ALT)) def __str__(self): cdef kstring_t s s.s, s.l, s.m = NULL, 0, 0 vcf_format(self.vcf.hdr, self.b, &s) try: return s.s[:s.l].decode() finally: stdlib.free(s.s) def __dealloc__(self): if self.b is not NULL: bcf_destroy(self.b) self.b = NULL if self._gt_types != NULL: stdlib.free(self._gt_types) if self._gt_ref_depths != NULL: stdlib.free(self._gt_ref_depths) if self._gt_alt_depths != NULL: stdlib.free(self._gt_alt_depths) if self._gt_alt_freqs != NULL: stdlib.free(self._gt_alt_freqs) if self._gt_phased != NULL: stdlib.free(self._gt_phased) if self._gt_quals != NULL: stdlib.free(self._gt_quals) if self._int_gt_quals != NULL: stdlib.free(self._int_gt_quals) if self._gt_idxs != NULL: stdlib.free(self._gt_idxs) if self._gt_pls != NULL: stdlib.free(self._gt_pls) if self._gt_gls != NULL: stdlib.free(self._gt_gls) property gt_bases: "numpy array indicating the alleles in each sample." def __get__(self): cdef np.ndarray gt_types = self.gt_types cdef int i, n = self.ploidy, j=-1, a, b cdef char **alleles = self.b.d.allele #cdef dict d = {i:alleles[i] for i in range(self.b.n_allele)} cdef list d = [from_bytes(alleles[i]) for i in range(self.b.n_allele)] d.append(".") # -1 gives . cdef list bases = ["./." for _ in range(self.vcf.n_samples)] cdef np.ndarray phased = (self.gt_phases).astype(int) cdef list lookup = ["/", "|"] cdef int unknown = 3 if self.vcf.gts012 else 2 for i in range(0, n * self.vcf.n_samples, n): j += 1 if n == 2: if (gt_types[j] == unknown) and (not self.vcf.strict_gt): continue else: a = self._gt_idxs[i] b = self._gt_idxs[i + 1] if a >= -1 and b >= -1: bases[j] = d[a] + lookup[phased[j]] + d[b] else: bases[j] = d[max(-1, a)] elif n == 1: bases[j] = d[self._gt_idxs[i]] else: raise Exception("gt_bases not implemented for ploidy > 2") return np.array(bases, str) def relatedness(self, int32_t[:, ::view.contiguous] ibs, int32_t[:, ::view.contiguous] n, int32_t[:] hets): if not self.vcf.gts012: raise Exception("must call relatedness with gts012") if self._gt_types == NULL: self.gt_types cdef double[:] alt_freqs = self.gt_alt_freqs return krelated(self._gt_types, &ibs[0, 0], &n[0, 0], &hets[0], self.vcf.n_samples, &alt_freqs[0]) property num_called: "number of samples that were not UNKNOWN." def __get__(self): if self._gt_types == NULL: self.gt_types cdef int n = 0, i = 0 if self.vcf.gts012: for i in range(self.vcf.n_samples): if self._gt_types[i] != 3: n+=1 else: for i in range(self.vcf.n_samples): if self._gt_types[i] != 2: n+=1 return n property call_rate: "proportion of samples that were not UNKNOWN." def __get__(self): if self.vcf.n_samples > 0: return float(self.num_called) / self.vcf.n_samples property aaf: "alternate allele frequency across samples in this VCF." def __get__(self): num_chroms = 2.0 * self.num_called if num_chroms == 0.0: return 0.0 return float(self.num_het + 2 * self.num_hom_alt) / num_chroms property nucl_diversity: def __get__(self): num_chroms = 2.0 * self.num_called p = self.aaf return (num_chroms / (num_chroms - 1.0)) * 2 * p * (1 - p) property num_hom_ref: "number homozygous reference samples at this variant." def __get__(self): if self._gt_types == NULL: self.gt_types cdef int n = 0, i = 0 for i in range(self.vcf.n_samples): if self._gt_types[i] == 0: n+=1 return n property num_het: "number heterozygous samples at this variant." def __get__(self): if self._gt_types == NULL: self.gt_types cdef int n = 0, i = 0 for i in range(self.vcf.n_samples): if self._gt_types[i] == 1: n+=1 return n property num_hom_alt: "number homozygous alternate samples at this variant." def __get__(self): if self._gt_types == NULL: self.gt_types cdef int n = 0, i = 0 if self.vcf.gts012: for i in range(self.vcf.n_samples): if self._gt_types[i] == 2: n+=1 else: for i in range(self.vcf.n_samples): if self._gt_types[i] == 3: n+=1 return n property num_unknown: "number unknown samples at this variant." def __get__(self): if self._gt_types == NULL: self.gt_types cdef int n = 0, i = 0 for i in range(self.vcf.n_samples): if self._gt_types[i] == 2: n+=1 return n property FORMAT: "VCF FORMAT field for this variant." def __get__(self): cdef int i cdef bcf_fmt_t fmt cdef char *key keys = [] for i in range(self.b.n_fmt): fmt = self.b.d.fmt[i]; key = bcf_hdr_int2id(self.vcf.hdr, BCF_DT_ID, fmt.id) keys.append(from_bytes(key)) return keys def format(self, field, vtype=None): """format returns a numpy array for the requested field. The numpy array shape will match the requested field. E.g. if the fields has number=3, then the shape will be (n_samples, 3). Parameters ---------- field: str FORMAT field to get the values. Returns ------- numpy array. """ if vtype is None: vtype = self.vcf.get_type(field) cdef bytes tag = to_bytes(field) cdef bcf_fmt_t *fmt = bcf_get_fmt(self.vcf.hdr, self.b, tag) cdef int n = 0, nret cdef void *buf = NULL; cdef int typenum = 0 if vtype == "Integer" or vtype == int: nret = bcf_get_format_int32(self.vcf.hdr, self.b, tag, &buf, &n) typenum = np.NPY_INT32 elif vtype == "Float" or vtype == float: nret = bcf_get_format_float(self.vcf.hdr, self.b, tag, &buf, &n) typenum = np.NPY_FLOAT32 elif vtype == "String" or vtype == str or vtype == "Character": vtype = str nret = bcf_get_format_string(self.vcf.hdr, self.b, tag, &buf, &n) typenum = np.NPY_STRING else: raise Exception("type %s not supported to format()" % vtype) if nret < 0: return None cdef char **dst cdef int i cdef np.npy_intp shape[2] shape[0] = self.vcf.n_samples shape[1] = fmt.n # values per sample if vtype == str: dst = buf v = [dst[i] for i in range(self.vcf.n_samples)] xret = np.array(v, dtype=str) stdlib.free(dst[0]) stdlib.free(dst) return xret iv = np.PyArray_SimpleNewFromData(2, shape, typenum, buf) iret = np.array(iv) stdlib.free(buf) return iret @property def genotype(self): if self.vcf.n_samples == 0: return None cdef int32_t *gts = NULL cdef int ndst = 0 cdef int nret = bcf_get_genotypes(self.vcf.hdr, self.b, >s, &ndst) if nret < 0: raise Exception("couldn't get genotypes for variant") return newGenotypes(gts, int(nret/self.vcf.n_samples), self.vcf.n_samples) @genotype.setter def genotype(self, Genotypes g): cdef int ret = bcf_update_genotypes(self.vcf.hdr, self.b, g._raw, self.vcf.n_samples * g.ploidy) if ret < 0: raise Exception("error setting genotypes with: %s" % g) property genotypes: """genotypes returns a list for each sample Indicating the allele and phasing. e.g. [0, 1, True] corresponds to 0|1 while [1, 2, False] corresponds to 1/2 """ def __get__(self): if self.vcf.n_samples == 0: return None if self._genotypes is not None: return self._genotypes cdef int32_t *gts = NULL cdef int i, j, nret, off = 0, ndst = 0, k = 0 cdef int n_samples = self.vcf.n_samples #self._genotypes = [] nret = bcf_get_genotypes(self.vcf.hdr, self.b, >s, &ndst) if nret < 0: raise Exception("error parsing genotypes") nret /= n_samples self._genotypes = [[] for _ in range(n_samples)] for i in range(n_samples): k = i * nret for j in range(nret): #assert k + j < ndst if bcf_gt_is_missing(gts[k + j]): self._genotypes[i].append(-1) continue if gts[k + j] == bcf_int32_vector_end: break self._genotypes[i].append(bcf_gt_allele(gts[k + j])) self._genotypes[i].append( bool(bcf_gt_is_phased(gts[k+1 if k+1 < ndst else k]))) stdlib.free(gts) return self._genotypes def __set__(self, gts): cdef int n_samples = self.vcf.n_samples if len(gts) != n_samples: raise Exception("genotypes: must set with a number of gts equal the number of samples in the vcf") elif len(gts) == 0: nret = 0 else: nret = max(len(gt)-1 for gt in gts) cdef int * cgts = stdlib.malloc(sizeof(int) * nret * n_samples) cdef int i, j, k self._genotypes = None for i in range(n_samples): k = i * nret for j in range(nret): if j == len(gts[i]) - 1: cgts[k + j] = bcf_int32_vector_end #bcf_gt_phased(-1) break else: cgts[k + j] = bcf_gt_phased(gts[i][j]) if gts[i][-1] else bcf_gt_unphased(gts[i][j]) ret = bcf_update_genotypes(self.vcf.hdr, self.b, cgts, n_samples * nret) if ret < 0: raise Exception("error setting genotypes with: %s" % gts) stdlib.free(cgts) def set_pos(self, int pos0): """ set the POS to the given 0-based position """ self.b.pos = pos0 self.POS = self.b.pos + 1 def set_format(self, name, np.ndarray data not None): """ set the format field given by name.. data must be a numpy array of type float, int or string (fixed length ASCII np.bytes_) """ cdef int n_samples = self.vcf.n_samples if len(data) % n_samples != 0: raise Exception("format: len(data) must be a multiple of number of samples in vcf.") cdef np.ndarray[np.float32_t, mode="c"] afloat cdef np.ndarray[np.int32_t, mode="c"] aint cdef char *bytesp cdef size_t i cdef int size cdef int ret if np.issubdtype(data.dtype, np.signedinteger) or np.issubdtype(data.dtype, np.unsignedinteger): size = data.shape[0] if len((data).shape) > 1: size *= data.shape[1] aint = data.astype(np.int32).reshape((size,)) ret = bcf_update_format_int32(self.vcf.hdr, self.b, to_bytes(name), &aint[0], size) elif np.issubdtype(data.dtype, np.floating): size = data.shape[0] if len((data).shape) > 1: size *= data.shape[1] afloat = data.astype(np.float32).reshape((size,)) isnan = np.isnan(afloat) for i in range(size): if isnan[i]: bcf_float_set(&afloat[i], bcf_float_missing) ret = bcf_update_format_float(self.vcf.hdr, self.b, to_bytes(name), &afloat[0], size) elif np.issubdtype(data.dtype, np.bytes_): if len((data).shape) > 1: raise Exception("Setting string type format fields with number>1 are currently not supported") if not data.flags['C_CONTIGUOUS']: data = np.ascontiguousarray(data) size = data.nbytes bytesp = data.data ret = bcf_update_format(self.vcf.hdr, self.b, to_bytes(name), bytesp, size, BCF_HT_STR) else: raise Exception("format: currently only float, int and string (fixed length ASCII np.bytes_) numpy arrays are supported. got %s", data.dtype) if ret < 0: raise Exception("error (%d) setting format with: %s" % (ret, data[:100])) property gt_types: """gt_types returns a numpy array indicating the type of each sample. HOM_REF=0, HET=1. For `gts012=True` HOM_ALT=2, UNKNOWN=3 """ def __get__(self): cdef int ndst = 0, ngts, n, i, nper, j = 0, k = 0 cdef int a if self.vcf.n_samples == 0: return np.array([]) if self._gt_types == NULL: self._gt_phased = stdlib.malloc(sizeof(int) * self.vcf.n_samples) ngts = bcf_get_genotypes(self.vcf.hdr, self.b, &self._gt_types, &ndst) nper = int(ngts / self.vcf.n_samples) self._ploidy = nper self._gt_idxs = stdlib.malloc(sizeof(int) * self.vcf.n_samples * nper) if ngts == 0 or nper == 0: return np.array([]) for i in range(0, ngts, nper): for k in range(i, i + nper): a = self._gt_types[k] if a >= 0: self._gt_idxs[k] = bcf_gt_allele(a) else: self._gt_idxs[k] = a self._gt_phased[j] = self._gt_types[i] > 0 and bcf_gt_is_phased(self._gt_types[i+1]) j += 1 if self.vcf.gts012: n = as_gts(self._gt_types, self.vcf.n_samples, nper, self.vcf.strict_gt, 2, 3) else: n = as_gts(self._gt_types, self.vcf.n_samples, nper, self.vcf.strict_gt, 3, 2) cdef np.npy_intp shape[1] shape[0] = self.vcf.n_samples return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_types) property ploidy: """get the ploidy of each sample for the given record.""" def __get__(self): if self._ploidy == -1: self.gt_types return self._ploidy property gt_phred_ll_homref: """get the PL of Hom ref for each sample as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] cdef int ndst = 0, nret=0, n, i, j, nper cdef int imax = np.iinfo(np.int32(0)).max if self._gt_pls == NULL and self._gt_gls == NULL: nret = bcf_get_format_int32(self.vcf.hdr, self.b, "PL", &self._gt_pls, &ndst) if nret < 0: nret = bcf_get_format_float(self.vcf.hdr, self.b, "GL", &self._gt_gls, &ndst) if nret < 0: return [] else: for i in range(nret): if self._gt_gls[i] <= -2147483646: # this gets translated on conversion to PL self._gt_gls[i] = imax / -10.0 else: for i in range(nret): if self._gt_pls[i] < 0: self._gt_pls[i] = imax self._gt_nper = int(nret / self.vcf.n_samples) cdef np.npy_intp shape[1] shape[0] = self._gt_nper * self.vcf.n_samples if self._gt_pls != NULL: pls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_pls)[::self._gt_nper] return pls else: gls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_gls)[::self._gt_nper] gls = (-10 * gls).round().astype(np.int32) return gls property gt_phred_ll_het: """get the PL of het for each sample as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] if self._gt_pls == NULL and self._gt_gls == NULL: # NOTE: the missing values for all homref, het, homalt are set # by this call. self.gt_phred_ll_homref cdef np.npy_intp shape[1] shape[0] = self._gt_nper * self.vcf.n_samples if self._gt_pls != NULL: if self._gt_nper > 1: ret = np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_pls)[1::self._gt_nper] return ret return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_pls) else: if self._gt_nper > 1: gls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_gls)[1::self._gt_nper] else: gls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_gls) gls = (-10 * gls).round().astype(np.int32) return gls property gt_phred_ll_homalt: """get the PL of hom_alt for each sample as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] if self._gt_pls == NULL and self._gt_gls == NULL: self.gt_phred_ll_homref cdef np.npy_intp shape[1] shape[0] = self._gt_nper * self.vcf.n_samples if self._gt_pls != NULL: if self._gt_nper > 1: return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_pls)[2::self._gt_nper] return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_pls) else: if self._gt_nper > 1: gls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_gls)[2::self._gt_nper] else: gls = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_gls) gls = (-10 * gls).round().astype(np.int32) return gls property gt_ref_depths: """get the count of reference reads as a numpy array.""" def __get__(self): cdef int ndst, nret = 0, n, i, j = 0, nper = 0 if self.vcf.n_samples == 0: return [] if self._gt_ref_depths == NULL: ndst = 0 # GATK nret = bcf_get_format_int32(self.vcf.hdr, self.b, "AD", &self._gt_ref_depths, &ndst) if nret > 0: nper = int(nret / self.vcf.n_samples) if nper == 1: stdlib.free(self._gt_ref_depths); self._gt_ref_depths = NULL return -1 + np.zeros(self.vcf.n_samples, np.int32) for i in range(0, nret, nper): self._gt_ref_depths[j] = self._gt_ref_depths[i] j += 1 elif nret == -1: # Freebayes # RO has to be 1:1 nret = bcf_get_format_int32(self.vcf.hdr, self.b, "RO", &self._gt_ref_depths, &ndst) if nret < 0: stdlib.free(self._gt_ref_depths); self._gt_ref_depths = NULL return -1 + np.zeros(self.vcf.n_samples, np.int32) # TODO: add new vcf standard. else: stdlib.free(self._gt_ref_depths); self._gt_ref_depths = NULL return -1 + np.zeros(self.vcf.n_samples, np.int32) for i in range(self.vcf.n_samples): if self._gt_ref_depths[i] < 0: self._gt_ref_depths[i] = -1 else: pass cdef np.npy_intp shape[1] shape[0] = self.vcf.n_samples return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_ref_depths) property gt_alt_depths: """get the count of alternate reads as a numpy array.""" def __get__(self): cdef int ndst, nret = 0, n, i, j = 0, k = 0, nper = 0 if self.vcf.n_samples == 0: return [] if self._gt_alt_depths == NULL: ndst = 0 # GATK nret = bcf_get_format_int32(self.vcf.hdr, self.b, "AD", &self._gt_alt_depths, &ndst) if nret > 0: nper = int(nret / self.vcf.n_samples) if nper == 1: stdlib.free(self._gt_alt_depths); self._gt_alt_depths = NULL return (-1 + np.zeros(self.vcf.n_samples, np.int32)) for i in range(0, nret, nper): self._gt_alt_depths[j] = self._gt_alt_depths[i+1] # add up all the alt alleles for k in range(2, nper): self._gt_alt_depths[j] += self._gt_alt_depths[i+k] j += 1 elif nret == -1: # Freebayes nret = bcf_get_format_int32(self.vcf.hdr, self.b, "AO", &self._gt_alt_depths, &ndst) nper = int(nret / self.vcf.n_samples) if nret < 0: stdlib.free(self._gt_alt_depths); self._gt_alt_depths = NULL return -1 + np.zeros(self.vcf.n_samples, np.int32) for i in range(0, nret, nper): self._gt_alt_depths[j] = self._gt_alt_depths[i] for k in range(1, nper): self._gt_alt_depths[j] += self._gt_alt_depths[i+k] j += 1 else: stdlib.free(self._gt_alt_depths); self._gt_alt_depths = NULL return -1 + np.zeros(self.vcf.n_samples, np.int32) # TODO: add new vcf standard. for i in range(self.vcf.n_samples): if self._gt_alt_depths[i] < 0: self._gt_alt_depths[i] = -1 cdef np.npy_intp shape[1] shape[0] = self.vcf.n_samples return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_alt_depths) property gt_alt_freqs: """get the freq of alternate reads as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] t = np.array(self.gt_depths, float) a = np.array(self.gt_alt_depths, float) # for which samples are the alt or total depths unknown? tU = t < 0 aU = a < 0 # for which samples is the total depth 0? t0 = t == 0 ## initialize alt_freq = t.astype(float) # default alt_freq[t0] = 0 alt_freq[aU] = 0 alt_freq[tU] = -1 # compute the alt_freq when not unknown and no div0 error clean = ~tU & ~aU & ~t0 alt_freq[clean] = (a[clean] / t[clean]) return alt_freq property gt_quals: """get the GQ for each sample as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] cdef int ndst = 0, nret, n, i cdef int *gq cdef np.ndarray[np.float32_t, ndim=1] a if self._gt_quals == NULL and self._int_gt_quals == NULL: nret = bcf_get_format_int32(self.vcf.hdr, self.b, "GQ", &self._int_gt_quals, &ndst) if nret == -2: # defined as int ndst = 0 nret = bcf_get_format_float(self.vcf.hdr, self.b, "GQ", &self._gt_quals, &ndst) if nret < 0 and nret != -2: return -1.0 + np.zeros(self.vcf.n_samples, np.float32) cdef np.npy_intp shape[1] shape[0] = self.vcf.n_samples if self._int_gt_quals != NULL: a = np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._int_gt_quals).astype(np.float32) a[a < 0] = -1 else: a = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT32, self._gt_quals) # this take up 10% of the total vcf parsing time. fix!! a[np.isnan(a)] = -1 return a property gt_depths: """get the read-depth for each sample as a numpy array.""" def __get__(self): if self.vcf.n_samples == 0: return [] # unfortunately need to create a new array here since we're modifying. r = np.array(self.gt_ref_depths, np.int32) a = np.array(self.gt_alt_depths, np.int32) # keep the -1 for empty. rl0 = r < 0 al0 = a < 0 r[rl0] = 0 a[al0] = 0 depth = r + a depth[rl0 & al0] = -1 return depth property gt_phases: """get a boolean indicating whether each sample is phased as a numpy array.""" def __get__(self): # run for side-effect if self._gt_phased == NULL: self.gt_types cdef np.npy_intp shape[1] shape[0] = self.vcf.n_samples return np.PyArray_SimpleNewFromData(1, shape, np.NPY_INT32, self._gt_phased).astype(bool) property REF: "the reference allele." def __get__(self): return self.b.d.allele[0].decode() def __set__(self, ref): # int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string); alleles = (ref + "," + ",".join(self.ALT)).encode() if bcf_update_alleles_str(self.vcf.hdr, self.b, alleles) != 0: raise ValueError("couldn't set reference to:" + str(ref)) property ALT: "the list of alternate alleles." def __get__(self): cdef int i return [self.b.d.allele[i].decode() for i in range(1, self.b.n_allele)] def __set__(self, alts): # int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string); if not isinstance(alts, list): alts = [alts] alleles = (self.REF + "," + ",".join(alts)).encode() if bcf_update_alleles_str(self.vcf.hdr, self.b, alleles) != 0: raise ValueError("couldn't set alternates to:" + str(alts)) property is_snp: "boolean indicating if the variant is a SNP." def __get__(self): cdef int i if len(self.b.d.allele[0]) > 1: return False for i in range(1, self.b.n_allele): if not self.b.d.allele[i] in (b"A", b"C", b"G", b"T"): return False return self.b.n_allele > 1 property is_mnp: "boolean indicating if the variant is a MNP." def __get__(self): cdef int i is_sv = self.is_sv if len(self.b.d.allele[0]) == 1 and not is_sv: return False if len(self.REF) == 1 and not is_sv: return False if all([len(x)==len(self.REF) for x in self.ALT]): if not is_sv: return True return False property is_indel: "boolean indicating if the variant is an indel." def __get__(self): cdef int i if self.is_sv: return False if len(self.b.d.allele[0]) > 1 and self.b.d.allele[0] != b'<': return True if len(self.REF) > 1: return True for i in range(1, self.b.n_allele): alt = self.b.d.allele[i] if alt[0] == b'<': continue if alt == b".": return True if len(alt) > 1: return True return False property is_transition: "boolean indicating if the variant is a transition." def __get__(self): if len(self.ALT) != 1: return False if not self.is_snp: return False ref = self.REF # just one alt allele alt_allele = self.ALT[0] if ((ref == 'A' and alt_allele == 'G') or (ref == 'G' and alt_allele == 'A') or (ref == 'C' and alt_allele == 'T') or (ref == 'T' and alt_allele == 'C')): return True return False property is_deletion: "boolean indicating if the variant is a deletion." def __get__(self): if len(self.ALT) > 1: return False if not self.is_indel: return False if len(self.ALT) == 0: return True alt = self.ALT[0] if alt is None or alt == ".": return True if len(self.REF) > len(alt): return True return False property is_sv: "boolean indicating if the variant is an SV." def __get__(self): return self.INFO.get(b'SVTYPE') is not None property CHROM: """Chromosome of the variant.""" def __get__(self): return bcf_hdr_id2name(self.vcf.hdr, self.b.rid).decode() def __set__(self, new_chrom): new_rid = bcf_hdr_id2int(self.vcf.hdr, BCF_DT_CTG, new_chrom.encode()) if new_rid < 0: self.vcf.add_to_header("##contig=".format(new_chrom)) new_rid = bcf_hdr_id2int(self.vcf.hdr, BCF_DT_CTG, new_chrom.encode()) if new_rid < 0: raise ValueError("Unable to add {} to CHROM".format(new_chrom)) warnings.warn("added new contig {} to header".format(new_chrom)) self.b.rid = new_rid property var_type: "type of variant (snp/indel/sv)" def __get__(self): if self.is_snp: return "snp" if self.is_mnp: return "mnp" elif self.is_indel: return "indel" elif self.is_sv: return "sv" else: return "unknown" property var_subtype: def __get__(self): if self.is_snp: if self.is_transition: return "ts" if len(self.ALT) == 1: return "tv" return "unknown" elif self.is_indel: if self.is_deletion: return "del" if len(self.ALT) == 1: return "ins" else: return "unknown" svt = self.INFO.get("SVTYPE") if svt is None: return "unknown" if svt == "BND": return "complex" if self.INFO.get('IMPRECISE') is None: return svt return self.ALT[0].strip('<>') property start: "0-based start of the variant." def __get__(self): return self.b.pos property end: "end of the variant. the INFO field is parsed for SVs." def __get__(self): return self.b.pos + self.b.rlen property ID: "the value of ID from the VCF field." def __get__(self): cdef char *id = self.b.d.id if id == b".": return None return from_bytes(id) def __set__(self, value): sanitized = str(value) if value is not None else '.' ret = bcf_update_id(self.vcf.hdr, self.b, to_bytes(sanitized)) if ret != 0: raise Exception("not able to set ID: %s", value) property FILTER: """the value of FILTER from the VCF field. a value of PASS or '.' in the VCF will give None for this function """ def __get__(self): cdef int i cdef int n = self.b.d.n_flt if n == 1: if self.vcf.PASS != -1: if self.b.d.flt[0] == self.vcf.PASS: return None else: v = bcf_hdr_int2id(self.vcf.hdr, BCF_DT_ID, self.b.d.flt[0]) if v == b"PASS": self.vcf.PASS = self.b.d.flt[0] return None return from_bytes(v) if n == 0: return None return from_bytes(b';'.join(bcf_hdr_int2id(self.vcf.hdr, BCF_DT_ID, self.b.d.flt[i]) for i in range(n))) def __set__(self, filters): if isinstance(filters, basestring): filters = filters.split(";") cdef bcf_hdr_t *h = self.vcf.hdr cdef int *flt_ids = stdlib.malloc(sizeof(int) * len(filters)) for i, fname in enumerate(filters): flt_ids[i] = bcf_hdr_id2int(h, BCF_DT_ID, to_bytes(fname)) ret = bcf_update_filter(h, self.b, flt_ids, len(filters)) stdlib.free(flt_ids) if ret != 0: raise Exception("not able to set filter: %s", filters) property FILTERS: """the FILTER values as a list from the VCF field. a value '.' in the VCF will return an empty list for this property """ def __get__(self): cdef int i cdef int n = self.b.d.n_flt return [from_bytes(bcf_hdr_int2id(self.vcf.hdr, BCF_DT_ID, self.b.d.flt[i])) for i in range(n)] property QUAL: "the float value of QUAL from the VCF field." def __get__(self): cdef float q = self.b.qual if bcf_float_is_missing(q): return None return q def __set__(self, value): if value is None: bcf_float_set(&self.b.qual, bcf_float_missing) else: self.b.qual = value cdef inline HREC newHREC(bcf_hrec_t *hrec, bcf_hdr_t *hdr): cdef HREC h = HREC.__new__(HREC) h.hdr = hdr h.hrec = hrec return h cdef class HREC(object): cdef bcf_hdr_t *hdr cdef bcf_hrec_t *hrec def __cinit__(HREC self): pass def __dealloc__(self): #bcf_hrec_destroy(self.hrec) self.hrec = NULL self.hdr = NULL @property def type(self): return ["FILTER", "INFO", "FORMAT", "CONTIG", "STR", "GENERIC"][self.hrec.type] def __getitem__(self, key): key = from_bytes(key) if key == "HeaderType": return self.type cdef int i for i in range(self.hrec.nkeys): if from_bytes(self.hrec.keys[i]) == key: return from_bytes(self.hrec.vals[i]) raise KeyError def info(self, extra=False): """ return a dict with commonly used stuffs """ d = {} for k in ('Type', 'Number', 'ID', 'Description'): try: d[k] = self[k] except KeyError: continue d['HeaderType'] = self.type if extra: for i in range(self.hrec.nkeys): k = self.hrec.keys[i] if k in d: continue d[k] = self.hrec.vals[i] return d def __repr__(self): return str(self.info()) cdef class INFO(object): """ INFO is create internally by accessing `Variant.INFO` is acts like a dictionary where keys are expected to be in the INFO field of the Variant and values are typed according to what is specified in the VCF header Items can be deleted with del v.INFO[key] and accessed with v.INFO[key] or v.INFO.get(key) """ cdef bcf_hdr_t *hdr cdef bcf1_t *b cdef int _i def __cinit__(INFO self): self._i = 0 def __delitem__(self, okey): okey = to_bytes(okey) cdef char *key = okey cdef bcf_info_t *info = bcf_get_info(self.hdr, self.b, key) if info == NULL: raise KeyError(key) cdef int htype = bcf_hdr_id2type(self.hdr, BCF_HL_INFO, info.key) cdef int ret = bcf_update_info(self.hdr, self.b, key,NULL,0,htype) if ret != 0: raise Exception("error deleting %s" % key) def __setitem__(self, key, value): # only support strings for now. if value is True or value is False: ret = bcf_update_info_flag(self.hdr, self.b, to_bytes(key), b"", int(value)) if ret != 0: raise Exception("not able to set: %s -> %s (%d)" % (key, value, ret)) return cdef int32_t iint cdef float ifloat if isinstance(value, int): iint = value ret = bcf_update_info_int32(self.hdr, self.b, to_bytes(key), &iint, 1) elif isinstance(value, float): ifloat = value ret = bcf_update_info_float(self.hdr, self.b, to_bytes(key), &ifloat, 1) else: ret = bcf_update_info_string(self.hdr, self.b, to_bytes(key), to_bytes(value)) if ret != 0: raise Exception("not able to set: %s -> %s (%d)", key, value, ret) cdef _getval(INFO self, bcf_info_t * info, char *key): if info.len == 1: if info.type == BCF_BT_INT8: if info.v1.i == INT8_MIN: return None return (info.v1.i) if info.type == BCF_BT_INT16: if info.v1.i == INT16_MIN: return None return (info.v1.i) if info.type == BCF_BT_INT32: if info.v1.i == INT32_MIN: return None return (info.v1.i) if info.type == BCF_BT_FLOAT: if bcf_float_is_missing(info.v1.f): return None return info.v1.f if info.type == BCF_BT_CHAR: v = info.vptr[:info.vptr_len] if len(v) > 0 and v[0] == 0x7: return None return from_bytes(v) # FLAG. if info.len == 0: return bcf_hdr_id2type(self.hdr, BCF_HL_INFO, info.key) == BCF_HT_FLAG return bcf_array_to_object(info.vptr, info.type, info.len) def __getitem__(self, okey): okey = to_bytes(okey) cdef char *key = okey cdef bcf_info_t *info = bcf_get_info(self.hdr, self.b, key) if info == NULL: raise KeyError(key) return self._getval(info, key) def get(self, key, default=None): try: return self.__getitem__(key) except KeyError: return default def __iter__(self): self._i = 0 return self def __next__(self): cdef bcf_info_t *info = NULL cdef char *name while info == NULL: if self._i >= self.b.n_info: raise StopIteration info = &(self.b.d.info[self._i]) self._i += 1 name = bcf_hdr_int2id(self.hdr, BCF_DT_ID, info.key) return name.decode(), self._getval(info, name) # this function is copied verbatim from pysam/cbcf.pyx cdef bcf_array_to_object(void *data, int type, int n, int scalar=0): cdef char *datac cdef int8_t *data8 cdef int16_t *data16 cdef int32_t *data32 cdef float *dataf cdef int i if not data or n <= 0: return None if type == BCF_BT_CHAR: datac = data value = datac[:n].decode() if datac[0] != bcf_str_missing else None else: value = [] if type == BCF_BT_INT8: data8 = data for i in range(n): if data8[i] == bcf_int8_vector_end: break value.append(data8[i] if data8[i] != bcf_int8_missing else None) elif type == BCF_BT_INT16: data16 = data for i in range(n): if data16[i] == bcf_int16_vector_end: break value.append(data16[i] if data16[i] != bcf_int16_missing else None) elif type == BCF_BT_INT32: data32 = data for i in range(n): if data32[i] == bcf_int32_vector_end: break value.append(data32[i] if data32[i] != bcf_int32_missing else None) elif type == BCF_BT_FLOAT: dataf = data for i in range(n): if bcf_float_is_vector_end(dataf[i]): break value.append(dataf[i] if not bcf_float_is_missing(dataf[i]) else None) else: raise TypeError('unsupported info type code') if not value: value = None elif scalar and len(value) == 1: value = value[0] else: value = tuple(value) return value cdef inline Variant newVariant(bcf1_t *b, VCF vcf): cdef Variant v = Variant.__new__(Variant) v.b = b if not vcf.lazy: with nogil: bcf_unpack(v.b, 15) else: with nogil: bcf_unpack(v.b, 1|2|4) v.vcf = vcf v.POS = v.b.pos + 1 cdef INFO i = INFO.__new__(INFO) i.b = b i.hdr = vcf.hdr v.INFO = i return v cdef to_bytes(s, enc=ENC): if not isinstance(s, bytes): return s.encode(enc) return s cdef from_bytes(s): if isinstance(s, bytes): try: return s.decode(ENC) except UnicodeDecodeError: return s.decode('utf8', errors='replace') return s # TODO: make Writer extend HTSFile not VCF by moving common methods into HTSFile cdef class Writer(VCF): """ Writer class makes a VCF Writer. Parameters ---------- fname: str path to file tmpl: VCF a template to use to create the output header. mode: str | Mode to use for writing the file. If ``None`` (default) is given, the mode is inferred from the filename extension. If stdout (``"-"``) is provided for ``fname`` and ``mode`` is left at default, uncompressed VCF will be produced. | Valid values are: | - ``"wbu"``: uncompressed BCF | - ``"wb"``: compressed BCF | - ``"wz"``: compressed VCF | - ``"w"``: uncompressed VCF | Compression level can also be indicated by adding a single integer to one of the compressed modes (e.g. ``"wz4"`` for VCF with compressions level 4). Note ---- File extensions ``.bcf`` and ``.bcf.gz`` will both return compressed BCF. If you want uncompressed BCF you must explicitly provide the appropriate ``mode``. Returns ------- VCF object for iterating and querying. """ #cdef htsFile *hts #cdef bcf_hdr_t *hdr cdef public bytes name cdef bint header_written cdef const bcf_hdr_t *ohdr def __init__(Writer self, fname, VCF tmpl, mode=None): mode = self._infer_file_mode(fname, mode) self._open_htsfile(fname, mode) bcf_hdr_sync(tmpl.hdr) self.ohdr = tmpl.hdr self.hdr = bcf_hdr_dup(tmpl.hdr) bcf_hdr_sync(self.hdr) self.header_written = False @staticmethod def _infer_file_mode(fname, mode=None): if mode is not None: return mode from_path = isinstance(fname, (basestring, Path)) if not from_path: return "w" fname = str(fname) is_compressed = fname.endswith(".gz") fmt_idx = -2 if is_compressed else -1 file_fmt = fname.split(".")[fmt_idx] # bcftools output write mode chars - https://github.com/samtools/bcftools/blob/76392b3014de70b7fa5c6b5c9d5bc47361951770/version.c#L64-L70 inferred_mode = "w" if file_fmt == "bcf": inferred_mode += "b" if is_compressed and file_fmt == "vcf": inferred_mode += "z" return inferred_mode @classmethod def from_string(Writer cls, fname, header_string, mode="w"): cdef Writer self = Writer.__new__(Writer) cdef char *hmode = "w" self._open_htsfile(fname, mode) self.hdr = bcf_hdr_init(hmode) self.ohdr = bcf_hdr_dup(self.hdr) if bcf_hdr_parse(self.hdr, to_bytes(header_string)) != 0: raise Exception("error parsing header:" + header_string) if bcf_hdr_sync(self.hdr) != 0: raise Exception("error syncing header:" + header_string) self.header_written = False self.n_samples = bcf_hdr_nsamples(self.hdr) return self def variant_from_string(self, variant_string): cdef bcf1_t *b = bcf_init() cdef kstring_t s tmp = to_bytes(variant_string) s.s = tmp s.l = len(variant_string) s.m = len(variant_string) ret = vcf_parse(&s, self.hdr, b) if ret > 0: bcf_destroy(b) raise Exception("error parsing:" + variant_string + " return value:" + ret) var = newVariant(b, self) if var.b.errcode == BCF_ERR_CTG_UNDEF: self.add_to_header("##contig=" % var.CHROM) var.b.errcode = 0 return var def write_header(Writer self): bcf_hdr_write(self.hts, self.hdr) self.header_written = True def write_record(Writer self, Variant var): "Write the variant to the writer." cdef bcf_hrec_t *h if not self.header_written: self.write_header() if var.b.errcode == BCF_ERR_CTG_UNDEF: h = bcf_hdr_id2hrec(self.ohdr, BCF_DT_CTG, 0, var.b.rid) if h == NULL: raise Exception("contig %d unknown and not found in header" % var.b.rid) if bcf_hdr_add_hrec(self.hdr, h) < 0: raise Exception("error adding contig %d to header" % var.b.rid) bcf_hdr_sync(self.hdr) elif var.b.errcode != 0: raise Exception("variant to be written has errorcode: %d" % var.b.errcode) return bcf_write(self.hts, self.hdr, var.b) def close(Writer self): if not self.header_written: self.write_header() super().close() cyvcf2-0.30.14/cyvcf2/cyvcf2.pxd0000644000175000017500000003054314154107376015523 0ustar nileshnileshfrom libc.stdint cimport int64_t, int32_t, uint32_t, int8_t, int16_t, uint8_t import numpy as np cimport numpy as np np.import_array() cdef extern from "relatedness.h": int related(int *gt_types, double *asum, int32_t *N, int32_t *ibs0, int32_t *ibs2, int32_t n_samples) float r_unphased(int32_t *a_gts, int32_t *b_gts, float f, int32_t n_samples) int ibd(int agt, int bgt, int run_length, float pi, int *bins, int32_t n_bins) int krelated(int32_t *gt_types, int32_t *ibs, int32_t *n, int32_t *hets, int32_t n_samples, double *ab) cdef extern from "helpers.h": int as_gts(int32_t *gts, int num_samples, int ploidy, int strict_gt, int HOM_ALT, int UNKNOWN); int32_t* bcf_hdr_seqlen(const bcf_hdr_t *hdr, int32_t *nseq) cdef extern from "htslib/kstring.h": ctypedef struct kstring_t: size_t l, m; char *s; char *ks_release(kstring_t *s) cdef extern from "htslib/hfile.h": ctypedef struct hFILE: pass hFILE *hdopen(int fd, const char *mode); cdef extern from "htslib/hts.h": int hts_set_threads(htsFile *fp, int n); cdef union ufp: hFILE *hfile; cdef enum htsExactFormat: unknown_format, binary_format, text_format, sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed ctypedef struct htsFormat: htsExactFormat format ctypedef struct htsFile: ufp fp htsFormat format int hts_detect_format(hFILE *fp, htsFormat *fmt); htsFile *hts_open(char *fn, char *mode); htsFile *hts_hopen(hFILE *fp, const char *fn, const char *mode); cdef int hts_verbose = 1 ctypedef struct hts_itr_t: pass ctypedef struct hts_idx_t: pass hts_idx_t *bcf_index_load(char *fn) hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx); #int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data); void hts_itr_destroy(hts_itr_t *iter); void hts_idx_destroy(hts_idx_t *idx); cdef extern from "htslib/tbx.h": ctypedef struct tbx_t: pass tbx_t *tbx_index_load(const char *fn); tbx_t *tbx_index_load2(const char *fn, const char *fnidx); hts_itr_t *tbx_itr_queryi(tbx_t *tbx, int tid, int64_t beg, int64_t end) hts_itr_t *tbx_itr_querys(tbx_t *tbx, char *reg) nogil int tbx_itr_next(htsFile *fp, tbx_t *tbx, hts_itr_t *iter, void *data) nogil; void tbx_destroy(tbx_t *tbx); cdef extern from "htslib/vcf.h": ctypedef struct hts_idx_t: pass int bcf_itr_next(htsFile *, hts_itr_t* iter, bcf1_t*) hts_itr_t *bcf_itr_querys(hts_idx_t *, void *, char *); const int BCF_DT_ID = 0; const int BCF_DT_CTG = 1 const int BCF_DT_SAMPLE = 2; uint32_t bcf_float_missing = 0x7F800001; const int BCF_ERR_CTG_UNDEF = 1 const int BCF_BT_NULL = 0 const int BCF_BT_INT8 = 1 const int BCF_BT_INT16 = 2 const int BCF_BT_INT32 = 3 const int BCF_BT_FLOAT = 5 const int BCF_BT_CHAR = 7 const int bcf_str_missing = 0x07 const int bcf_str_vector_end = 0 const int INT8_MIN = -128 const int INT16_MIN = -32768 const int INT32_MIN = -2147483648 const int bcf_int8_vector_end = -127 const int bcf_int16_vector_end = -32767 const int bcf_int32_vector_end = -2147483647 const int bcf_int8_missing = INT8_MIN const int bcf_int16_missing = INT16_MIN const int32_t bcf_int32_missing = INT32_MIN ctypedef union uv1: int32_t i; # integer value float f; # float value ctypedef struct variant_t: pass ctypedef struct bcf_fmt_t: int id; int n; # n ctypedef struct bcf_info_t: int key; # key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key int type; # type: one of BCF_BT_* types; len: vector length, 1 for scalars #} v1; # only set if $len==1; for easier access uv1 v1 uint8_t *vptr; # pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes uint32_t vptr_len; # length of the vptr block or, when set, of the vptr_mod block, excluding offset uint32_t vptr_off; uint32_t vptr_free; # vptr offset, i.e., the size of the INFO key plus size+type bytes int len; # indicates that vptr-vptr_off must be freed; set only when modified and the new ctypedef struct bcf_dec_t: int m_fmt, m_info, m_id, m_als, m_allele, m_flt; # allocated size (high-water mark); do not change int n_flt; # Number of FILTER fields int *flt; # FILTER keys in the dictionary char *id; # ID block (\0-seperated) char *als; # REF+ALT block (\0-seperated) char **allele; # allele[0] is the REF (allele[] pointers to the als block); all null terminated bcf_info_t *info; # INFO bcf_fmt_t *fmt; # FORMAT and individual sample variant_t *var; # $var and $var_type set only when set_variant_types called int n_var, var_type; int shared_dirty; # if set, shared.s must be recreated on BCF output int indiv_dirty; # if set, indiv.s must be recreated on BCF output ctypedef struct bcf1_t: int64_t pos; #// POS int64_t rlen; #// length of REF int32_t rid; #// CHROM float qual; #// QUAL uint32_t n_info, n_allele; uint32_t n_fmt #//:8 #//, n_sample:24; #kstring_t shared, indiv; bcf_dec_t d; #// lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack() int max_unpack; # // Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields wont be needed int unpacked; # // remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work int unpack_size[3]; # // the original block size of ID, REF+ALT and FILTER int errcode; # // one of BCF_ERR_* codes ctypedef struct bcf_idpair_t: pass const int BCF_HL_FLT = 0 # header line const int BCF_HL_INFO = 1 const int BCF_HL_FMT = 2 const int BCF_HL_CTG = 3 const int BCF_HL_STR = 4 # structured header line TAG= const int BCF_HL_GEN = 5 # generic header line const int BCF_HT_FLAG = 0 # header type const int BCF_HT_INT = 1 const int BCF_HT_REAL = 2 const int BCF_HT_STR = 3 ctypedef struct bcf_hrec_t: int type; # One of the BCF_HL_* type char *key; # The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc. char *value; # Set only for generic lines, NULL for FILTER/INFO, etc. int nkeys; # Number of structured fields char **keys; # The key=value pairs char **vals; # The key=value pairs ctypedef struct kstring_t: pass ctypedef struct bcf_hdr_t: int32_t n[3]; bcf_idpair_t *id[3]; void *dict[3]; # ID dictionary, contig dict and sample dict char **samples; bcf_hrec_t **hrec; int nhrec, dirty; int ntransl; # for bcf_translate() int *transl[2]; # for bcf_translate() int nsamples_ori; # for bcf_hdr_set_samples() uint8_t *keep_samples; kstring_t mem; int32_t m[3]; void bcf_float_set(float *ptr, uint32_t value) bint bcf_float_is_missing(float f) bint bcf_float_is_vector_end(float f) void bcf_destroy(bcf1_t *v); bcf1_t * bcf_init() nogil; int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v) nogil; int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec); int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals); int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string); bcf_hdr_t *bcf_hdr_read(htsFile *fp); int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); int bcf_hdr_nsamples(const bcf_hdr_t *hdr); void bcf_hdr_destroy(const bcf_hdr_t *hdr) char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len); int bcf_hdr_format(const bcf_hdr_t *hdr, int is_bcf, kstring_t *str); bcf_hdr_t *bcf_hdr_init(const char *mode); int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt); int bcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v); int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s); bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class); void bcf_hrec_destroy(bcf_hrec_t *) bcf_hrec_t *bcf_hdr_id2hrec(const bcf_hdr_t *hdr, int type, int idx, int rid); int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); int hts_close(htsFile *fp); int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v) nogil; const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid); const char *bcf_hdr_int2id(const bcf_hdr_t *hdr, int type, int int_id) int bcf_hdr_id2int(const bcf_hdr_t *hdr, int type, const char *id); int bcf_hdr_id2type(bcf_hdr_t * hdr,int type, int int_id) int bcf_unpack(bcf1_t *b, int which) nogil; bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key); int bcf_get_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, int32_t **dst, int *ndst); int bcf_get_format_int32(const bcf_hdr_t *hdr, bcf1_t *line, char * tag, int **dst, int *ndst); int bcf_get_format_float(const bcf_hdr_t *hdr, bcf1_t *line, char * tag, float **dst, int *ndst) int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst); int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type); int bcf_gt_is_phased(int); int bcf_gt_is_missing(int); int bcf_gt_allele(int); bint bcf_float_is_missing(float); bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key); int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n); ## genotypes void bcf_gt2alleles(int igt, int *a, int *b); int bcf_update_genotypes(const bcf_hdr_t *hdr, bcf1_t *line, const void *values, int n); # idx is 0 for ref, 1... for alts... int bcf_gt_phased(int idx); int bcf_gt_unphased(int idx); # sample/format fields int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type); int bcf_update_format_int32(const bcf_hdr_t * hdr, bcf1_t * line, const char * key, const void * values, int n) int bcf_update_format_float(const bcf_hdr_t * hdr, bcf1_t * line, const char * key, const void * values, int n) int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n); int bcf_update_format_char(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char**values, int n); int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id); int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id); int bcf_hdr_append(bcf_hdr_t * hdr, char *); int bcf_hdr_sync(bcf_hdr_t *h); bcf_hdr_t *bcf_hdr_dup(bcf_hdr_t *h); int bcf_update_info_int32(const bcf_hdr_t *hdr, bcf1_t * line, const char *key, const int32_t *values, int n) int bcf_update_info_float(const bcf_hdr_t *hdr, bcf1_t * line, const char *key, const float *values, int n) int bcf_update_info_flag(const bcf_hdr_t *hdr, bcf1_t * line, const char *key, const char *value, int n) int bcf_update_info_string(const bcf_hdr_t *hdr, bcf1_t * line, const char *key, const char *values) #define bcf_update_info_flag(hdr,line,key,string,n) bcf_update_info((hdr),(line),(key),(string),(n),BCF_HT_FLAG) #define bcf_update_info_float(hdr,line,key,values,n) bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_REAL) #define bcf_update_info_flag(hdr,line,key,string,n) bcf_update_info((hdr),(line),(key),(string),(n),BCF_HT_FLAG) #define bcf_update_info_string(hdr,line,key,string) bcf_update_info((hdr),(line),(key),(string),1,BCF_HT_STR) # free the array, not the values. char **bcf_index_seqnames(hts_idx_t *idx, bcf_hdr_t *hdr, int *n); char **tbx_seqnames(tbx_t *tbx, int *n) char **bcf_hdr_seqnames(bcf_hdr_t *hdr, int *n); cyvcf2-0.30.14/cyvcf2/tests/0000755000175000017500000000000014154107376014747 5ustar nileshnileshcyvcf2-0.30.14/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz0000644000175000017500000000056014154107376023201 0ustar nileshnileshBCSn0EWXdF!.睊B#An%vX9cێsl8ewa:\?'Nz]/Ilêr#Tiu#E0 9'FSeJaj4aZh+Jl;T("L\I+jvj8rG , DE33ȋ\`vNa[MߗvukA;3Ԧ؋Rԋ(Nt4[Yd-*H"0s)^<.G)œbb1Y-AVØA +b<,џ3|#j"5Ѯ=F;*8BCcyvcf2-0.30.14/cyvcf2/tests/test-invalid-header.vcf0000644000175000017500000000055014154107376021300 0ustar nileshnilesh##fileformat=VCFv4.0 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FOO 20 10001292 rs1 G A 42.22 . AF=0.50;AC=1 GT:RD:GQ 1/0:23:19.28 20 10002963 . C G 42.22 . AF=0.30 GT:RD:GQ 0/1:30:33.07 20 10005008 rs2 A T 123.78 . AF=1.00 GT:RD:GQ 1/1:30:8.26 20 10044557 rs3 C T 42.22 . AC=2 GT:RD:GQ 0/1:31:15.01 20 10048580 . T A 42.22 . AF=0.75 GT:RD:GQ 1/0:33:23.49 cyvcf2-0.30.14/cyvcf2/tests/seg.vcf.gz0000644000175000017500000000155614154107376016653 0ustar nileshnileshBCQV]o0}vjҦB[Tb$t $ $[3a֤l˺=Bs=>s\3i<=e"ADYB LN$.bdRsVoaS6M gX~5UKTDAwŠ]'ْ {Ȓ/,F+u.-:B9}lPg2n7탃f} o8ܞn[u\OY oE2jN~s=)5zᆜ}8>lCRAoN Թ8?>9?&QZ/ BCcyvcf2-0.30.14/cyvcf2/tests/issue_198.vcf0000644000175000017500000000042714154107376017203 0ustar nileshnilesh##fileformat=VCFv4.2 ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_1 chr1 231373681 rs560634812 T C 12816.8 PASS . GT 0/. chr1 231373681 rs560634812 T C 12816.8 PASS . 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TCGGT 0 . AC=0 chr1 146999 . TCGGT TGGGG 0 . AC=0 chr1 146999 . T TG 0 . AC=0 chr1 146999 . TG T 0 . AC=0 chr1 146999 . T G 0 . 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[ӡi͈g37%Un3?2XTRb\P n%"Et)!2[U3'߂b ()pbpTLz+Mɣwu>Bv럐n3)Bˍ;tt;av槧; i3w㓋T0russSpaw4CӟOgzMg{ߝ)16azvٽ^|4{d黷ȉ[ax&yw,feү`쭛?~0?;~v2?|~zx?=O ǣf~W/'35O7{¹×۫nq?;\/nW釳ZR?vOg]ǵSҒ⾓UWU+`1彆,/2jEdQ9lP#z&n=#ܔжDW^FtmW/uM=[ƕ̖[n{qenBF%`Γ;̍)ownl1omS޸}w/; oяG*C-٤{bC_g֩Is'_T< ütBqR$ZnN_ODM Cv37ۆ*@3RbJASP93P.ˬZ+g ^goڏbC̪'VMK)SRIKxiÿ*U7n8ljFE1s.Y. kYmRvX`1t[}Ҡ6__l$|Vi:|{1VK۝|ѼZ<7]G#b;Boi+Vc{qr!//A`zLZu| 3{o2hFR|+_#ަ8R>ȓ0 /}"&FwPE]QvJھ)7045u_ aAG,qDH/t;S J%p7PDp;$xqZTɅ~cz M {*V%1UY +ԍge!6}A.,f]Kʊ<z2Xf )m  "m $G"]ڙv7r5zj-_. tfc"9Rk'c!]ʴ࢟~>;w7Do{xCKIto73Zc+M=kŪ)`,6*jjY7V/ ܗCjb{Np(jF@SS HPRʩ{LcЋ]6 ##ALT= ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 3 81262 . G A 1826147.32 . . GT 0/. ./0 1/. ./1 ./. cyvcf2-0.30.14/cyvcf2/tests/test_hemi.py0000644000175000017500000000133214154107376017301 0ustar nileshnileshimport numpy as np from cyvcf2 import VCF, Variant, Writer import os.path HERE = os.path.dirname(__file__) HEM_PATH = os.path.join(HERE, "test-hemi.vcf") VCF_PATH = os.path.join(HERE, "test.vcf.gz") def check_var(v): s = [x.split(":")[0] for x in str(v).split("\t")[9:]] lookup = {'0/0': 0, '0/1': 1, './1': 1, '1/.': 1, '0/.': 0, './0': 0, '1/1': 3, '.': 2, './.': 2} expected = np.array([lookup[ss] for ss in s]) obs = v.gt_types assert np.all(expected == obs), zip(expected, obs) def test_hemi(): """ make sure that we are getting the correct gt_types for hemizygous variants """ for p in (HEM_PATH, VCF_PATH): vcf = VCF(p) for v in vcf: check_var(v) cyvcf2-0.30.14/cyvcf2/tests/test-format-string.vcf0000644000175000017500000000156114154107376021223 0ustar nileshnilesh##fileformat=VCFv4.2 ##FILTER= ##FORMAT= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Tumor Normal 7 55086956 . C G 0 . . GT:ADP_ALL:RULE 0/0:6728,1:F 1|1:22,1:G 7 55086957 . T A,C,G 0 . . GT:ADP_ALL:RULE 1/2:6768,2,2,1:F2,F3,F4 2|3:1,2,3,4:G2,G3,G4 7 55086958 . T G 0 . . GT:ADP_ALL:RULE 0/1/.:6768,2,2,1:F2,F3,F4 0:1,2,3,4:G2,G3,G4 7 55086959 . T G,T 0 . . GT:ADP_ALL:RULE . 0|2:1,2,3,4:G2,G3,G4 cyvcf2-0.30.14/cyvcf2/tests/test.comp_het.3.vcf0000644000175000017500000004531014154107376020367 0ustar nileshnilesh##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=20 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta ##SnpEffVersion="SnpEff 3.2 (build 2013-03-14), by Pablo Cingolani" ##SnpEffCmd="SnpEff -i vcf -o vcf GRCh37.66 /if2/arq5x/cphg-quinlan/projects/sms-elsea/varCalling/all.vcf " ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child_1 child_2 dad_2 mom_2 dad_1 mom_1 child_3 dad_3 mom_3 child_4 dad_4 mom_4 1 17363 . TTCT T 628.85 . AC=2;AF=0.083;AN=24;BaseQRankSum=4.577;DP=2951;DS;FS=10.112;HRun=0;HaplotypeScore=316.7300;InbreedingCoeff=-0.0909;MQ=22.73;MQ0=27;MQRankSum=1.681;QD=1.33;ReadPosRankSum=0.329;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|8|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|6|1) GT:AD:DP:GQ:PL 0|0:250,0:70:99:0,169,3371 0|0:250,0:78:99:0,199,4105 0|0:250,0:70:99:0,187,3984 0|0:250,0:63:99:0,166,3406 0|0:243,0:89:99:0,262,5364 0|0:250,0:62:99:0,172,3575 0|1:205,27:73:99:371,0,3406 0|1:225,16:74:99:318,0,3528 0|0:250,0:64:99:0,193,3988 0|1:205,27:73:99:371,0,3406 0|1:225,16:74:99:318,0,3528 0|0:250,0:64:99:0,193,3988 1 17730 . C A 102.87 . AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1) GT:AD:DP:GQ:PL 0|0:246,4:250:36.11:0,36,464 0|0:244,5:249:57.17:0,57,727 0|0:244,6:250:48.15:0,48,628 0|0:247,3:250:51.13:0,51,621 0|1:242,8:250:26.26:26,0,830 0|0:246,4:250:48.14:0,48,601 1|0:221,13:234:13.85:14,0,482 0|1:232,11:243:7:7,0,501 0|1:238,12:250:73.18:73,0,368 1|0:221,13:234:13.85:14,0,482 0|1:232,11:243:7:7,0,501 0|1:238,12:250:73.18:73,0,368 1 17740 . C A 102.87 . XX=;AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1) GT:XX:AD:DP:GQ:PL 0/0:TTTT 0|0:.:244,5:249:57.17:0,57,727 0/0:.:244,6:250:48.15:0,48,628 0|0:.:247,3:250:51.13:0,51,621 0/1:.:242,8:250:26.26:26,0,830 0|0:.:246,4:250:48.14:0,48,601 1/0:.:221,13:234:13.85:14,0,482 0|1:.:232,11:243:7:7,0,501 0/1:.:238,12:250:73.18:73,0,368 1|0:.:221,13:234:13.85:14,0,482 0/1:.:232,11:243:7:7,0,501 0|1:.:238,12:250:73.18:73,0,368 1 17750 . C A 102.87 . AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1) GT:AD:DP:GQ:PL 0/0:246,4:250:36.11:0,36,464 0/0:244,5:249:57.17:0,57,727 0/0:244,6:250:48.15:0,48,628 0/0:247,3:250:51.13:0,51,621 0/1:242,8:250:26.26:26,0,830 0/0:246,4:250:48.14:0,48,601 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0|1:238,12:250:73.18:73,0,368 1 17760 . C A 102.87 . AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1) GT:AD:DP:GQ:PL 0/0:246,4:250:36.11:0,36,464 0/0:244,5:249:57.17:0,57,727 0/0:244,6:250:48.15:0,48,628 0/0:247,3:250:51.13:0,51,621 0/1:242,8:250:26.26:26,0,830 0/0:246,4:250:48.14:0,48,601 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 2 17760 . C A 102.87 . AC=5;AF=0.208;AN=24;BaseQRankSum=-11.508;DP=2968;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.0610;InbreedingCoeff=-0.2498;MQ=13.12;MQ0=24;MQRankSum=-4.433;QD=0.08;ReadPosRankSum=1.952;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242||1),DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655||1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|4|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|5|1),EXON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|4|1),INTRON(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|7|1) GT:AD:DP:GQ:PL 0/0:246,4:250:36.11:0,36,464 0/0:244,5:249:57.17:0,57,727 0/0:244,6:250:48.15:0,48,628 0/0:247,3:250:51.13:0,51,621 0/1:242,8:250:26.26:26,0,830 0/0:246,4:250:48.14:0,48,601 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 1/0:221,13:234:13.85:14,0,482 0/1:232,11:243:7:7,0,501 0/1:238,12:250:73.18:73,0,368 cyvcf2-0.30.14/cyvcf2/tests/test.snpeff.bcf0000644000175000017500000001200114154107376017654 0ustar nileshnileshBC[ku]I+,[(8cv;cJ;NJ.KR/?2X 53v"]p"hp.C6ZE!$F:vM@#("FypHꚒe( pι~9w8ZJ禧 u@lt /u<;+$]+l)h>Z rkLJm }Tٝ.(M`X5 dZNҭ7kdzZWn>RXisk!r@oyVga3K'h,ks=s"ZfhiV7AݐBߣ)Ov7L6gX期͎YPQ=~2ڛ Ot'(=ɚmՒQuTu0hlBkcЫF9 EAm[SVhLpeS? 27@vgtyӃȎB|O9V>,\qZ!,qcm5n +m벃܅VUHw:>J6 ڱKUZt kuS,j@(*O)d*z#,G?gc4 3b._n5km&w0x빨蘀^FyͺUtfͳlB FС^/P1nopjpi_{SKonPO|N4իmvZǭTH!H>:3 sOݚ}N0LǵAA9 TDZ&FgQ;OkeBnxyLw:.+G,'5Yclbn`[st8;P-Rl 8$"ɗ)yXjJyP))(+T  Rnn`(Mby̞3A6J2'  TJqD c{yȞ'/AR$0/(,1 K Ƈd?qX%/M7?i8~DK CI*H Rd4\? |~ӟ4~\L?6?=$q1T($ _D>>#C)'O7a$o;L`*<>XCI$q<|b%O?CRҔ'2u3uB:'N:AB#!Lb X' X+k%Ob ǣ Y:au21](X'ĬSDbT ;9T9{TSyrkD|7YX˲6ǑRoi>V՞ٮr,; WkFmijm2;znrRRp̅8]`G\Z0MդMlAΣ Ia璖]5$ yVL;Z$=k050j4P͋[4]lX@2?Rpֿ>Hzŏ\2z +vݶt˰jӲufnTp2^OKC/tM?A8>(2J|aL?Iz?t߮Zkxv&:-7m:WN6;)|L*u I$@qO6:>Z*ή˳l)V*Ǵ Y0s, kiC]ToETS>GQSz艣K{ij;Eye*1v oNܑ;1_NL^JPý}-3{ݯ&{ZK|lߧcI==)(+zpR~VY^] +^~*,`ZENO~j?{5l7%y|+/ 5^WpLٓMY."TNQ졹|Ry72ϋ vsl4ZY1<]6$ oC[p+* l(oC!KCңS-I/MQ[<9/6|u۝UPXX_ygC+$+/}&Bʕl/=p [XԶ߲hn pßԃ;A{3>\gx^jW/..}~Q@yۨn,u6qJ i\-,i$h4h}9@&oZ>H_w]uA/_ZZ S;6gw֯,~_|q3ԣTwoRaq~`q8JJN7%ӗa#qq1Z(/*fPIߞlMSm߀FQB uS>|yz i{7ѺE{"U|%;?zZ<; D3ZĀBْVɂe!*ނs,˧o ]4UNPq!.8 ᮎ u7Tj'EKrE=4uiHݯ)?ˉq^ &c@Gݝ~(}QwW}c{jrWXnuc:?.)ݺW]K:CLuVfX~ݼ?2nO\K{O_#)jꟾ;;#UaU޾+m?X=~CaԼfg8N8~4)jfj7ڹ{ֿx&Ӟ]z 66v-^>Neqa?zaq| 5m3?iEۯk?{A2O\ܞ ##ALT= ##FILTER= ##FILTER= 200.0 || ReadPosRankSum < -20.0"> ##FILTER= 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || HaplotypeScore > 13.0"> ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##reference=file:///gpfs/data/cypre253/cypre253u1/./BIODATA/ucsc.hg19.fasta ##source=SelectVariants ##INFO= ##INFO= ##VEP=v81 cache=/home/athinat/.vep/homo_sapiens/81_GRCh37 db=homo_sapiens_core_81_37@ensembldb.ensembl.org gencode=GENCODE 19 HGMD-PUBLIC=20144 genebuild=2011-04 polyphen=2.2.2 ClinVar=201501 dbSNP=142 COSMIC=71 ESP=20141103 assembly=GRCh37.p13 regbuild=13 sift=sift5.2.2 ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 37150 37165 38008 chrX 2700157 . G A 3450.64 PASS AC=3;AF=1;AN=3;DP=119;FS=0;GQ_MEAN=1159.33;GQ_STDDEV=474.37;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.49;SOR=0.781;set=variant2;CSQ=missense_variant|Gac/Aac|D/N|ENSG00000124343|XG|ENST00000381174|4/10|benign(0)|tolerated(0.97)|60/180|protein_coding,missense_variant|Gac/Aac|D/N|ENSG00000124343|XG|ENST00000509484|2/7|benign(0)|tolerated(0.46)|38/148|protein_coding,missense_variant|Gac/Aac|D/N|ENSG00000124343|XG|ENST00000426774|4/10|benign(0.001)||60/181|protein_coding,missense_variant|Gac/Aac|D/N|ENSG00000124343|XG|ENST00000419513|4/11|benign(0)|tolerated(0.87)|60/195|protein_coding GT:AD:DP:GQ:PL 1:0,52:52:99:1701,0 1:0,38:38:99:818,0 1:0,27:27:99:959,0 chrX 2724760 . T C 985.64 PASS AC=3;AF=1;AN=3;DP=34;FS=0;GQ_MEAN=337.67;GQ_STDDEV=147.02;MLEAC=3;MLEAF=1;MQ=59.66;MQ0=0;NCC=0;QD=28.99;SOR=1.284;set=variant2;CSQ=missense_variant|cTc/cCc|L/P|ENSG00000124343|XG|ENST00000419513|8/11|benign(0)|tolerated(0.32)|131/195|protein_coding,intron_variant|||ENSG00000124343|XG|ENST00000426774||||-/181|protein_coding,intron_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000124343|XG|ENST00000519244|||||retained_intron,intron_variant|||ENSG00000124343|XG|ENST00000381174||||-/180|protein_coding GT:AD:DP:GQ:PL 1:0,10,0:10:99:335,0 1:0,8,2:10:99:192,0 1:0,14,0:14:99:486,0 chrX 2733109 . T G 1477.64 PASS AC=1;AF=1;AN=1;DP=55;FS=0;GQ_MEAN=1505;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.87;SOR=0.729;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,55:55:99:1505,0 .:0,0:.:.:. chrX 2733210 . G A 416.64 PASS AC=1;AF=1;AN=1;DP=16;FS=0;GQ_MEAN=444;MLEAC=1;MLEAF=1;MQ=52.1;MQ0=0;NCC=2;QD=26.04;SOR=0.941;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,16:16:99:444,0 .:0,0:.:.:. chrX 2733276 . G A 443.64 PASS AC=1;AF=1;AN=1;DP=21;FS=0;GQ_MEAN=471;MLEAC=1;MLEAF=1;MQ=56.89;MQ0=0;NCC=2;QD=22.18;SOR=1.127;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:471,0 .:0,0:.:.:. chrX 2733641 . A G 938.64 PASS AC=1;AF=1;AN=1;DP=32;FS=0;GQ_MEAN=966;MLEAC=1;MLEAF=1;MQ=49.86;MQ0=0;NCC=2;QD=29.33;SOR=1.112;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,32:32:99:966,0 .:0,0:.:.:. chrX 2733668 . G A 589.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=617;MLEAC=1;MLEAF=1;MQ=44.17;MQ0=0;NCC=2;QD=25.64;SOR=0.776;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:617,0 .:0,0:.:.:. chrX 2733845 . C T 119.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=147;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=14.96;SOR=1.863;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:147,0 .:0,0:.:.:. chrX 2733862 . A C 240.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.39;ClippingRankSum=-0.696;DP=10;FS=6.99;GQ_MEAN=268;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.696;NCC=2;QD=24.06;ReadPosRankSum=1.39;SOR=3.02;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124343|XG|ENST00000509484||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000381174|10/10|||-/180|protein_coding,downstream_gene_variant|||ENSG00000124343|XG|ENST00000419513||||-/195|protein_coding,3_prime_UTR_variant|||ENSG00000124343|XG|ENST00000426774|10/10|||-/181|protein_coding,downstream_gene_variant|||ENSG00000251848|snoU13|ENST00000516039|||||snoRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,9:10:99:268,0 .:0,0:.:.:. chrX 2777985 . C T 3190.65 PASS AC=3;AF=1;AN=3;DP=104;FS=0;GQ_MEAN=1072.67;GQ_STDDEV=485.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.98;SOR=1.413;set=variant2;CSQ=downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000469234|||||processed_transcript,missense_variant|gCg/gTg|A/V|ENSG00000056998|GYG2|ENST00000381157|3/6|benign(0.005)|deleterious(0.02)|89/244|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000520904||||-/137|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000381161|6/8||||processed_transcript,missense_variant|gCg/gTg|A/V|ENSG00000056998|GYG2|ENST00000542787|8/10|benign(0.172)||270/430|protein_coding,missense_variant|gCg/gTg|A/V|ENSG00000056998|GYG2|ENST00000381163|8/12|benign(0.018)|tolerated(0.37)|270/501|protein_coding,missense_variant|gCg/gTg|A/V|ENSG00000056998|GYG2|ENST00000338623|8/11|benign(0.002)||270/465|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000453106|4/7||||processed_transcript,missense_variant|gCg/gTg|A/V|ENSG00000056998|GYG2|ENST00000398806|7/11|benign(0.145)|tolerated(0.37)|239/470|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000353656|6/8||||processed_transcript GT:AD:DP:GQ:PL 1:0,46:46:99:1577,0 1:0,27:27:99:609,0 1:0,30:30:99:1032,0 chrX 2779570 . A G 1265.64 PASS AC=3;AF=1;AN=3;DP=40;FS=0;GQ_MEAN=431;GQ_STDDEV=282.9;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.45;SOR=1.387;set=variant2;CSQ=missense_variant|cAc/cGc|H/R|ENSG00000056998|GYG2|ENST00000542787|9/10|benign(0.003)||313/430|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000381161|7/8||||processed_transcript,missense_variant|cAc/cGc|H/R|ENSG00000056998|GYG2|ENST00000381157|4/6|benign(0.001)|tolerated(0.79)|132/244|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000469234|||||processed_transcript,missense_variant|cAc/cGc|H/R|ENSG00000056998|GYG2|ENST00000338623|9/11|benign(0)||313/465|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000056998|GYG2|ENST00000381163|9/12|benign(0)|tolerated(0.62)|313/501|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000056998|GYG2|ENST00000398806|8/11|benign(0)|tolerated(0.54)|282/470|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000453106|5/7||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000353656|7/8||||processed_transcript GT:AD:DP:GQ:PL 1:0,20:20:99:666,0 1:0,4:4:99:117,0 1:0,15:15:99:510,0 chrX 2800295 . G C 153.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=181;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.95;SOR=0.941;set=variant2;CSQ=downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000398806||||-/470|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000453106|||||processed_transcript,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000353656|||||processed_transcript,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000542787|10/10|||-/430|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000381161|8/8||||processed_transcript,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000381157||||-/244|protein_coding,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000338623|11/11|||-/465|protein_coding,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000381163|12/12|||-/501|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:181,0 .:0,0:.:.:. chrX 2800624 . G T 183.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=211;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.23;SOR=2.584;set=variant2;CSQ=downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000398806||||-/470|protein_coding,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000542787|10/10|||-/430|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000381161|8/8||||processed_transcript,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000381157||||-/244|protein_coding,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000338623|11/11|||-/465|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000353656|||||processed_transcript,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000381163|12/12|||-/501|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:211,0 .:0,0:.:.:. chrX 2800677 . A G 1055.64 PASS AC=1;AF=1;AN=1;DP=40;FS=0;GQ_MEAN=1083;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.07;SOR=0.743;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000338623|11/11|||-/465|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000353656|||||processed_transcript,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000381163|12/12|||-/501|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000398806||||-/470|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000056998|GYG2|ENST00000381161|8/8||||processed_transcript,3_prime_UTR_variant|||ENSG00000056998|GYG2|ENST00000542787|10/10|||-/430|protein_coding,downstream_gene_variant|||ENSG00000056998|GYG2|ENST00000381157||||-/244|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,39:39:99:1083,0 .:0,0:.:.:. chrX 2832742 . G C 4780.64 PASS AC=3;AF=1;AN=3;DP=138;FS=0;GQ_MEAN=1602.67;GQ_STDDEV=207.39;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.64;SOR=0.722;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000495294|||||processed_transcript,upstream_gene_variant|||ENSG00000006756|ARSD|ENST00000458014||||-/159|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000481340|2/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000217890|7/7||||processed_transcript,intron_variant|||ENSG00000006756|ARSD|ENST00000381154||||-/593|protein_coding GT:AD:DP:GQ:PL 1:0,44:44:99:1705,0 1:0,44:44:99:1364,0 1:0,50:50:99:1739,0 chrX 2832771 . C T 145.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=1.35;ClippingRankSum=0.083;DP=46;FS=3.111;GQ_MEAN=139.33;GQ_STDDEV=36.69;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;MQRankSum=1.25;NCC=0;QD=4.17;ReadPosRankSum=-0.317;SOR=0.309;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000481340|2/2||||processed_transcript,upstream_gene_variant|||ENSG00000006756|ARSD|ENST00000458014||||-/159|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000495294|||||processed_transcript,intron_variant|||ENSG00000006756|ARSD|ENST00000381154||||-/593|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000217890|7/7||||processed_transcript GT:AD:DP:GQ:PL 1:15,20:35:99:178,0 0:5,0:5:99:0,135 0:6,0:6:99:0,105 chrX 2835863 . G T 51.87 PASS AC=1;AF=0.333;AN=3;DP=11;FS=0;GQ_MEAN=112.33;GQ_STDDEV=29.02;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=17.29;SOR=1.179;set=variant2;CSQ=missense_variant|gCt/gAt|A/D|ENSG00000006756|ARSD|ENST00000381154|5/10|probably_damaging(0.984)|deleterious(0)|282/593|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000217890|5/7||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000481340|1/2||||processed_transcript,downstream_gene_variant|||ENSG00000006756|ARSD|ENST00000559324||||-/82|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000006756|ARSD|ENST00000494870|||||retained_intron,intron_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000495294|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,111 1:0,3:3:84:84,0 0:5,0:5:99:0,142 chrX 2836037 . G C 105.64 my_snp_filter AC=2;AF=1;AN=2;BaseQRankSum=-0.359;ClippingRankSum=-0.047;DP=136;FS=2.195;GQ_MEAN=66.5;GQ_STDDEV=20.51;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.14;NCC=1;QD=1.6;ReadPosRankSum=-0.581;SOR=0.446;set=FilteredInAll;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000217890|5/7||||processed_transcript,missense_variant|tCt/tGt|S/C|ENSG00000006756|ARSD|ENST00000381154|5/10|benign(0.053)|tolerated(0.13)|224/593|protein_coding,upstream_gene_variant|||ENSG00000006756|ARSD|ENST00000481340|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000006756|ARSD|ENST00000495294|||||processed_transcript,downstream_gene_variant|||ENSG00000006756|ARSD|ENST00000559324||||-/82|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000006756|ARSD|ENST00000494870|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:81:81,0 1:28,36:64:52:52,0 chrX 2852951 . G A 88.87 PASS AC=1;AF=0.333;AN=3;DP=10;FS=0;GQ_MEAN=113.67;GQ_STDDEV=6.35;MLEAC=1;MLEAF=0.333;MQ=49.67;MQ0=0;NCC=0;QD=22.22;SOR=1.609;set=variant2;CSQ=synonymous_variant|aaC/aaT|N|ENSG00000157399|ARSE|ENST00000545496|12/12|||589/614|protein_coding,synonymous_variant|aaC/aaT|N|ENSG00000157399|ARSE|ENST00000540563|10/10|||519/544|protein_coding,synonymous_variant|aaC/aaT|N|ENSG00000157399|ARSE|ENST00000381134|11/11|||564/589|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,110 1:0,4:4:99:121,0 0:3,0:3:99:0,110 chrX 2856155 . C T 271.64 PASS AC=3;AF=1;AN=3;DP=10;FS=0;GQ_MEAN=99.67;GQ_STDDEV=43.89;MLEAC=3;MLEAF=1;MQ=58.04;MQ0=0;NCC=0;QD=27.16;SOR=2.303;set=variant2;CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000157399|ARSE|ENST00000545496|10/12|benign(0.23)|tolerated(0.17)|449/614|protein_coding,missense_variant|Ggc/Agc|G/S|ENSG00000157399|ARSE|ENST00000540563|8/10|benign(0.15)|tolerated(0.16)|379/544|protein_coding,missense_variant|Ggc/Agc|G/S|ENSG00000157399|ARSE|ENST00000381134|9/11|probably_damaging(0.98)|tolerated(0.18)|424/589|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:49:49,0 1:0,4:4:99:126,0 1:0,4:4:99:124,0 chrX 2942109 . T C 1274.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=434;GQ_STDDEV=323.4;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.19;SOR=4.921;set=variant2;CSQ=synonymous_variant|Ttg/Ctg|L|ENSG00000205667|ARSH|ENST00000381130|6/9|||317/562|protein_coding GT:AD:DP:GQ:PL 1:0,20:20:99:716,0 1:0,3:3:81:81,0 1:0,13:13:99:505,0 chrX 3002687 . A G 965.87 PASS AC=2;AF=0.667;AN=3;DP=31;FS=0;GQ_MEAN=374.33;GQ_STDDEV=252.56;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.42;SOR=1.302;set=variant2;CSQ=synonymous_variant|gaA/gaG|E|ENSG00000062096|ARSF|ENST00000359361|6/11|||270/590|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000062096|ARSF|ENST00000381127|6/11|||270/590|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000062096|ARSF|ENST00000537104|5/10|||270/590|protein_coding GT:AD:DP:GQ:PL 1:0,17:17:99:630,0 0:4,0:4:99:0,125 1:0,10:10:99:368,0 chrX 3228411 . G A 698.87 PASS AC=2;AF=0.667;AN=3;DP=24;FS=0;GQ_MEAN=273.67;GQ_STDDEV=167.19;MLEAC=2;MLEAF=0.667;MQ=42.73;MQ0=0;NCC=0;QD=34.94;SOR=4.615;set=variant2;CSQ=synonymous_variant|gcC/gcT|A|ENSG00000101825|MXRA5|ENST00000217939|7/7|||2611/2828|protein_coding GT:AD:DP:GQ:PL 1:0,9:9:99:314,0 0:4,0:4:90:0,90 1:0,11:11:99:417,0 chrX 3228891 . A G 1565.64 PASS AC=2;AF=1;AN=2;DP=52;FS=0;GQ_MEAN=796.5;GQ_STDDEV=242.54;MLEAC=2;MLEAF=1;MQ=55.68;MQ0=0;NCC=1;QD=30.11;SOR=2.215;set=variant2;CSQ=synonymous_variant|acT/acC|T|ENSG00000101825|MXRA5|ENST00000217939|7/7|||2451/2828|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:625,0 .:0,0:.:.:. 1:0,31:31:99:968,0 chrX 3235724 . C T 2816.87 PASS AC=2;AF=0.667;AN=3;DP=88;FS=0;GQ_MEAN=984;GQ_STDDEV=784.96;MLEAC=2;MLEAF=0.667;MQ=59.92;MQ0=0;NCC=0;QD=33.14;SOR=0.765;set=variant2;CSQ=missense_variant|Ggc/Agc|G/S|ENSG00000101825|MXRA5|ENST00000217939|6/7|benign(0.206)|tolerated(0.4)|2000/2828|protein_coding GT:AD:DP:GQ:PL 1:0,47:47:99:1609,0 0:3,0:3:99:0,103 1:0,38:38:99:1240,0 chrX 3238167 . T G 3877.87 PASS AC=2;AF=0.667;AN=3;DP=114;FS=0;GQ_MEAN=1339;GQ_STDDEV=1120.42;MLEAC=2;MLEAF=0.667;MQ=59.73;MQ0=0;NCC=0;QD=27.9;SOR=0.806;set=variant2;CSQ=synonymous_variant|ccA/ccC|P|ENSG00000101825|MXRA5|ENST00000217939|5/7|||1853/2828|protein_coding GT:AD:DP:GQ:PL 1:0,63:63:99:2297,0 0:4,0:4:99:0,107 1:0,47:47:99:1613,0 chrX 3238733 . G A 3711.87 PASS AC=2;AF=0.667;AN=3;DP=115;FS=0;GQ_MEAN=1263;GQ_STDDEV=1055.16;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.74;SOR=1.386;set=variant2;CSQ=missense_variant|Cca/Tca|P/S|ENSG00000101825|MXRA5|ENST00000217939|5/7|probably_damaging(0.977)|deleterious(0.02)|1665/2828|protein_coding GT:AD:DP:GQ:PL 1:0,54:54:99:1845,0 0:4,0:4:45:0,45 1:0,56:56:99:1899,0 chrX 3239545 . C T 2794.87 PASS AC=2;AF=0.667;AN=3;DP=82;FS=0;GQ_MEAN=961;GQ_STDDEV=792.66;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.94;SOR=0.743;set=variant2;CSQ=missense_variant|gGc/gAc|G/D|ENSG00000101825|MXRA5|ENST00000217939|5/7|benign(0)|tolerated(1)|1394/2828|protein_coding GT:AD:DP:GQ:PL 1:0,44:44:99:1532,0 0:2,0:2:56:0,56 1:0,36:36:99:1295,0 chrX 3239828 . T C 2570.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-0.941;ClippingRankSum=-1.337;DP=81;FS=0;GQ_MEAN=880.33;GQ_STDDEV=777.67;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-0.743;NCC=0;QD=32.14;ReadPosRankSum=-0.446;SOR=0.263;set=variant2;CSQ=missense_variant|Aga/Gga|R/G|ENSG00000101825|MXRA5|ENST00000217939|5/7|benign(0.002)|tolerated(0.35)|1300/2828|protein_coding GT:AD:DP:GQ:PL 1:1,34:35:99:1032,0 0:1,0:1:38:0,38 1:0,45:45:99:1571,0 chrX 3240343 . G A 3184.87 PASS AC=2;AF=0.667;AN=3;DP=100;FS=0;GQ_MEAN=1106.33;GQ_STDDEV=870.15;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.18;SOR=1.076;set=variant2;CSQ=missense_variant|gCa/gTa|A/V|ENSG00000101825|MXRA5|ENST00000217939|5/7|benign(0.1)|tolerated(0.2)|1128/2828|protein_coding GT:AD:DP:GQ:PL 1:0,49:49:99:1583,0 0:4,0:4:99:0,102 1:0,47:47:99:1634,0 chrX 3241050 . G A 2815.87 PASS AC=2;AF=0.667;AN=3;DP=82;FS=0;GQ_MEAN=972.33;GQ_STDDEV=792.08;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.26;SOR=1.236;set=variant2;CSQ=synonymous_variant|tcC/tcT|S|ENSG00000101825|MXRA5|ENST00000217939|5/7|||892/2828|protein_coding GT:AD:DP:GQ:PL 1:0,45:45:99:1548,0 0:2,0:2:69:0,69 1:0,35:35:99:1300,0 chrX 3241256 . T C 2773 PASS AC=2;AF=0.667;AN=3;DP=85;FS=0;GQ_MEAN=941.67;GQ_STDDEV=819.23;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.01;SOR=0.791;set=variant2;CSQ=missense_variant|Att/Gtt|I/V|ENSG00000101825|MXRA5|ENST00000217939|5/7|benign(0)|tolerated(1)|824/2828|protein_coding GT:AD:DP:GQ:PL 1:0,46:46:99:1587,0 0:1,0:1:20:0,20 1:0,38:38:99:1218,0 chrX 3241284 . A G 2960.9 PASS AC=2;AF=0.667;AN=3;DP=89;FS=0;GQ_MEAN=1006.33;GQ_STDDEV=884.33;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.65;SOR=0.836;set=variant2;CSQ=synonymous_variant|agT/agC|S|ENSG00000101825|MXRA5|ENST00000217939|5/7|||814/2828|protein_coding GT:AD:DP:GQ:PL 1:0,51:51:99:1744,0 0:1,0:1:26:0,26 1:0,37:37:99:1249,0 chrX 3241317 . T C 3070.87 PASS AC=2;AF=0.667;AN=3;DP=95;FS=0;GQ_MEAN=1071.67;GQ_STDDEV=851.11;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.75;SOR=0.855;set=variant2;CSQ=synonymous_variant|ccA/ccG|P|ENSG00000101825|MXRA5|ENST00000217939|5/7|||803/2828|protein_coding GT:AD:DP:GQ:PL 1:0,51:51:99:1735,0 0:4,0:4:99:0,112 1:0,40:40:99:1368,0 chrX 3241791 . G A 3166.87 PASS AC=2;AF=0.667;AN=3;DP=93;FS=0;GQ_MEAN=1101.67;GQ_STDDEV=888.31;MLEAC=2;MLEAF=0.667;MQ=57.84;MQ0=0;NCC=0;QD=30.05;SOR=1.863;set=variant2;CSQ=synonymous_variant|gaC/gaT|D|ENSG00000101825|MXRA5|ENST00000217939|5/7|||645/2828|protein_coding GT:AD:DP:GQ:PL 1:0,49:49:99:1813,0 0:4,0:4:99:0,106 1:0,39:39:99:1386,0 chrX 3524309 . T C 1814.64 PASS AC=1;AF=1;AN=1;DP=71;FS=0;GQ_MEAN=1842;MLEAC=1;MLEAF=1;MQ=58.38;MQ0=0;NCC=2;QD=25.56;SOR=0.779;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000183943|PRKX|ENST00000262848|9/9|||-/358|protein_coding,downstream_gene_variant|||ENSG00000183943|PRKX|ENST00000496648|||||processed_transcript,downstream_gene_variant|||ENSG00000207332|RNU6-146P|ENST00000384602|||||snRNA,downstream_gene_variant|||ENSG00000183943|PRKX|ENST00000462736|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,71:71:99:1842,0 .:0,0:.:.:. chrX 3524737 . TAC T 447.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=475;MLEAC=1;MLEAF=1;MQ=60.98;MQ0=0;NCC=2;QD=26.44;SOR=0.859;set=variant;CSQ=downstream_gene_variant|||ENSG00000183943|PRKX|ENST00000496648|||||processed_transcript,downstream_gene_variant|||ENSG00000207332|RNU6-146P|ENST00000384602|||||snRNA,downstream_gene_variant|||ENSG00000183943|PRKX|ENST00000462736|||||processed_transcript,3_prime_UTR_variant|||ENSG00000183943|PRKX|ENST00000262848|9/9|||-/358|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:475,0 .:0,0:.:.:. chrX 3592725 . G A 4687.64 PASS AC=3;AF=1;AN=3;DP=156;FS=0;GQ_MEAN=1571.67;GQ_STDDEV=189.03;MLEAC=3;MLEAF=1;MQ=58.49;MQ0=0;NCC=0;QD=30.05;SOR=1.261;set=variant2;CSQ=synonymous_variant|ccC/ccT|P|ENSG00000183943|PRKX|ENST00000262848|2/9|||83/358|protein_coding,upstream_gene_variant|||ENSG00000183943|PRKX|ENST00000425240|||||processed_transcript GT:AD:DP:GQ:PL 1:0,48:48:99:1588,0 1:0,71:71:99:1752,0 1:0,37:37:99:1375,0 chrX 3631167 . A G 975.87 PASS AC=2;AF=0.667;AN=3;DP=34;FS=0;GQ_MEAN=383.33;GQ_STDDEV=219.78;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.85;SOR=1.382;set=variant2;CSQ=upstream_gene_variant|||ENSG00000182888|RP11-558O12.1|ENST00000329806|||||processed_pseudogene,missense_variant|gTg/gCg|V/A|ENSG00000183943|PRKX|ENST00000262848|1/9|benign(0)|tolerated(0.85)|43/358|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:572,0 0:6,0:6:99:0,142 1:0,12:12:99:436,0 chrX 6145855 . C G 56.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=84;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=14.16;SOR=1.609;set=variant2;CSQ=upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000538097||||-/816|protein_coding,intron_variant|||ENSG00000146938|NLGN4X|ENST00000381092||||-/816|protein_coding,5_prime_UTR_variant|||ENSG00000146938|NLGN4X|ENST00000381093|1/7|||-/836|protein_coding,intron_variant|||ENSG00000146938|NLGN4X|ENST00000381095||||-/816|protein_coding,5_prime_UTR_variant|||ENSG00000146938|NLGN4X|ENST00000275857|1/6|||-/816|protein_coding,upstream_gene_variant|||ENSG00000146938|NLGN4X|ENST00000469740|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:84:84,0 .:0,0:.:.:. chrX 6995315 . C T 1965.87 PASS AC=2;AF=0.667;AN=3;DP=62;FS=0;GQ_MEAN=701.33;GQ_STDDEV=515.61;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.49;SOR=3.219;set=variant2;CSQ=synonymous_variant|ccG/ccA|P|ENSG00000130021|HDHD1|ENST00000540122|3/4|||152/208|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000130021|HDHD1|ENST00000486446|3/4|||152/191|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000130021|HDHD1|ENST00000412827|3/4|||109/185|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000130021|HDHD1|ENST00000424830|4/5|||175/251|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000130021|HDHD1|ENST00000381077|3/4|||152/228|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:1005,0 0:4,0:4:99:0,106 1:0,29:29:99:993,0 chrX 6995438 . C T 3119.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.67;ClippingRankSum=1.06;DP=108;FS=0;GQ_MEAN=1086;GQ_STDDEV=864.6;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=1.51;NCC=0;QD=30;ReadPosRankSum=1.2;SOR=1.157;set=variant2;CSQ=synonymous_variant|ctG/ctA|L|ENSG00000130021|HDHD1|ENST00000424830|4/5|||134/251|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000130021|HDHD1|ENST00000412827|3/4|||68/185|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000130021|HDHD1|ENST00000381077|3/4|||111/228|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000130021|HDHD1|ENST00000486446|3/4|||111/191|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000130021|HDHD1|ENST00000540122|3/4|||111/208|protein_coding GT:AD:DP:GQ:PL 1:1,45:46:99:1411,0 0:4,0:4:99:0,106 1:1,57:58:99:1741,0 chrX 7270996 . A G 623.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=651;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.99;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101846|STS|ENST00000217961|10/10|||-/583|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:651,0 .:0,0:.:.:. chrX 8138080 . G C 1524.64 PASS AC=1;AF=1;AN=1;DP=58;FS=0;GQ_MEAN=1552;MLEAC=1;MLEAF=1;MQ=58.18;MQ0=0;NCC=2;QD=26.29;SOR=1.179;set=variant2;CSQ=missense_variant|aCc/aGc|T/S|ENSG00000177504|VCX2|ENST00000317103|3/3|unknown(0)|tolerated_low_confidence(1)|138/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,58:58:99:1552,0 .:0,0:.:.:. chrX 8138160 . T C 878.64 PASS AC=1;AF=1;AN=1;DP=24;FS=0;GQ_MEAN=906;MLEAC=1;MLEAF=1;MQ=52.11;MQ0=0;NCC=2;QD=24.48;SOR=1.051;set=variant2;CSQ=synonymous_variant|gaA/gaG|E|ENSG00000177504|VCX2|ENST00000317103|3/3|||111/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,24:24:99:906,0 .:0,0:.:.:. chrX 8138165 . C G 745.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=773;MLEAC=1;MLEAF=1;MQ=47.56;MQ0=0;NCC=2;QD=32.96;SOR=2.985;set=variant2;CSQ=missense_variant|Gtg/Ctg|V/L|ENSG00000177504|VCX2|ENST00000317103|3/3|unknown(0)|tolerated_low_confidence(1)|110/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,14:14:99:773,0 .:0,0:.:.:. chrX 8138170 . C G 602.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=630;MLEAC=1;MLEAF=1;MQ=46.47;MQ0=0;NCC=2;QD=33.17;SOR=2.833;set=variant2;CSQ=missense_variant|aGc/aCc|S/T|ENSG00000177504|VCX2|ENST00000317103|3/3|unknown(0)|tolerated_low_confidence(1)|108/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:630,0 .:0,0:.:.:. chrX 8138171 . T C 557.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=585;MLEAC=1;MLEAF=1;MQ=46.47;MQ0=0;NCC=2;QD=28.39;SOR=2.833;set=variant2;CSQ=missense_variant|Agc/Ggc|S/G|ENSG00000177504|VCX2|ENST00000317103|3/3|unknown(0)|deleterious_low_confidence(0.01)|108/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:585,0 .:0,0:.:.:. chrX 8139196 . C T 532.64 my_snp_filter AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=560;MLEAC=1;MLEAF=1;MQ=34.27;MQ0=0;NCC=2;QD=23.16;SOR=0.776;set=FilteredInAll;CSQ=5_prime_UTR_variant|||ENSG00000177504|VCX2|ENST00000317103|1/3|||-/139|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:560,0 .:0,0:.:.:. chrX 8498979 . G A 910.64 PASS AC=1;AF=1;AN=1;DP=36;FS=0;GQ_MEAN=938;MLEAC=1;MLEAF=1;MQ=58.26;MQ0=0;NCC=2;QD=25.3;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000011201|KAL1|ENST00000262648|14/14|||-/680|protein_coding,downstream_gene_variant|||ENSG00000011201|KAL1|ENST00000481896|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,36:36:99:938,0 .:0,0:.:.:. chrX 8503641 . G A 357.64 PASS AC=3;AF=1;AN=3;DP=12;FS=0;GQ_MEAN=128.33;GQ_STDDEV=72.23;MLEAC=3;MLEAF=1;MQ=55.18;MQ0=0;NCC=0;QD=29.8;SOR=3.611;set=variant2;CSQ=synonymous_variant|atC/atT|I|ENSG00000011201|KAL1|ENST00000262648|12/14|||611/680|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000011201|KAL1|ENST00000481896|2/2||||processed_transcript GT:AD:DP:GQ:PL 1:0,6:6:99:207,0 1:0,3:3:65:65,0 1:0,3:3:99:113,0 chrX 8504833 . C T 1136.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=388;GQ_STDDEV=150.84;MLEAC=3;MLEAF=1;MQ=57.99;MQ0=0;NCC=0;QD=32.48;SOR=2.964;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000011201|KAL1|ENST00000481896|1/2||||processed_transcript,missense_variant|Gtt/Att|V/I|ENSG00000011201|KAL1|ENST00000262648|11/14|benign(0.001)|tolerated(1)|534/680|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:557,0 1:0,13:13:99:340,0 1:0,7:7:99:267,0 chrX 9859098 . A G 4711.64 PASS AC=3;AF=1;AN=3;DP=166;FS=0;GQ_MEAN=1579.67;GQ_STDDEV=265.37;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.73;SOR=0.743;set=variant2;CSQ=synonymous_variant|ccA/ccG|P|ENSG00000146950|SHROOM2|ENST00000380913|3/10|||133/1616|protein_coding GT:AD:DP:GQ:PL 1:0,55:55:99:1696,0 1:0,55:55:99:1276,0 1:0,54:54:99:1767,0 chrX 10085674 . T C 377.64 PASS AC=2;AF=1;AN=2;DP=14;FS=0;GQ_MEAN=202.5;GQ_STDDEV=10.61;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.97;SOR=2.303;set=variant2;CSQ=synonymous_variant|gaT/gaC|D|ENSG00000047644|WWC3|ENST00000454666|10/22|||525/1092|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000047644|WWC3|ENST00000380861|11/23|||525/1092|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:210,0 .:0,0:.:.:. 1:0,7:7:99:195,0 chrX 10201780 . A G 525.88 PASS AC=2;AF=0.667;AN=3;DP=15;FS=0;GQ_MEAN=196.33;GQ_STDDEV=184.91;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.83;SOR=2.985;set=variant2;CSQ=downstream_gene_variant|||ENSG00000073464|CLCN4|ENST00000380829||||-/729|protein_coding,3_prime_UTR_variant|||ENSG00000073464|CLCN4|ENST00000380833|13/13|||-/760|protein_coding,downstream_gene_variant|||ENSG00000073464|CLCN4|ENST00000421085||||-/666|protein_coding GT:AD:DP:GQ:PL 1:0,10:10:99:396,0 0:1,0:1:31:0,31 1:0,4:4:99:162,0 chrX 11129475 . A AGGC 937.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=1.18;ClippingRankSum=1.18;DP=29;FS=0;GQ_MEAN=482.5;GQ_STDDEV=454.67;MLEAC=2;MLEAF=1;MQ=58.98;MQ0=0;MQRankSum=1.18;NCC=1;QD=34.73;ReadPosRankSum=1.18;SOR=0.941;set=variant;CSQ=upstream_gene_variant|||ENSG00000234129|RP11-120D5.1|ENST00000608576|||||lincRNA,5_prime_UTR_variant|||ENSG00000004961|HCCS|ENST00000321143|1/7|||-/268|protein_coding,upstream_gene_variant|||ENSG00000234129|RP11-120D5.1|ENST00000608176|||||lincRNA,downstream_gene_variant|||ENSG00000207151|Y_RNA|ENST00000384422|||||misc_RNA,upstream_gene_variant|||ENSG00000234129|RP11-120D5.1|ENST00000433747|||||lincRNA,5_prime_UTR_variant|||ENSG00000004961|HCCS|ENST00000380763|1/7|||-/268|protein_coding,upstream_gene_variant|||ENSG00000234129|RP11-120D5.1|ENST00000608916|||||lincRNA,upstream_gene_variant|||ENSG00000004961|HCCS|ENST00000380762||||-/268|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,18:18:99:804,0 1:2,7:9:99:161,0 chrX 11156292 . A G 856.64 PASS AC=1;AF=1;AN=1;DP=31;FS=0;GQ_MEAN=884;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.63;SOR=1.044;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000047648|ARHGAP6|ENST00000495242|15/15|||-/690|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000047648|ARHGAP6|ENST00000303025|13/13|||-/771|protein_coding,3_prime_UTR_variant|||ENSG00000047648|ARHGAP6|ENST00000337414|13/13|||-/974|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000047648|ARHGAP6|ENST00000489330|14/14||||retained_intron,intron_variant|||ENSG00000047648|ARHGAP6|ENST00000534860||||-/604|protein_coding,3_prime_UTR_variant|||ENSG00000047648|ARHGAP6|ENST00000380736|13/13|||-/771|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:884,0 .:0,0:.:.:. chrX 11157535 . G C 2206.64 PASS AC=3;AF=1;AN=3;DP=70;FS=0;GQ_MEAN=744.67;GQ_STDDEV=232.71;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.52;SOR=1.011;set=variant2;CSQ=downstream_gene_variant|||ENSG00000047648|ARHGAP6|ENST00000380717||||-/601|protein_coding,downstream_gene_variant|||ENSG00000047648|ARHGAP6|ENST00000380718||||-/765|protein_coding,downstream_gene_variant|||ENSG00000047648|ARHGAP6|ENST00000413512||||-/467|protein_coding,missense_variant|gaC/gaG|D/E|ENSG00000047648|ARHGAP6|ENST00000380736|13/13|benign(0.027)|tolerated_low_confidence(0.34)|588/771|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000047648|ARHGAP6|ENST00000489330|14/14||||retained_intron,intron_variant|||ENSG00000047648|ARHGAP6|ENST00000534860||||-/604|protein_coding,missense_variant|gaC/gaG|D/E|ENSG00000047648|ARHGAP6|ENST00000337414|13/13|benign(0.027)|tolerated_low_confidence(0.37)|791/974|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000047648|ARHGAP6|ENST00000495242|15/15|||-/690|nonsense_mediated_decay,missense_variant|gaC/gaG|D/E|ENSG00000047648|ARHGAP6|ENST00000303025|13/13|benign(0.027)|tolerated_low_confidence(0.34)|588/771|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:858,0 1:0,18:18:99:477,0 1:0,27:27:99:899,0 chrX 12739294 . A G 4461.87 PASS AC=2;AF=0.667;AN=3;DP=135;FS=0;GQ_MEAN=1536;GQ_STDDEV=1240.35;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.32;SOR=0.892;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000169933|FRMPD4|ENST00000380682|17/17|||-/1322|protein_coding GT:AD:DP:GQ:PL 1:0,61:61:99:2099,0 0:5,0:5:99:0,114 1:0,69:69:99:2395,0 chrX 12740118 . T C 290.87 PASS AC=2;AF=0.667;AN=3;DP=11;FS=0;GQ_MEAN=144;GQ_STDDEV=88.83;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=25.73;SOR=4.407;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000169933|FRMPD4|ENST00000380682|17/17|||-/1322|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:78:78,0 0:3,0:3:99:0,109 1:0,6:6:99:245,0 chrX 12809661 . G A 2441.64 PASS AC=3;AF=1;AN=3;DP=98;FS=0;GQ_MEAN=823;GQ_STDDEV=285.51;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=25.7;SOR=0.714;set=variant2;CSQ=synonymous_variant|ctG/ctA|L|ENSG00000101911|PRPS2|ENST00000398491|1/7|||15/321|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000101911|PRPS2|ENST00000380663|1/4|||15/147|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000101911|PRPS2|ENST00000380668|1/7|||15/318|protein_coding,synonymous_variant|ctG/ctA|L|ENSG00000101911|PRPS2|ENST00000489404|1/4|||15/200|protein_coding GT:AD:DP:GQ:PL 1:0,37:37:99:1067,0 1:0,43:43:99:893,0 1:0,15:15:99:509,0 chrX 12924826 . A G 311.87 PASS AC=1;AF=0.333;AN=3;DP=20;FS=0;GQ_MEAN=188.33;GQ_STDDEV=134.83;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=22.28;SOR=0.976;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000233338|TLR8-AS1|ENST00000451564|||||antisense,start_lost&splice_region_variant|Atg/Gtg|M/V|ENSG00000101916|TLR8|ENST00000218032|1/2|benign(0)|tolerated_low_confidence(0.32)|1/1041|protein_coding,splice_region_variant&5_prime_UTR_variant|||ENSG00000101916|TLR8|ENST00000311912|1/3|||-/1059|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,108 1:0,14:14:99:344,0 0:3,0:3:99:0,113 chrX 12939928 . T C 2494.64 PASS AC=3;AF=1;AN=3;DP=75;FS=0;GQ_MEAN=840.67;GQ_STDDEV=588.21;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.26;SOR=1.091;set=variant2;CSQ=synonymous_variant|gaT/gaC|D|ENSG00000101916|TLR8|ENST00000218032|2/2|||923/1041|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000101916|TLR8|ENST00000311912|3/3|||941/1059|protein_coding GT:AD:DP:GQ:PL 1:0,40:40:99:1301,0 1:0,5:5:99:178,0 1:0,30:30:99:1043,0 chrX 12993286 . C T 386.87 PASS AC=1;AF=0.333;AN=3;DP=25;FS=0;GQ_MEAN=219.33;GQ_STDDEV=173.61;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=21.49;SOR=0.914;set=variant2;CSQ=upstream_gene_variant|||ENSG00000205542|TMSB4X|ENST00000380633||||-/44|protein_coding,splice_region_variant&5_prime_UTR_variant|||ENSG00000205542|TMSB4X|ENST00000451311|1/3|||-/44|protein_coding,upstream_gene_variant|||ENSG00000205542|TMSB4X|ENST00000380635||||-/44|protein_coding,5_prime_UTR_variant|||ENSG00000205542|TMSB4X|ENST00000380636|1/2|||-/44|protein_coding GT:AD:DP:GQ:PL 0:4,0:4:99:0,135 1:0,18:18:99:419,0 0:3,0:3:99:0,104 chrX 13062722 . C T 246.63 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;GQ_MEAN=156.5;GQ_STDDEV=170.41;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=22.42;SOR=0.859;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000187268|FAM9C|ENST00000380625|1/8|||-/166|protein_coding,upstream_gene_variant|||ENSG00000187268|FAM9C|ENST00000438997||||-/126|protein_coding,upstream_gene_variant|||ENSG00000187268|FAM9C|ENST00000333995||||-/166|protein_coding,5_prime_UTR_variant|||ENSG00000187268|FAM9C|ENST00000542843|1/6|||-/128|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000187268|FAM9C|ENST00000468287|1/7||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:277,0 0:1,0:1:36:0,36 chrX 13337115 . C T 36.87 PASS AC=1;AF=0.333;AN=3;DP=9;FS=0;GQ_MEAN=94.67;GQ_STDDEV=22.28;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=12.29;SOR=1.179;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000231216|GS1-600G8.3|ENST00000431486|||||antisense,synonymous_variant|agG/agA|R|ENSG00000123594|ATXN3L|ENST00000380622|1/1|||313/355|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,106 1:0,3:3:69:69,0 0:3,0:3:99:0,109 chrX 13587829 . T G 378.87 PASS AC=2;AF=0.667;AN=3;DP=18;FS=0;GQ_MEAN=190.33;GQ_STDDEV=87.53;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.57;SOR=1.981;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000198759|EGFL6|ENST00000361306|1/12|||-/553|protein_coding,5_prime_UTR_variant|||ENSG00000198759|EGFL6|ENST00000380602|1/12|||-/554|protein_coding GT:AD:DP:GQ:PL 1:0,4:4:99:122,0 0:6,0:6:99:0,160 1:0,8:8:99:289,0 chrX 13681115 . C T 2183.87 PASS AC=2;AF=0.667;AN=3;DP=66;FS=0;GQ_MEAN=774;GQ_STDDEV=578.59;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.32;SOR=1.329;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000176896|TCEANC|ENST00000490617|3/3||||processed_transcript,missense_variant|tCg/tTg|S/L|ENSG00000176896|TCEANC|ENST00000545566|5/5|benign(0.173)|tolerated(0.07)|163/351|protein_coding,missense_variant|tCg/tTg|S/L|ENSG00000176896|TCEANC|ENST00000314720|4/4|benign(0.324)|tolerated(0.05)|193/381|protein_coding,upstream_gene_variant|||ENSG00000176896|TCEANC|ENST00000463321|||||processed_transcript,missense_variant|tCg/tTg|S/L|ENSG00000176896|TCEANC|ENST00000380600|2/2|benign(0.173)|tolerated(0.07)|163/351|protein_coding,missense_variant&NMD_transcript_variant|tCg/tTg|S/L|ENSG00000176896|TCEANC|ENST00000467590|1/5|benign(0.401)|deleterious(0.03)|85/272|nonsense_mediated_decay,missense_variant|tCg/tTg|S/L|ENSG00000176896|TCEANC|ENST00000544987|3/3|benign(0.173)|tolerated(0.07)|163/351|protein_coding GT:AD:DP:GQ:PL 1:0,31:31:99:1118,0 0:4,0:4:99:0,106 1:0,31:31:99:1098,0 chrX 13681638 . C T 1177.87 PASS AC=2;AF=0.667;AN=3;DP=36;FS=0;GQ_MEAN=439.67;GQ_STDDEV=300.18;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=25.86;SOR=1.681;set=variant2;CSQ=synonymous_variant|aaC/aaT|N|ENSG00000176896|TCEANC|ENST00000314720|4/4|||367/381|protein_coding,synonymous_variant|aaC/aaT|N|ENSG00000176896|TCEANC|ENST00000545566|5/5|||337/351|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000176896|TCEANC|ENST00000490617|3/3||||processed_transcript,synonymous_variant|aaC/aaT|N|ENSG00000176896|TCEANC|ENST00000380600|2/2|||337/351|protein_coding,synonymous_variant&NMD_transcript_variant|aaC/aaT|N|ENSG00000176896|TCEANC|ENST00000467590|1/5|||259/272|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000176896|TCEANC|ENST00000463321|||||processed_transcript,synonymous_variant|aaC/aaT|N|ENSG00000176896|TCEANC|ENST00000544987|3/3|||337/351|protein_coding GT:AD:DP:GQ:PL 1:0,13:13:99:515,0 0:4,0:4:99:0,109 1:0,19:19:99:695,0 chrX 13681679 . G T 929.87 PASS AC=2;AF=0.667;AN=3;DP=29;FS=0;GQ_MEAN=357;GQ_STDDEV=214.83;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=27.29;SOR=1.136;set=variant2;CSQ=upstream_gene_variant|||ENSG00000176896|TCEANC|ENST00000463321|||||processed_transcript,missense_variant|tGg/tTg|W/L|ENSG00000176896|TCEANC|ENST00000380600|2/2|benign(0)|tolerated_low_confidence(0.16)|351/351|protein_coding,stop_lost&splice_region_variant&NMD_transcript_variant|tGa/tTa|*/L|ENSG00000176896|TCEANC|ENST00000467590|1/5|||273/272|nonsense_mediated_decay,missense_variant|tGg/tTg|W/L|ENSG00000176896|TCEANC|ENST00000544987|3/3|benign(0)|tolerated_low_confidence(0.16)|351/351|protein_coding,missense_variant|tGg/tTg|W/L|ENSG00000176896|TCEANC|ENST00000545566|5/5|benign(0)|tolerated_low_confidence(0.16)|351/351|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000176896|TCEANC|ENST00000490617|3/3||||processed_transcript,missense_variant|tGg/tTg|W/L|ENSG00000176896|TCEANC|ENST00000314720|4/4|benign(0)|tolerated_low_confidence(0.17)|381/381|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:476,0 0:4,0:4:99:0,109 1:0,13:13:99:486,0 chrX 13730787 . G C 362.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=390;MLEAC=1;MLEAF=1;MQ=57.85;MQ0=0;NCC=2;QD=25.9;SOR=1.329;set=variant2;CSQ=downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000380578|||||retained_intron,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000458511||||-/174|protein_coding,3_prime_UTR_variant|||ENSG00000196459|TRAPPC2|ENST00000359680|5/5|||-/140|protein_coding,downstream_gene_variant|||ENSG00000123595|RAB9A|ENST00000464506||||-/201|protein_coding,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000519885||||-/113|protein_coding,3_prime_UTR_variant|||ENSG00000196459|TRAPPC2|ENST00000453655|6/6|||-/147|protein_coding,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000517553|||||retained_intron,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000519382|||||retained_intron,3_prime_UTR_variant|||ENSG00000196459|TRAPPC2|ENST00000358231|6/6|||-/140|protein_coding,3_prime_UTR_variant|||ENSG00000196459|TRAPPC2|ENST00000380579|6/6|||-/140|protein_coding,downstream_gene_variant|||ENSG00000123595|RAB9A|ENST00000243325|||||processed_transcript,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000518847||||-/74|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,14:14:99:390,0 .:0,0:.:.:. chrX 13734539 . T C 1342.64 PASS AC=3;AF=1;AN=3;DP=40;FS=0;GQ_MEAN=456.67;GQ_STDDEV=206.98;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.57;SOR=2.419;set=variant2;CSQ=intron_variant|||ENSG00000196459|TRAPPC2|ENST00000358231||||-/140|protein_coding,intron_variant|||ENSG00000196459|TRAPPC2|ENST00000380579||||-/140|protein_coding,downstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000518847||||-/74|protein_coding,intron_variant|||ENSG00000196459|TRAPPC2|ENST00000453655||||-/147|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000196459|TRAPPC2|ENST00000517553|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000196459|TRAPPC2|ENST00000519382|4/4||||retained_intron,intron_variant|||ENSG00000196459|TRAPPC2|ENST00000359680||||-/140|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000196459|TRAPPC2|ENST00000380578|||||retained_intron,intron_variant|||ENSG00000196459|TRAPPC2|ENST00000458511||||-/174|protein_coding,intron_variant|||ENSG00000196459|TRAPPC2|ENST00000519885||||-/113|protein_coding GT:AD:DP:GQ:PL 1:0,17:17:99:587,0 1:0,7:7:99:218,0 1:0,16:16:99:565,0 chrX 13752895 . G T 39.63 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;GQ_MEAN=91;GQ_STDDEV=29.7;MLEAC=1;MLEAF=0.5;MQ=46.52;MQ0=0;NCC=1;QD=19.82;SOR=2.303;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000046651|OFD1|ENST00000398395|1/11|||-/367|protein_coding,upstream_gene_variant|||ENSG00000046651|OFD1|ENST00000466534|||||processed_transcript,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000519885||||-/113|protein_coding,5_prime_UTR_variant|||ENSG00000046651|OFD1|ENST00000340096|1/23|||-/1012|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000359680||||-/140|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000458511||||-/174|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000046651|OFD1|ENST00000490265|1/23||||processed_transcript,5_prime_UTR_variant|||ENSG00000046651|OFD1|ENST00000380550|1/22|||-/972|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000518847||||-/74|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000380579||||-/140|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000358231||||-/140|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000519382|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000046651|OFD1|ENST00000485052|1/4||||processed_transcript,5_prime_UTR_variant|||ENSG00000046651|OFD1|ENST00000380567|1/24|||-/872|protein_coding,upstream_gene_variant|||ENSG00000196459|TRAPPC2|ENST00000453655||||-/147|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:70:70,0 0:4,0:4:99:0,112 .:0,0:.:.:. chrX 13835096 . T C 308.87 PASS AC=1;AF=0.333;AN=3;DP=21;FS=0;GQ_MEAN=190.33;GQ_STDDEV=130.58;MLEAC=1;MLEAF=0.333;MQ=59.87;MQ0=0;NCC=0;QD=22.06;SOR=2.303;set=variant2;CSQ=intron_variant|||ENSG00000046653|GPM6B|ENST00000493085||||-/94|protein_coding,intron_variant|||ENSG00000046653|GPM6B|ENST00000454189||||-/246|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000355135|1/8|||-/305|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000493677|1/9|||-/302|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000475307|2/4|||-/107|protein_coding,intron_variant|||ENSG00000046653|GPM6B|ENST00000398361||||-/179|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000316715|1/8|||-/328|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000356942|1/7|||-/265|protein_coding,intron_variant|||ENSG00000046653|GPM6B|ENST00000468080||||-/76|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,120 1:0,14:14:99:341,0 0:3,0:3:99:0,110 chrX 13956661 . CG C 242.63 PASS AC=1;AF=0.5;AN=2;DP=12;FS=0;GQ_MEAN=204;GQ_STDDEV=97.58;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=30.33;SOR=1.863;set=variant;CSQ=upstream_gene_variant|||ENSG00000046653|GPM6B|ENST00000398361||||-/179|protein_coding,5_prime_UTR_variant|||ENSG00000046653|GPM6B|ENST00000454189|1/7|||-/246|protein_coding GT:AD:DP:GQ:PL 1:0,8:8:99:273,0 0:4,0:4:99:0,135 .:0,0:.:.:. chrX 14627144 . T C 87.87 PASS AC=1;AF=0.333;AN=3;DP=13;FS=0;GQ_MEAN=122.33;GQ_STDDEV=11.68;MLEAC=1;MLEAF=0.333;MQ=57.97;MQ0=0;NCC=0;QD=21.97;SOR=3.258;set=variant2;CSQ=synonymous_variant|caT/caC|H|ENSG00000101958|GLRA2|ENST00000355020|7/9|||249/452|protein_coding,downstream_gene_variant|||ENSG00000101958|GLRA2|ENST00000415367||||-/215|protein_coding,synonymous_variant|caT/caC|H|ENSG00000101958|GLRA2|ENST00000443437|9/11|||160/363|protein_coding,synonymous_variant|caT/caC|H|ENSG00000101958|GLRA2|ENST00000218075|7/9|||249/452|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,112 1:0,4:4:99:120,0 0:5,0:5:99:0,135 chrX 14749604 . T C 60.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=88;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.21;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101958|GLRA2|ENST00000355020||||-/452|protein_coding,3_prime_UTR_variant|||ENSG00000101958|GLRA2|ENST00000443437|11/11|||-/363|protein_coding,3_prime_UTR_variant|||ENSG00000101958|GLRA2|ENST00000218075|9/9|||-/452|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:88:88,0 .:0,0:.:.:. chrX 14887147 . C G 503.64 PASS AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=531;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.51;SOR=1.292;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130150|MOSPD2|ENST00000380492||||-/518|protein_coding,upstream_gene_variant|||ENSG00000130150|MOSPD2|ENST00000482354||||-/486|protein_coding,5_prime_UTR_variant|||ENSG00000181544|FANCB|ENST00000452869|2/10|||-/818|protein_coding,intron_variant|||ENSG00000181544|FANCB|ENST00000324138||||-/859|protein_coding,upstream_gene_variant|||ENSG00000130150|MOSPD2|ENST00000461777|||||retained_intron,upstream_gene_variant|||ENSG00000130150|MOSPD2|ENST00000497603||||-/39|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000181544|FANCB|ENST00000489126|1/2||||retained_intron,5_prime_UTR_variant|||ENSG00000181544|FANCB|ENST00000398334|2/10|||-/859|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:531,0 .:0,0:.:.:. chrX 15262372 . T A 181.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=209;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.95;SOR=2.584;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380483|7/7|||-/252|protein_coding,downstream_gene_variant|||ENSG00000102048|ASB9|ENST00000473862|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380485|7/7|||-/262|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000546332|8/8|||-/262|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380488|7/7|||-/294|protein_coding,intron_variant|||ENSG00000102048|ASB9|ENST00000477346||||-/211|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:209,0 .:0,0:.:.:. chrX 15262432 . A C 1225.64 PASS AC=3;AF=1;AN=3;DP=41;FS=0;GQ_MEAN=417.67;GQ_STDDEV=390.17;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.64;SOR=2.191;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380485|7/7|||-/262|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102048|ASB9|ENST00000473862|7/7||||processed_transcript,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380483|7/7|||-/252|protein_coding,intron_variant|||ENSG00000102048|ASB9|ENST00000477346||||-/211|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380488|7/7|||-/294|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000546332|8/8|||-/262|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:232,0 1:0,30:30:99:866,0 1:0,4:4:99:155,0 chrX 15266819 . C T 1686.87 PASS AC=2;AF=0.667;AN=3;DP=48;FS=0;GQ_MEAN=584.33;GQ_STDDEV=480.06;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.85;SOR=3.306;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102048|ASB9|ENST00000484017|||||processed_transcript,intron_variant|||ENSG00000102048|ASB9|ENST00000380488||||-/294|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380485|6/7|||-/262|protein_coding,downstream_gene_variant|||ENSG00000102048|ASB9|ENST00000481384|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380483|6/7|||-/252|protein_coding,downstream_gene_variant|||ENSG00000102048|ASB9|ENST00000470015|||||processed_transcript,intron_variant|||ENSG00000102048|ASB9|ENST00000477346||||-/211|protein_coding,3_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000546332|7/8|||-/262|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102048|ASB9|ENST00000473862|||||processed_transcript GT:AD:DP:GQ:PL 1:0,24:24:99:917,0 0:1,0:1:34:0,34 1:0,23:23:99:802,0 chrX 15288193 . T C 494.64 PASS AC=2;AF=1;AN=2;DP=15;FS=0;GQ_MEAN=261;GQ_STDDEV=175.36;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.98;SOR=5.549;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102048|ASB9|ENST00000473862|||||processed_transcript,upstream_gene_variant|||ENSG00000102048|ASB9|ENST00000380485||||-/262|protein_coding,upstream_gene_variant|||ENSG00000102048|ASB9|ENST00000380483||||-/252|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102048|ASB9|ENST00000470015|||||processed_transcript,intron_variant|||ENSG00000102048|ASB9|ENST00000546332||||-/262|protein_coding,5_prime_UTR_variant|||ENSG00000102048|ASB9|ENST00000380488|1/7|||-/294|protein_coding GT:AD:DP:GQ:PL 1:0,11:11:99:385,0 .:0,0:.:.:. 1:0,4:4:99:137,0 chrX 15332558 . A G 1912.87 PASS AC=2;AF=0.667;AN=3;DP=57;FS=0;GQ_MEAN=688.67;GQ_STDDEV=491.62;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=27.39;SOR=0.853;set=variant2;CSQ=intron_variant|||ENSG00000165192|ASB11|ENST00000380470||||-/306|protein_coding,synonymous_variant|cgT/cgC|R|ENSG00000165192|ASB11|ENST00000344384|1/7|||17/302|protein_coding,intron_variant|||ENSG00000165192|ASB11|ENST00000480796||||-/323|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000165192|ASB11|ENST00000485437||||-/224|nonsense_mediated_decay,synonymous_variant|cgT/cgC|R|ENSG00000165192|ASB11|ENST00000537676|1/8|||17/302|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:974,0 0:5,0:5:99:0,121 1:0,27:27:99:971,0 chrX 15415583 . C T 1519.64 PASS AC=3;AF=1;AN=3;DP=48;FS=0;GQ_MEAN=515.67;GQ_STDDEV=71.5;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.66;SOR=0.963;set=variant2;CSQ=synonymous_variant|caG/caA|Q|ENSG00000087842|PIR|ENST00000380420|8/10|||227/290|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000087842|PIR|ENST00000484433|2/3||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000087842|PIR|ENST00000492432|2/4||||processed_transcript,synonymous_variant|caG/caA|Q|ENSG00000087842|PIR|ENST00000380421|8/10|||227/290|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:567,0 1:0,17:17:99:434,0 1:0,16:16:99:546,0 chrX 15706830 . C A 84.63 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;GQ_MEAN=120;GQ_STDDEV=7.07;MLEAC=1;MLEAF=0.5;MQ=47.61;MQ0=0;NCC=1;QD=28.21;SOR=2.833;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000380334|2/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000380336|2/4||||processed_transcript,upstream_gene_variant|||ENSG00000169239|CA5B|ENST00000498004||||-/76|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000435806|2/5||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000448692|3/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000380333|2/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186312|CA5BP1|ENST00000380331|3/5||||processed_transcript GT:AD:DP:GQ:PL 1:0,3:3:99:115,0 0:4,0:4:99:0,125 .:0,0:.:.:. chrX 15800751 . G A 2185.87 PASS AC=2;AF=0.667;AN=3;DP=72;FS=0;GQ_MEAN=784.67;GQ_STDDEV=565.86;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.62;SOR=0.723;set=variant2;CSQ=synonymous_variant|gcG/gcA|A|ENSG00000169239|CA5B|ENST00000318636|8/8|||306/317|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000169239|CA5B|ENST00000454127|7/8|||306/317|protein_coding GT:AD:DP:GQ:PL 1:0,32:32:99:1041,0 0:5,0:5:99:0,136 1:0,35:35:99:1177,0 chrX 15801330 . A C 83.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=111;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.88;SOR=2.833;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000169239|CA5B|ENST00000454127|7/8|||-/317|protein_coding,3_prime_UTR_variant|||ENSG00000169239|CA5B|ENST00000318636|8/8|||-/317|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:99:111,0 .:0,0:.:.:. chrX 15802800 . C G 68.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=96;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=17.16;SOR=1.609;set=variant2;CSQ=downstream_gene_variant|||ENSG00000169239|CA5B|ENST00000454127||||-/317|protein_coding,3_prime_UTR_variant|||ENSG00000169239|CA5B|ENST00000318636|8/8|||-/317|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:96:96,0 .:0,0:.:.:. chrX 15838366 . C T 2372.64 PASS AC=3;AF=1;AN=3;DP=81;FS=0;GQ_MEAN=800;GQ_STDDEV=224.72;MLEAC=3;MLEAF=1;MQ=57.98;MQ0=0;NCC=0;QD=29.29;SOR=1.124;set=variant2;CSQ=synonymous_variant|aaC/aaT|N|ENSG00000169249|ZRSR2|ENST00000307771|10/11|||288/482|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:832,0 1:0,41:41:99:1007,0 1:0,16:16:99:561,0 chrX 16171381 . T A 645.64 PASS AC=1;AF=1;AN=1;DP=22;FS=0;GQ_MEAN=673;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=32.28;SOR=0.892;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000435789|6/6||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000422438|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000454712|4/4||||antisense,downstream_gene_variant|||ENSG00000126010|GRPR|ENST00000380289||||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:673,0 .:0,0:.:.:. chrX 16171382 . T A 795.64 PASS AC=1;AF=1;AN=1;DP=22;FS=0;GQ_MEAN=823;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=30.63;SOR=0.892;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000435789|6/6||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000454712|4/4||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000422438|||||antisense,downstream_gene_variant|||ENSG00000126010|GRPR|ENST00000380289||||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20,0:20:99:823,0 .:0,0:.:.:. chrX 16171594 . GA G 658.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.844;ClippingRankSum=-0.683;DP=32;FS=0;GQ_MEAN=686;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.086;NCC=2;QD=21.25;ReadPosRankSum=-0.121;SOR=0.906;set=variant;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000454712|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000422438|||||antisense,downstream_gene_variant|||ENSG00000126010|GRPR|ENST00000380289||||-/384|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000238178|RP11-431J24.2|ENST00000435789|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,29:31:99:686,0 .:0,0:.:.:. chrX 16859628 . G A 535.87 PASS AC=1;AF=0.333;AN=3;DP=30;FS=0;GQ_MEAN=262;GQ_STDDEV=265.05;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=22.33;SOR=1.051;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000086712|TXLNG|ENST00000485153|2/2||||processed_transcript,synonymous_variant|caG/caA|Q|ENSG00000086712|TXLNG|ENST00000380122|10/10|||442/528|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000481586|||||retained_intron,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000404022||||-/416|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000380087||||-/425|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000330735|||||retained_intron,synonymous_variant|caG/caA|Q|ENSG00000086712|TXLNG|ENST00000398155|8/8|||310/396|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000465244|||||retained_intron,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000380084||||-/469|protein_coding,intron_variant|||ENSG00000102054|RBBP7|ENST00000425696||||-/85|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,114 1:0,24:24:99:568,0 0:3,0:3:99:0,104 chrX 16860134 . T C 1250.64 PASS AC=1;AF=1;AN=1;DP=48;FS=0;GQ_MEAN=1278;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.06;SOR=0.776;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000404022||||-/416|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000481586|||||retained_intron,3_prime_UTR_variant|||ENSG00000086712|TXLNG|ENST00000380122|10/10|||-/528|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000086712|TXLNG|ENST00000485153|2/2||||processed_transcript,3_prime_UTR_variant|||ENSG00000086712|TXLNG|ENST00000398155|8/8|||-/396|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000380084||||-/469|protein_coding,intron_variant|||ENSG00000102054|RBBP7|ENST00000425696||||-/85|protein_coding,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000465244|||||retained_intron,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000330735|||||retained_intron,downstream_gene_variant|||ENSG00000102054|RBBP7|ENST00000380087||||-/425|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,48:48:99:1278,0 .:0,0:.:.:. chrX 17166219 . C T 544.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=572;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.68;SOR=0.776;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000169891|REPS2|ENST00000303843|18/18|||-/659|protein_coding,downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000470686|||||retained_intron,downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000380064||||-/459|protein_coding,3_prime_UTR_variant|||ENSG00000169891|REPS2|ENST00000357277|18/18|||-/660|protein_coding,downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000469714|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:572,0 .:0,0:.:.:. chrX 17166795 . A G 718.64 PASS AC=3;AF=1;AN=3;DP=28;FS=0;GQ_MEAN=248.67;GQ_STDDEV=219.42;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=25.67;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000469714|||||processed_transcript,3_prime_UTR_variant|||ENSG00000169891|REPS2|ENST00000303843|18/18|||-/659|protein_coding,downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000380064||||-/459|protein_coding,downstream_gene_variant|||ENSG00000169891|REPS2|ENST00000470686|||||retained_intron,3_prime_UTR_variant|||ENSG00000169891|REPS2|ENST00000357277|18/18|||-/660|protein_coding GT:AD:DP:GQ:PL 1:0,5:5:99:163,0 1:0,20:20:99:498,0 1:0,3:3:85:85,0 chrX 17753436 . A T 255.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=283;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.24;SOR=2.494;set=variant2;CSQ=upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000398080||||-/208|protein_coding,upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000419185||||-/147|protein_coding,upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000380041||||-/329|protein_coding,upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000427362|||||retained_intron,upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000380045||||-/208|protein_coding,3_prime_UTR_variant|||ENSG00000188158|NHS|ENST00000380060|8/8|||-/1630|protein_coding,3_prime_UTR_variant|||ENSG00000188158|NHS|ENST00000398097|9/9|||-/1474|protein_coding,upstream_gene_variant|||ENSG00000047634|SCML1|ENST00000380043||||-/302|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:283,0 .:0,0:.:.:. chrX 17819377 . T C 1993.64 PASS AC=3;AF=1;AN=3;DP=59;FS=0;GQ_MEAN=673.67;GQ_STDDEV=583.62;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.79;SOR=0.95;set=variant2;CSQ=missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000451717|2/2|unknown(0)|tolerated(1)|252/530|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000545871|3/3|unknown(0)|tolerated(1)|252/530|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000331511|3/3|unknown(0)|tolerated(1)|252/530|protein_coding,downstream_gene_variant|||ENSG00000131831|RAI2|ENST00000509491||||-/81|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000360011|3/3|unknown(0)|tolerated(1)|252/530|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000131831|RAI2|ENST00000415486|3/3|unknown(0)|tolerated(1)|202/480|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1205,0 1:0,2:2:49:49,0 1:0,21:21:99:767,0 chrX 18659184 . G A 613.64 PASS AC=1;AF=1;AN=1;DP=28;FS=0;GQ_MEAN=641;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.6;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102104|RS1|ENST00000379984|6/6|||-/224|protein_coding,downstream_gene_variant|||ENSG00000102104|RS1|ENST00000476595|||||processed_transcript,intron_variant|||ENSG00000008086|CDKL5|ENST00000379989||||-/1030|protein_coding,intron_variant|||ENSG00000008086|CDKL5|ENST00000379996||||-/1030|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:641,0 .:0,0:.:.:. chrX 19482476 . C T 2477.64 PASS AC=3;AF=1;AN=3;DP=85;FS=0;GQ_MEAN=835;GQ_STDDEV=156.98;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.15;SOR=1.101;set=variant2;CSQ=missense_variant|Gct/Act|A/T|ENSG00000180815|MAP3K15|ENST00000469203|2/27|possibly_damaging(0.687)|deleterious(0.02)|24/1145|protein_coding,upstream_gene_variant|||ENSG00000180815|MAP3K15|ENST00000359173||||-/748|protein_coding,missense_variant|Gct/Act|A/T|ENSG00000180815|MAP3K15|ENST00000338883|4/29|possibly_damaging(0.687)|deleterious(0.02)|192/1313|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000180815|MAP3K15|ENST00000518578|3/30||||processed_transcript GT:AD:DP:GQ:PL 1:0,27:27:99:917,0 1:0,28:28:99:654,0 1:0,30:30:99:934,0 chrX 21861434 . A G 2456.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.347;ClippingRankSum=0.924;DP=74;FS=5.502;GQ_MEAN=828;GQ_STDDEV=705.82;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.04;NCC=0;QD=33.65;ReadPosRankSum=0.809;SOR=1.89;set=variant2;CSQ=splice_region_variant&synonymous_variant|caA/caG|Q|ENSG00000012174|MBTPS2|ENST00000379484|2/11|||74/519|protein_coding,splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000012174|MBTPS2|ENST00000465888|2/6||||processed_transcript,splice_region_variant&synonymous_variant|caA/caG|Q|ENSG00000012174|MBTPS2|ENST00000365779|2/7|||74/330|protein_coding GT:AD:DP:GQ:PL 1:1,29:30:99:1010,0 1:0,2:2:49:49,0 1:0,41:41:99:1425,0 chrX 21901903 . G A 634.64 PASS AC=1;AF=1;AN=1;DP=28;FS=0;GQ_MEAN=662;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.67;SOR=0.836;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000012174|MBTPS2|ENST00000379484|11/11|||-/519|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,28:28:99:662,0 .:0,0:.:.:. chrX 21958851 . A G 142.64 PASS AC=1;AF=1;AN=1;DP=9;FS=0;GQ_MEAN=170;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.77;SOR=1.329;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102172|SMS|ENST00000457085||||-/311|protein_coding,upstream_gene_variant|||ENSG00000102172|SMS|ENST00000478094|||||processed_transcript,5_prime_UTR_variant|||ENSG00000102172|SMS|ENST00000379404|1/9|||-/313|protein_coding,5_prime_UTR_variant|||ENSG00000102172|SMS|ENST00000404933|1/11|||-/366|protein_coding,downstream_gene_variant|||ENSG00000271286|LL0XNC01-39B3.1|ENST00000603134|||||processed_pseudogene,upstream_gene_variant|||ENSG00000102172|SMS|ENST00000415881||||-/275|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:170,0 .:0,0:.:.:. .:0,0:.:.:. chrX 22012912 . TA T 956.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-1.288;ClippingRankSum=0.578;DP=40;FS=0;GQ_MEAN=984;MLEAC=1;MLEAF=1;MQ=58;MQ0=0;MQRankSum=-1.2;NCC=2;QD=24.53;ReadPosRankSum=0.489;SOR=0.527;set=variant;CSQ=intron_variant|||ENSG00000102172|SMS|ENST00000415881||||-/275|protein_coding,3_prime_UTR_variant|||ENSG00000102172|SMS|ENST00000404933|11/11|||-/366|protein_coding,downstream_gene_variant|||ENSG00000102172|SMS|ENST00000379404||||-/313|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,38:39:99:984,0 .:0,0:.:.:. chrX 22051034 . A G 3886.64 PASS AC=3;AF=1;AN=3;DP=116;FS=0;GQ_MEAN=1304.67;GQ_STDDEV=850.1;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.51;SOR=1.692;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000102174|PHEX|ENST00000379374|1/22|||-/749|protein_coding,5_prime_UTR_variant|||ENSG00000102174|PHEX|ENST00000537599|1/21|||-/695|protein_coding GT:AD:DP:GQ:PL 1:0,52:52:99:1848,0 1:0,12:12:99:325,0 1:0,52:52:99:1741,0 chrX 22051091 . C T 4284.64 PASS AC=3;AF=1;AN=3;DP=140;FS=0;GQ_MEAN=1437.33;GQ_STDDEV=856.14;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.82;SOR=0.797;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000102174|PHEX|ENST00000537599|1/21|||-/695|protein_coding,5_prime_UTR_variant|||ENSG00000102174|PHEX|ENST00000379374|1/22|||-/749|protein_coding GT:AD:DP:GQ:PL 1:0,57:57:99:1888,0 1:0,20:20:99:450,0 1:0,62:62:99:1974,0 chrX 23412685 . T C 101.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=129;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.33;SOR=1.022;set=variant2;CSQ=downstream_gene_variant|||ENSG00000165186|PTCHD1|ENST00000456522||||-/103|protein_coding,3_prime_UTR_variant|||ENSG00000165186|PTCHD1|ENST00000379361|3/3|||-/888|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:129,0 .:0,0:.:.:. chrX 23412936 . T C 220.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=248;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.52;SOR=0.941;set=variant2;CSQ=downstream_gene_variant|||ENSG00000165186|PTCHD1|ENST00000456522||||-/103|protein_coding,3_prime_UTR_variant|||ENSG00000165186|PTCHD1|ENST00000379361|3/3|||-/888|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:248,0 .:0,0:.:.:. chrX 23928489 . C T 1709.64 PASS AC=3;AF=1;AN=3;DP=63;FS=0;GQ_MEAN=579;GQ_STDDEV=315.92;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.57;SOR=0.693;set=variant2;CSQ=upstream_gene_variant|||ENSG00000184831|APOO|ENST00000379220||||-/179|protein_coding,missense_variant|Cgc/Tgc|R/C|ENSG00000165182|CXorf58|ENST00000379211|2/9|benign(0.008)|tolerated_low_confidence(0.19)|24/332|protein_coding,upstream_gene_variant|||ENSG00000165182|CXorf58|ENST00000435707||||-/126|protein_coding,upstream_gene_variant|||ENSG00000184831|APOO|ENST00000379226||||-/198|protein_coding,upstream_gene_variant|||ENSG00000184831|APOO|ENST00000490078||||-/114|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,10:10:99:359,0 1:0,38:38:99:941,0 1:0,14:14:99:437,0 chrX 24073761 . C T 1691.64 PASS AC=3;AF=1;AN=3;DP=57;FS=0;GQ_MEAN=573;GQ_STDDEV=284.88;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.68;SOR=1.047;set=variant2;CSQ=synonymous_variant|caC/caT|H|ENSG00000130741|EIF2S3|ENST00000423068|2/5|||33/183|protein_coding,synonymous_variant|caC/caT|H|ENSG00000130741|EIF2S3|ENST00000253039|2/12|||33/472|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130741|EIF2S3|ENST00000487075|2/3||||processed_transcript GT:AD:DP:GQ:PL 1:0,13:13:99:479,0 1:0,34:34:99:893,0 1:0,10:10:99:347,0 chrX 24578306 . G A 1563.64 PASS AC=2;AF=1;AN=2;DP=68;FS=0;GQ_MEAN=795.5;GQ_STDDEV=1018.94;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=22.99;SOR=1.098;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102230|PCYT1B|ENST00000379145|8/8|||-/351|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000379144||||-/369|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000356768||||-/330|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000496020||||-/177|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,66:66:99:1516,0 1:0,2:2:75:75,0 chrX 24578551 . T A 41.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=69;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=13.88;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000379144||||-/369|protein_coding,3_prime_UTR_variant|||ENSG00000102230|PCYT1B|ENST00000379145|8/8|||-/351|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000356768||||-/330|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000496020||||-/177|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:69:69,0 .:0,0:.:.:. chrX 24578803 . C T 351.64 PASS AC=1;AF=1;AN=1;DP=15;FS=0;GQ_MEAN=379;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.44;SOR=0.818;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102230|PCYT1B|ENST00000379145|8/8|||-/351|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000379144||||-/369|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000356768||||-/330|protein_coding,downstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000496020||||-/177|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,15:15:99:379,0 .:0,0:.:.:. chrX 24665381 . A AC 205.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=233;MLEAC=1;MLEAF=1;MQ=65.19;MQ0=0;NCC=2;QD=34.27;SOR=3.912;set=variant;CSQ=upstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000496020||||-/177|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000379144||||-/369|protein_coding,intron_variant|||ENSG00000102230|PCYT1B|ENST00000379145||||-/351|protein_coding,upstream_gene_variant|||ENSG00000236836|PCYT1B-AS1|ENST00000432626|||||antisense,upstream_gene_variant|||ENSG00000102230|PCYT1B|ENST00000356768||||-/330|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:233,0 .:0,0:.:.:. .:0,0:.:.:. chrX 24844699 . C A 1565.64 PASS AC=3;AF=1;AN=3;DP=47;FS=0;GQ_MEAN=531;GQ_STDDEV=313.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.31;SOR=2.786;set=variant2;CSQ=synonymous_variant|gtC/gtA|V|ENSG00000101868|POLA1|ENST00000379068|32/37|||1239/1468|protein_coding,synonymous_variant|gtC/gtA|V|ENSG00000101868|POLA1|ENST00000379059|32/37|||1233/1462|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101868|POLA1|ENST00000494204|4/5||||processed_transcript GT:AD:DP:GQ:PL 1:0,21:21:99:740,0 1:0,6:6:99:170,0 1:0,20:20:99:683,0 chrX 26157220 . C T 4427.64 PASS AC=3;AF=1;AN=3;DP=128;FS=0;GQ_MEAN=1485;GQ_STDDEV=1236.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.59;SOR=0.724;set=variant2;CSQ=missense_variant|Cct/Tct|P/S|ENSG00000176774|MAGEB18|ENST00000325250|2/3|benign(0.003)|tolerated(1)|40/343|protein_coding GT:AD:DP:GQ:PL 1:0,73:73:99:2534,0 1:0,4:4:99:122,0 1:0,51:51:99:1799,0 chrX 26157792 . C T 3955.64 PASS AC=3;AF=1;AN=3;DP=110;FS=0;GQ_MEAN=1327.67;GQ_STDDEV=1076.01;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.01;SOR=1.505;set=variant2;CSQ=synonymous_variant|gcC/gcT|A|ENSG00000176774|MAGEB18|ENST00000325250|2/3|||230/343|protein_coding GT:AD:DP:GQ:PL 1:0,58:58:99:2126,0 1:0,3:3:99:104,0 1:0,49:49:99:1753,0 chrX 26213364 . T TTTGTC 557.64 PASS AC=2;AF=1;AN=2;DP=14;FS=0;GQ_MEAN=292.5;GQ_STDDEV=159.1;MLEAC=2;MLEAF=1;MQ=55.75;MQ0=0;NCC=1;QD=25.74;SOR=5.283;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000176746|MAGEB6|ENST00000379034|2/2|||-/407|protein_coding,upstream_gene_variant|||ENSG00000232644|GS1-466O4.3|ENST00000450430|||||unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,9:9:99:405,0 .:0,0:.:.:. 1:0,4:4:99:180,0 chrX 26577838 . C A 742.64 PASS AC=1;AF=1;AN=1;DP=31;FS=0;GQ_MEAN=770;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.96;SOR=0.756;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000259849|VENTXP1|ENST00000569334|1/1||||lincRNA,downstream_gene_variant|||ENSG00000230265|RP11-702C7.1|ENST00000420915|||||processed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:770,0 .:0,0:.:.:. chrX 27478720 . C T 744.64 PASS AC=1;AF=1;AN=1;DP=21;FS=0;GQ_MEAN=772;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=33.59;SOR=1.292;set=variant2;CSQ=downstream_gene_variant|||ENSG00000224960|SMEK3P|ENST00000412172|||||processed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:772,0 .:0,0:.:.:. chrX 27478736 . G A 694.64 PASS AC=1;AF=1;AN=1;DP=17;FS=0;GQ_MEAN=722;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=30.45;SOR=1.371;set=variant2;CSQ=downstream_gene_variant|||ENSG00000224960|SMEK3P|ENST00000412172|||||processed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,17:17:99:722,0 .:0,0:.:.:. chrX 27479339 . A G 6573.64 PASS AC=3;AF=1;AN=3;DP=198;FS=0;GQ_MEAN=2200.33;GQ_STDDEV=944.17;MLEAC=3;MLEAF=1;MQ=59.58;MQ0=0;NCC=0;QD=33.2;SOR=1.094;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224960|SMEK3P|ENST00000412172|1/1||||processed_pseudogene GT:AD:DP:GQ:PL 1:0,92:92:99:3134,0 1:0,45:45:99:1246,0 1:0,61:61:99:2221,0 chrX 27996301 . C T 670.64 my_snp_filter AC=1;AF=1;AN=1;BaseQRankSum=-0.924;ClippingRankSum=1.39;DP=31;FS=0;GQ_MEAN=698;MLEAC=1;MLEAF=1;MQ=39.83;MQ0=0;MQRankSum=-1.733;NCC=2;QD=22.35;SOR=0.314;set=FilteredInAll;CSQ=3_prime_UTR_variant|||ENSG00000226372|DCAF8L1|ENST00000441525|1/1|||-/600|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,29:30:99:698,0 .:0,0:.:.:. chrX 28807442 . G A 2610.64 PASS AC=3;AF=1;AN=3;DP=82;FS=0;GQ_MEAN=879.33;GQ_STDDEV=36.14;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.84;SOR=1.697;set=variant2;CSQ=upstream_gene_variant|||ENSG00000169306|IL1RAPL1|ENST00000302196||||-/696|protein_coding,5_prime_UTR_variant|||ENSG00000169306|IL1RAPL1|ENST00000378993|2/11|||-/696|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:895,0 1:0,33:33:99:838,0 1:0,25:25:99:905,0 chrX 30236878 . G A 2014.64 PASS AC=3;AF=1;AN=3;DP=65;FS=0;GQ_MEAN=680.67;GQ_STDDEV=229.53;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.99;SOR=1;set=variant2;CSQ=missense_variant|Gag/Aag|E/K|ENSG00000099399|MAGEB2|ENST00000378988|2/2|benign(0.004)|tolerated(0.78)|61/319|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:848,0 1:0,28:28:99:775,0 1:0,14:14:99:419,0 chrX 30269887 . T A 870.64 PASS AC=2;AF=1;AN=2;DP=31;FS=0;GQ_MEAN=449;GQ_STDDEV=347.9;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=29.02;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000214107|MAGEB1|ENST00000378981|4/4|||-/347|protein_coding,3_prime_UTR_variant|||ENSG00000214107|MAGEB1|ENST00000397548|2/2|||-/347|protein_coding,3_prime_UTR_variant|||ENSG00000214107|MAGEB1|ENST00000397550|3/3|||-/347|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,25:25:99:695,0 1:0,5:5:99:203,0 chrX 30326983 . C T 2060.64 PASS AC=2;AF=1;AN=2;DP=66;FS=0;GQ_MEAN=1044;GQ_STDDEV=275.77;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.34;SOR=1.255;set=variant2;CSQ=upstream_gene_variant|||ENSG00000169297|NR0B1|ENST00000378963||||-/105|protein_coding,synonymous_variant|cgG/cgA|R|ENSG00000169297|NR0B1|ENST00000453287|1/2|||166/400|protein_coding,synonymous_variant|cgG/cgA|R|ENSG00000169297|NR0B1|ENST00000378970|1/2|||166/470|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1239,0 .:0,0:.:.:. 1:0,24:24:99:849,0 chrX 30577224 . C T 83.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=111;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.88;SOR=2.833;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000120280|CXorf21|ENST00000378962|3/3|||-/301|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:99:111,0 .:0,0:.:.:. chrX 30577846 . A C 1803.64 PASS AC=3;AF=1;AN=3;DP=50;FS=0;GQ_MEAN=610.33;GQ_STDDEV=361.18;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.1;SOR=1.27;set=variant2;CSQ=synonymous_variant|gtT/gtG|V|ENSG00000120280|CXorf21|ENST00000378962|3/3|||209/301|protein_coding GT:AD:DP:GQ:PL 1:0,26:26:99:929,0 1:0,6:6:99:218,0 1:0,18:18:99:684,0 chrX 30748284 . T C 631.64 PASS AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=659;MLEAC=1;MLEAF=1;MQ=54.71;MQ0=0;NCC=2;QD=33.24;SOR=1.981;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000198814|GK|ENST00000378943|20/20|||-/553|protein_coding,downstream_gene_variant|||ENSG00000198814|GK|ENST00000481024||||-/102|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000198814|GK|ENST00000427190||||-/354|protein_coding,3_prime_UTR_variant|||ENSG00000198814|GK|ENST00000378946|20/20|||-/530|protein_coding,downstream_gene_variant|||ENSG00000198814|GK|ENST00000378945||||-/524|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:659,0 .:0,0:.:.:. chrX 30872602 . A G 4183.64 PASS AC=3;AF=1;AN=3;DP=134;FS=0;GQ_MEAN=1403.67;GQ_STDDEV=783.59;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.69;SOR=1;set=variant2;CSQ=missense_variant|Tgg/Cgg|W/R|ENSG00000157625|TAB3|ENST00000378933|3/8|benign(0)||394/712|protein_coding,missense_variant|Tgg/Cgg|W/R|ENSG00000157625|TAB3|ENST00000378932|7/11|benign(0)||394/684|protein_coding,missense_variant|Tgg/Cgg|W/R|ENSG00000157625|TAB3|ENST00000288422|7/12|benign(0)||394/712|protein_coding,upstream_gene_variant|||ENSG00000157625|TAB3|ENST00000378928||||-/83|protein_coding,missense_variant|Tgg/Cgg|W/R|ENSG00000157625|TAB3|ENST00000378930|2/7|benign(0)||394/712|protein_coding,missense_variant&NMD_transcript_variant|Tgg/Cgg|W/R|ENSG00000157625|TAB3|ENST00000467136|5/8|benign(0)||394/608|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000235512|TAB3-AS2|ENST00000445240|2/2||||antisense GT:AD:DP:GQ:PL 1:0,61:61:99:1968,0 1:0,20:20:99:509,0 1:0,51:51:99:1734,0 chrX 31139079 . ATACTT A 287.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=315;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.65;SOR=1.609;set=variant;CSQ=downstream_gene_variant|||ENSG00000198947|DMD|ENST00000474231||||-/1243|protein_coding,downstream_gene_variant|||ENSG00000198947|DMD|ENST00000361471||||-/622|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000357033|79/79|||-/3685|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000378707|36/36|||-/1225|protein_coding,downstream_gene_variant|||ENSG00000198947|DMD|ENST00000378680||||-/525|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000359836|34/34|||-/1230|protein_coding,downstream_gene_variant|||ENSG00000198947|DMD|ENST00000378702||||-/617|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000343523|31/31|||-/1133|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000378723|17/17|||-/635|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000541735|32/32|||-/1115|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198947|DMD|ENST00000481143|||||processed_transcript,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000378677|79/79|||-/3681|protein_coding,3_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000358062|30/30|||-/1386|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:315,0 .:0,0:.:.:. chrX 31496350 . C T 3881.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.514;ClippingRankSum=-1.097;DP=126;FS=0;GQ_MEAN=1303;GQ_STDDEV=753.2;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.62;NCC=0;QD=30.81;ReadPosRankSum=1.31;SOR=1.392;set=variant2;CSQ=missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000541735|16/32|benign(0.001)|tolerated(0.87)|477/1115|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000358062|12/30|benign(0.001)|tolerated(0.85)|633/1386|protein_coding,downstream_gene_variant|||ENSG00000198947|DMD|ENST00000445312|||||processed_transcript,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000378677|59/79|benign(0)||2933/3681|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000378707|16/36|benign(0.001)|tolerated(0.89)|477/1225|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000474231|16/35|benign(0.001)|tolerated(0.83)|477/1243|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000357033|59/79|benign(0)||2937/3685|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000359836|16/34|benign(0.001)|tolerated(0.86)|477/1230|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000198947|DMD|ENST00000343523|16/31|benign(0)||477/1133|protein_coding GT:AD:DP:GQ:PL 1:0,46:46:99:1474,0 1:2,22:24:99:479,0 1:0,56:56:99:1956,0 chrX 31986607 . G A 1389.64 PASS AC=3;AF=1;AN=3;DP=44;FS=0;GQ_MEAN=472.33;GQ_STDDEV=35.02;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.58;SOR=0.693;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000198947|DMD|ENST00000488902|4/5||||processed_transcript,missense_variant|Cgg/Tgg|R/W|ENSG00000198947|DMD|ENST00000378677|45/79|possibly_damaging(0.898)||2151/3681|protein_coding,5_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000541735|2/32|||-/1115|protein_coding,5_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000359836|2/34|||-/1230|protein_coding,5_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000343523|2/31|||-/1133|protein_coding,5_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000474231|2/35|||-/1243|protein_coding,missense_variant|Cgg/Tgg|R/W|ENSG00000198947|DMD|ENST00000357033|45/79|possibly_damaging(0.835)||2155/3685|protein_coding,5_prime_UTR_variant|||ENSG00000198947|DMD|ENST00000378707|2/36|||-/1225|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:495,0 1:0,15:15:99:432,0 1:0,14:14:99:490,0 chrX 32503194 . T C 1263.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=430.33;GQ_STDDEV=154.02;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.84;SOR=2.712;set=variant2;CSQ=intron_variant|||ENSG00000198947|DMD|ENST00000420596||||-/101|protein_coding,missense_variant|gAt/gGt|D/G|ENSG00000198947|DMD|ENST00000378677|21/79|benign(0)||878/3681|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198947|DMD|ENST00000488902|||||processed_transcript,intron_variant|||ENSG00000198947|DMD|ENST00000448370||||-/41|protein_coding,missense_variant|gAt/gGt|D/G|ENSG00000198947|DMD|ENST00000357033|21/79|benign(0)||882/3685|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:605,0 1:0,9:9:99:314,0 1:0,11:11:99:372,0 chrX 32613963 . C G 2041.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-1.348;ClippingRankSum=0.77;DP=62;FS=0;GQ_MEAN=735.33;GQ_STDDEV=581.85;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-1.059;NCC=0;QD=33.02;ReadPosRankSum=-0.096;SOR=0.898;set=variant2;CSQ=intron_variant|||ENSG00000198947|DMD|ENST00000420596||||-/101|protein_coding,intron_variant|||ENSG00000198947|DMD|ENST00000448370||||-/41|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000198947|DMD|ENST00000357033|13/79|possibly_damaging(0.558)||505/3685|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198947|DMD|ENST00000480751|||||processed_transcript,missense_variant|Gtc/Ctc|V/L|ENSG00000198947|DMD|ENST00000378677|13/79|probably_damaging(0.935)||501/3681|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198947|DMD|ENST00000488902|||||processed_transcript,intron_variant|||ENSG00000198947|DMD|ENST00000447523||||-/125|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000198947|DMD|ENST00000288447|13/18|possibly_damaging(0.544)|tolerated(0.13)|497/772|protein_coding GT:AD:DP:GQ:PL 1:1,35:36:99:1293,0 0:5,0:5:99:0,132 1:0,21:21:99:781,0 chrX 34648280 . G A 616.87 PASS AC=1;AF=0.333;AN=3;DP=36;FS=0;GQ_MEAN=288;GQ_STDDEV=312.64;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=20.56;SOR=1.536;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147027|TMEM47|ENST00000275954|3/3|||-/181|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,107 1:0,30:30:99:649,0 0:3,0:3:99:0,108 chrX 34674970 . C G 1418.64 PASS AC=3;AF=1;AN=3;DP=45;FS=0;GQ_MEAN=482;GQ_STDDEV=277.25;MLEAC=3;MLEAF=1;MQ=50.87;MQ0=0;NCC=0;QD=31.53;SOR=1.559;set=variant2;CSQ=synonymous_variant|cgG/cgC|R|ENSG00000147027|TMEM47|ENST00000275954|1/3|||59/181|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:564,0 1:0,7:7:99:173,0 1:0,20:20:99:709,0 chrX 35820265 . C T 2017.64 PASS AC=3;AF=1;AN=3;DP=60;FS=0;GQ_MEAN=681.67;GQ_STDDEV=478.04;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.63;SOR=2.546;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399987|3/3|||-/324|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000189023|MAGEB16|ENST00000399992|3/3|||16/356|protein_coding,5_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399985|2/2|||-/324|protein_coding,5_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399989|2/2|||-/324|protein_coding,5_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399988|2/2|||-/324|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:941,0 1:0,4:4:99:130,0 1:0,28:28:99:974,0 chrX 35820425 . C T 3323.64 PASS AC=3;AF=1;AN=3;DP=99;FS=0;GQ_MEAN=1117;GQ_STDDEV=803.67;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.57;SOR=0.985;set=variant2;CSQ=missense_variant|Ctc/Ttc|L/F|ENSG00000189023|MAGEB16|ENST00000399985|2/2|benign(0.002)|tolerated(0.73)|38/324|protein_coding,missense_variant|Ctc/Ttc|L/F|ENSG00000189023|MAGEB16|ENST00000399992|3/3|benign(0.002)|tolerated(0.74)|70/356|protein_coding,missense_variant|Ctc/Ttc|L/F|ENSG00000189023|MAGEB16|ENST00000399987|3/3|benign(0.002)|tolerated(0.73)|38/324|protein_coding,missense_variant|Ctc/Ttc|L/F|ENSG00000189023|MAGEB16|ENST00000399989|2/2|benign(0.002)|tolerated(0.73)|38/324|protein_coding,missense_variant|Ctc/Ttc|L/F|ENSG00000189023|MAGEB16|ENST00000399988|2/2|benign(0.002)|tolerated(0.73)|38/324|protein_coding GT:AD:DP:GQ:PL 1:0,48:48:99:1580,0 1:0,8:8:99:189,0 1:0,43:43:99:1582,0 chrX 35820696 . G A 2457.64 PASS AC=3;AF=1;AN=3;DP=76;FS=0;GQ_MEAN=828.33;GQ_STDDEV=530.72;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.34;SOR=1.432;set=variant2;CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000189023|MAGEB16|ENST00000399988|2/2|benign(0)|tolerated(1)|128/324|protein_coding,missense_variant|tGt/tAt|C/Y|ENSG00000189023|MAGEB16|ENST00000399992|3/3|benign(0)|tolerated(1)|160/356|protein_coding,missense_variant|tGt/tAt|C/Y|ENSG00000189023|MAGEB16|ENST00000399985|2/2|benign(0)|tolerated(1)|128/324|protein_coding,missense_variant|tGt/tAt|C/Y|ENSG00000189023|MAGEB16|ENST00000399987|3/3|benign(0)|tolerated(1)|128/324|protein_coding,missense_variant|tGt/tAt|C/Y|ENSG00000189023|MAGEB16|ENST00000399989|2/2|benign(0)|tolerated(1)|128/324|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1171,0 1:0,8:8:99:217,0 1:0,32:32:99:1097,0 chrX 35820795 . A G 2139.64 PASS AC=3;AF=1;AN=3;DP=71;FS=0;GQ_MEAN=722.33;GQ_STDDEV=280.81;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.14;SOR=0.84;set=variant2;CSQ=missense_variant|cAc/cGc|H/R|ENSG00000189023|MAGEB16|ENST00000399988|2/2|benign(0.001)|tolerated(0.37)|161/324|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000189023|MAGEB16|ENST00000399989|2/2|benign(0.001)|tolerated(0.37)|161/324|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000189023|MAGEB16|ENST00000399987|3/3|benign(0.001)|tolerated(0.37)|161/324|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000189023|MAGEB16|ENST00000399985|2/2|benign(0.001)|tolerated(0.37)|161/324|protein_coding,missense_variant|cAc/cGc|H/R|ENSG00000189023|MAGEB16|ENST00000399992|3/3|benign(0.001)|tolerated(0.5)|193/356|protein_coding GT:AD:DP:GQ:PL 1:0,32:32:99:1031,0 1:0,18:18:99:482,0 1:0,21:21:99:654,0 chrX 35821055 . A G 3551.64 PASS AC=3;AF=1;AN=3;DP=80;FS=0;GQ_MEAN=1193;GQ_STDDEV=736.77;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.5;SOR=1.639;set=variant2;CSQ=missense_variant|Atg/Gtg|M/V|ENSG00000189023|MAGEB16|ENST00000399987|3/3|benign(0.002)|deleterious(0)|248/324|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000189023|MAGEB16|ENST00000399992|3/3|benign(0.001)|deleterious(0)|280/356|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000189023|MAGEB16|ENST00000399985|2/2|benign(0.002)|deleterious(0)|248/324|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000189023|MAGEB16|ENST00000399989|2/2|benign(0.002)|deleterious(0)|248/324|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000189023|MAGEB16|ENST00000399988|2/2|benign(0.002)|deleterious(0)|248/324|protein_coding GT:AD:DP:GQ:PL 1:0,34:34:99:1530,0 1:0,8:8:99:348,0 1:0,38:38:99:1701,0 chrX 35821056 . T A 3551.64 PASS AC=3;AF=1;AN=3;DP=79;FS=0;GQ_MEAN=1193;GQ_STDDEV=736.77;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.53;SOR=1.7;set=variant2;CSQ=missense_variant|aTg/aAg|M/K|ENSG00000189023|MAGEB16|ENST00000399989|2/2|benign(0)|tolerated(1)|248/324|protein_coding,missense_variant|aTg/aAg|M/K|ENSG00000189023|MAGEB16|ENST00000399987|3/3|benign(0)|tolerated(1)|248/324|protein_coding,missense_variant|aTg/aAg|M/K|ENSG00000189023|MAGEB16|ENST00000399992|3/3|benign(0)|tolerated(1)|280/356|protein_coding,missense_variant|aTg/aAg|M/K|ENSG00000189023|MAGEB16|ENST00000399985|2/2|benign(0)|tolerated(1)|248/324|protein_coding,missense_variant|aTg/aAg|M/K|ENSG00000189023|MAGEB16|ENST00000399988|2/2|benign(0)|tolerated(1)|248/324|protein_coding GT:AD:DP:GQ:PL 1:0,34:34:99:1530,0 1:0,8:8:99:348,0 1:0,37:37:99:1701,0 chrX 35821127 . C T 3517.64 PASS AC=3;AF=1;AN=3;DP=100;FS=0;GQ_MEAN=1181.67;GQ_STDDEV=750.57;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.58;SOR=1.225;set=variant2;CSQ=stop_gained|Cga/Tga|R/*|ENSG00000189023|MAGEB16|ENST00000399988|2/2|||272/324|protein_coding,stop_gained|Cga/Tga|R/*|ENSG00000189023|MAGEB16|ENST00000399989|2/2|||272/324|protein_coding,stop_gained|Cga/Tga|R/*|ENSG00000189023|MAGEB16|ENST00000399987|3/3|||272/324|protein_coding,stop_gained|Cga/Tga|R/*|ENSG00000189023|MAGEB16|ENST00000399985|2/2|||272/324|protein_coding,stop_gained|Cga/Tga|R/*|ENSG00000189023|MAGEB16|ENST00000399992|3/3|||304/356|protein_coding GT:AD:DP:GQ:PL 1:0,44:44:99:1619,0 1:0,12:12:99:315,0 1:0,44:44:99:1611,0 chrX 35821302 . C G 3556.64 PASS AC=3;AF=1;AN=3;DP=81;FS=0;GQ_MEAN=1194.67;GQ_STDDEV=411.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.84;SOR=1.668;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399988|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399987|3/3|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399985|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399992|3/3|||-/356|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399989|2/2|||-/324|protein_coding GT:AD:DP:GQ:PL 1:0,33:33:99:1452,0 1:0,16:16:99:720,0 1:0,32:32:99:1412,0 chrX 35821308 . C T 3498.64 PASS AC=3;AF=1;AN=3;DP=76;FS=0;GQ_MEAN=1175.33;GQ_STDDEV=394.79;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.51;SOR=1.704;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399989|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399987|3/3|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399985|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399992|3/3|||-/356|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399988|2/2|||-/324|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1384,0 1:0,16:16:99:720,0 1:0,30:30:99:1422,0 chrX 35821464 . A G 622.64 PASS AC=3;AF=1;AN=3;DP=18;FS=0;GQ_MEAN=216.67;GQ_STDDEV=162.67;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.59;SOR=1.179;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399992|3/3|||-/356|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399985|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399987|3/3|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399989|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399988|2/2|||-/324|protein_coding GT:AD:DP:GQ:PL 1:0,5:5:99:172,0 1:0,11:11:99:397,0 1:0,2:2:81:81,0 chrX 35821558 . G A 1029.64 PASS AC=2;AF=1;AN=2;DP=40;FS=0;GQ_MEAN=528.5;GQ_STDDEV=635.69;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.4;SOR=0.743;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399989|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399985|2/2|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399992|3/3|||-/356|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399987|3/3|||-/324|protein_coding,3_prime_UTR_variant|||ENSG00000189023|MAGEB16|ENST00000399988|2/2|||-/324|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:79:79,0 1:0,37:37:99:978,0 .:0,0:.:.:. chrX 35938045 . C T 2910.87 PASS AC=2;AF=0.667;AN=3;DP=92;FS=0;GQ_MEAN=997.33;GQ_STDDEV=839.82;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.34;SOR=0.883;set=variant2;CSQ=synonymous_variant|atC/atT|I|ENSG00000165164|CXorf22|ENST00000297866|1/16|||43/976|protein_coding,synonymous_variant&NMD_transcript_variant|atC/atT|I|ENSG00000165164|CXorf22|ENST00000493930|1/16|||43/754|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,49:49:99:1647,0 0:2,0:2:49:0,49 1:0,41:41:99:1296,0 chrX 35969297 . G A 1471.87 PASS AC=2;AF=0.667;AN=3;DP=50;FS=0;GQ_MEAN=543.67;GQ_STDDEV=364.16;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.71;SOR=1.559;set=variant2;CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000165164|CXorf22|ENST00000297866|5/16|probably_damaging(0.996)|deleterious(0)|236/976|protein_coding,missense_variant&NMD_transcript_variant|Gtg/Atg|V/M|ENSG00000165164|CXorf22|ENST00000493930|5/16|probably_damaging(0.996)|deleterious(0)|236/754|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,24:24:99:801,0 0:5,0:5:99:0,127 1:0,21:21:99:703,0 chrX 35988996 . T C 949.87 PASS AC=2;AF=0.667;AN=3;DP=31;FS=0;GQ_MEAN=368;GQ_STDDEV=216.58;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.9;SOR=2.753;set=variant2;CSQ=synonymous_variant|ctT/ctC|L|ENSG00000165164|CXorf22|ENST00000297866|11/16|||642/976|protein_coding,synonymous_variant&NMD_transcript_variant|ctT/ctC|L|ENSG00000165164|CXorf22|ENST00000493930|11/16|||642/754|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,13:13:99:452,0 0:4,0:4:99:0,122 1:0,14:14:99:530,0 chrX 35993454 . C T 865.87 PASS AC=2;AF=0.667;AN=3;DP=31;FS=0;GQ_MEAN=348.33;GQ_STDDEV=199.04;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.63;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000165164|CXorf22|ENST00000493930|14/16|||-/754|nonsense_mediated_decay,synonymous_variant|gaC/gaT|D|ENSG00000165164|CXorf22|ENST00000297866|14/16|||815/976|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:545,0 0:6,0:6:99:0,147 1:0,9:9:99:353,0 chrX 36007614 . T G 2530.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.58;ClippingRankSum=1.71;DP=85;FS=2.379;GQ_MEAN=888.33;GQ_STDDEV=681.26;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=0.776;NCC=0;QD=31.64;ReadPosRankSum=1.58;SOR=0.787;set=variant2;CSQ=missense_variant|ttT/ttG|F/L|ENSG00000165164|CXorf22|ENST00000297866|16/16|benign(0)|tolerated_low_confidence(1)|964/976|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000165164|CXorf22|ENST00000493930|16/16|||-/754|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:2,38:40:99:1262,0 0:4,0:4:99:0,102 1:1,39:40:99:1301,0 chrX 36371719 . T A 1946.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=0.204;ClippingRankSum=0.306;DP=62;FS=4.921;GQ_MEAN=694.67;GQ_STDDEV=528.85;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=0;NCC=0;QD=33;ReadPosRankSum=0.408;SOR=1.591;set=variant2;CSQ=missense_variant|tTt/tAt|F/Y|ENSG00000205081|CXorf30|ENST00000378657|14/18|benign(0)|tolerated(0.75)|371/633|protein_coding,missense_variant|tTt/tAt|F/Y|ENSG00000205081|CXorf30|ENST00000378653|15/19|benign(0)|tolerated(0.61)|656/918|protein_coding GT:AD:DP:GQ:PL 1:1,33:34:99:1127,0 0:3,0:3:99:0,105 1:0,25:25:99:852,0 chrX 36385156 . A G 3193.94 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=0.042;ClippingRankSum=-0.718;DP=99;FS=0;GQ_MEAN=1112.67;GQ_STDDEV=911.02;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-1.141;NCC=0;QD=33.62;ReadPosRankSum=-0.211;SOR=0.278;set=variant2;CSQ=synonymous_variant|gaA/gaG|E|ENSG00000205081|CXorf30|ENST00000378657|16/18|||479/633|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000205081|CXorf30|ENST00000378653|17/19|||764/918|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000205081|CXorf30|ENST00000446478|2/3||||retained_intron,intron_variant&non_coding_transcript_variant|||ENSG00000226484|RP11-87M18.2|ENST00000455438|||||antisense GT:AD:DP:GQ:PL 1:0,54:54:99:1894,0 0:4,0:4:99:0,112 1:1,40:41:99:1332,0 chrX 36403036 . A G 3499.87 PASS AC=2;AF=0.667;AN=3;DP=111;FS=0;GQ_MEAN=1214.67;GQ_STDDEV=955.03;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.02;SOR=1.48;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000226484|RP11-87M18.2|ENST00000455438|||||antisense,missense_variant|cAt/cGt|H/R|ENSG00000205081|CXorf30|ENST00000378657|18/18|benign(0.001)|tolerated(1)|606/633|protein_coding,missense_variant|cAt/cGt|H/R|ENSG00000205081|CXorf30|ENST00000378653|19/19|benign(0)|tolerated(1)|891/918|protein_coding GT:AD:DP:GQ:PL 1:0,56:56:99:1779,0 0:4,0:4:99:0,112 1:0,50:50:99:1753,0 chrX 37028127 . A G 2445.87 PASS AC=2;AF=0.667;AN=3;DP=77;FS=0;GQ_MEAN=860.67;GQ_STDDEV=658.41;MLEAC=2;MLEAF=0.667;MQ=53.51;MQ0=0;NCC=0;QD=33.05;SOR=0.992;set=variant2;CSQ=synonymous_variant|ccA/ccG|P|ENSG00000198173|FAM47C|ENST00000358047|1/1|||548/1035|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1175,0 0:3,0:3:99:0,104 1:0,39:39:99:1303,0 chrX 37029254 . A C 4599.87 PASS AC=2;AF=0.667;AN=3;DP=137;FS=0;GQ_MEAN=1578.67;GQ_STDDEV=1278.65;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.59;SOR=1.136;set=variant2;CSQ=missense_variant|aAt/aCt|N/T|ENSG00000198173|FAM47C|ENST00000358047|1/1|benign(0)|tolerated(0.96)|924/1035|protein_coding GT:AD:DP:GQ:PL 1:0,69:69:99:2379,0 0:3,0:3:99:0,104 1:0,64:64:99:2253,0 chrX 37430932 . AGCCCGGC A 59.63 PASS AC=1;AF=0.5;AN=2;DP=5;FS=0;GQ_MEAN=95.5;GQ_STDDEV=7.78;MLEAC=1;MLEAF=0.5;MQ=53.03;MQ0=0;NCC=1;QD=12.78;SOR=0.693;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000147036|LANCL3|ENST00000378619|1/5|||-/420|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,5_prime_UTR_variant|||ENSG00000147036|LANCL3|ENST00000378621|1/6|||-/388|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:90:90,0 0:3,0:3:99:0,101 .:0,0:.:.:. chrX 37518806 . C T 1803.87 PASS AC=2;AF=0.667;AN=3;DP=61;FS=0;GQ_MEAN=649.33;GQ_STDDEV=465.34;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.21;SOR=1.528;set=variant2;CSQ=synonymous_variant|agC/agT|S|ENSG00000147036|LANCL3|ENST00000378621|3/6|||263/388|protein_coding,synonymous_variant|agC/agT|S|ENSG00000147036|LANCL3|ENST00000378619|3/5|||263/420|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:918,0 0:4,0:4:99:0,112 1:0,26:26:99:918,0 chrX 37701048 . G A 918.87 PASS AC=2;AF=0.667;AN=3;DP=29;FS=0;GQ_MEAN=352.67;GQ_STDDEV=212.8;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.01;SOR=3.528;set=variant2;CSQ=synonymous_variant|gcC/gcT|A|ENSG00000165169|DYNLT3|ENST00000378581|3/6|||61/152|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000165169|DYNLT3|ENST00000432389|3/5|||67/122|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000165169|DYNLT3|ENST00000378578|3/5|||61/116|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:471,0 0:4,0:4:99:0,107 1:0,13:13:99:480,0 chrX 37932886 . A G 1147.64 PASS AC=3;AF=1;AN=3;DP=46;FS=0;GQ_MEAN=391.67;GQ_STDDEV=576.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=24.95;SOR=0.874;set=variant2;CSQ=intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147041|SYTL5|ENST00000297875|5/17|||163/730|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147041|SYTL5|ENST00000456733|4/17|||163/752|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147041|SYTL5|ENST00000357972|5/17|||163/730|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:69:69,0 1:0,42:42:99:1057,0 1:0,2:2:49:49,0 chrX 37948832 . A G 859.87 PASS AC=2;AF=0.667;AN=3;DP=28;FS=0;GQ_MEAN=324.33;GQ_STDDEV=290.53;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.39;SOR=1.893;set=variant2;CSQ=intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,missense_variant|Atc/Gtc|I/V|ENSG00000147041|SYTL5|ENST00000357972|7/17|benign(0.012)|tolerated(0.5)|275/730|protein_coding,missense_variant|Atc/Gtc|I/V|ENSG00000147041|SYTL5|ENST00000456733|6/17|benign(0.012)|tolerated(0.5)|275/752|protein_coding,missense_variant|Atc/Gtc|I/V|ENSG00000147041|SYTL5|ENST00000297875|7/17|benign(0.012)|tolerated(0.5)|275/730|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:646,0 0:3,0:3:81:0,81 1:0,7:7:99:246,0 chrX 37967868 . T C 2908.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.177;ClippingRankSum=0.742;DP=93;FS=0;GQ_MEAN=978.67;GQ_STDDEV=561.26;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.53;NCC=0;QD=31.62;ReadPosRankSum=-1.732;SOR=0.853;set=variant2;CSQ=synonymous_variant|taT/taC|Y|ENSG00000147041|SYTL5|ENST00000297875|12/17|||450/730|protein_coding,synonymous_variant|taT/taC|Y|ENSG00000147041|SYTL5|ENST00000456733|12/17|||472/752|protein_coding,synonymous_variant|taT/taC|Y|ENSG00000147041|SYTL5|ENST00000357972|12/17|||450/730|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding GT:AD:DP:GQ:PL 1:1,48:49:99:1556,0 1:0,17:17:99:435,0 1:0,26:26:99:945,0 chrX 37986733 . A G 462.64 PASS AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=490;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.35;SOR=0.793;set=variant2;CSQ=intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,3_prime_UTR_variant|||ENSG00000147041|SYTL5|ENST00000357972|17/17|||-/730|protein_coding,3_prime_UTR_variant|||ENSG00000147041|SYTL5|ENST00000456733|17/17|||-/752|protein_coding,3_prime_UTR_variant|||ENSG00000147041|SYTL5|ENST00000297875|17/17|||-/730|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:490,0 .:0,0:.:.:. chrX 38008727 . G C 869.64 PASS AC=3;AF=1;AN=3;DP=32;FS=0;GQ_MEAN=299;GQ_STDDEV=334.32;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.18;SOR=0.818;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101955|SRPX|ENST00000343800|9/9|||-/451|protein_coding,3_prime_UTR_variant|||ENSG00000101955|SRPX|ENST00000538295|9/9|||-/379|protein_coding,3_prime_UTR_variant|||ENSG00000101955|SRPX|ENST00000378533|10/10|||-/464|protein_coding,3_prime_UTR_variant|||ENSG00000101955|SRPX|ENST00000432886|9/9|||-/405|protein_coding,downstream_gene_variant|||ENSG00000101955|SRPX|ENST00000461865|||||processed_transcript,3_prime_UTR_variant|||ENSG00000101955|SRPX|ENST00000544439|9/9|||-/444|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101955|SRPX|ENST00000479015|3/3||||processed_transcript GT:AD:DP:GQ:PL 1:0,4:4:99:131,0 1:0,26:26:99:684,0 1:0,2:2:82:82,0 chrX 38079975 . CGCA C 267.87 PASS AC=2;AF=0.667;AN=3;DP=13;FS=0;GQ_MEAN=132.67;GQ_STDDEV=33.56;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.31;SOR=2.584;set=variant;CSQ=upstream_gene_variant|||ENSG00000226679|RP13-43E11.1|ENST00000423919|||||antisense,inframe_deletion|cTGCgc/cgc|LR/R|ENSG00000101955|SRPX|ENST00000544439|1/9|||23-24/444|protein_coding,inframe_deletion|cTGCgc/cgc|LR/R|ENSG00000101955|SRPX|ENST00000378533|1/10|||23-24/464|protein_coding,inframe_deletion|cTGCgc/cgc|LR/R|ENSG00000101955|SRPX|ENST00000432886|1/9|||23-24/405|protein_coding,inframe_deletion|cTGCgc/cgc|LR/R|ENSG00000101955|SRPX|ENST00000538295|1/9|||23-24/379|protein_coding,intron_variant|||ENSG00000250349|TM4SF2|ENST00000465127||||-/279|protein_coding,intron_variant|||ENSG00000101955|SRPX|ENST00000343800||||-/451|protein_coding GT:AD:DP:GQ:PL 1:0,4:4:99:165,0 0:4,0:4:98:0,98 1:0,3:3:99:135,0 chrX 38663104 . T C 48.63 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;GQ_MEAN=107;GQ_STDDEV=39.6;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=24.32;SOR=2.303;set=variant2;CSQ=intron_variant|||ENSG00000165175|MID1IP1|ENST00000457894||||-/183|protein_coding,intron_variant|||ENSG00000165175|MID1IP1|ENST00000378474||||-/183|protein_coding,downstream_gene_variant|||ENSG00000235806|RP4-646N3.1|ENST00000432359|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000238123|MID1IP1-AS1|ENST00000436893|1/2||||antisense,5_prime_UTR_variant|||ENSG00000165175|MID1IP1|ENST00000336949|1/2|||-/183|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 0:5,0:5:99:0,135 1:0,2:2:79:79,0 chrX 38664817 . CT C 37.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DP=13;FS=0;GQ_MEAN=98;GQ_STDDEV=24.27;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;MQRankSum=-0.731;NCC=0;QD=7.57;ReadPosRankSum=0.731;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000165175|MID1IP1|ENST00000336949|2/2|||-/183|protein_coding,upstream_gene_variant|||ENSG00000238123|MID1IP1-AS1|ENST00000436893|||||antisense,3_prime_UTR_variant|||ENSG00000165175|MID1IP1|ENST00000457894|2/2|||-/183|protein_coding,3_prime_UTR_variant|||ENSG00000165175|MID1IP1|ENST00000378474|3/3|||-/183|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,113 1:1,4:5:70:70,0 0:3,0:3:99:0,111 chrX 39932907 . T C 2373.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.57;ClippingRankSum=-0.846;DP=79;FS=3.126;GQ_MEAN=839;GQ_STDDEV=651.2;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-1.249;NCC=0;QD=31.24;ReadPosRankSum=-0.766;SOR=0.35;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000183337|BCOR|ENST00000490976|3/3||||retained_intron,synonymous_variant|gcA/gcG|A|ENSG00000183337|BCOR|ENST00000378455|4/14|||564/1703|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000183337|BCOR|ENST00000378444|4/15|||564/1755|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000183337|BCOR|ENST00000406200|4/9|||564/1287|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000183337|BCOR|ENST00000397354|4/15|||564/1721|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000183337|BCOR|ENST00000342274|4/15|||564/1721|protein_coding,downstream_gene_variant|||ENSG00000183337|BCOR|ENST00000412952||||-/28|protein_coding GT:AD:DP:GQ:PL 1:1,42:43:99:1366,0 0:3,0:3:99:0,111 1:0,33:33:99:1040,0 chrX 39933339 . A G 4333.64 PASS AC=3;AF=1;AN=3;DP=121;FS=0;GQ_MEAN=1453.67;GQ_STDDEV=1019.96;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.32;SOR=1.336;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000183337|BCOR|ENST00000490976|3/3||||retained_intron,synonymous_variant|gaT/gaC|D|ENSG00000183337|BCOR|ENST00000378444|4/15|||420/1755|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000183337|BCOR|ENST00000406200|4/9|||420/1287|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000183337|BCOR|ENST00000342274|4/15|||420/1721|protein_coding,downstream_gene_variant|||ENSG00000183337|BCOR|ENST00000412952||||-/28|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000183337|BCOR|ENST00000397354|4/15|||420/1721|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000183337|BCOR|ENST00000378455|4/14|||420/1703|protein_coding GT:AD:DP:GQ:PL 1:0,65:65:99:2302,0 1:0,9:9:99:322,0 1:0,47:47:99:1737,0 chrX 40506697 . A G 3193.66 PASS AC=3;AF=1;AN=3;DP=102;FS=0;GQ_MEAN=1073.67;GQ_STDDEV=467.54;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.31;SOR=1.27;set=variant2;CSQ=synonymous_variant|Tta/Cta|L|ENSG00000185753|CXorf38|ENST00000378418|1/3|||26/155|protein_coding,downstream_gene_variant|||ENSG00000180182|MED14|ENST00000416199||||-/155|protein_coding,5_prime_UTR_variant|||ENSG00000185753|CXorf38|ENST00000378426|1/5|||-/200|protein_coding,5_prime_UTR_variant|||ENSG00000185753|CXorf38|ENST00000378421|1/7|||-/200|protein_coding,synonymous_variant|Tta/Cta|L|ENSG00000185753|CXorf38|ENST00000327877|1/7|||26/319|protein_coding,downstream_gene_variant|||ENSG00000180182|MED14|ENST00000324817||||-/1454|protein_coding,synonymous_variant|Tta/Cta|L|ENSG00000185753|CXorf38|ENST00000440784|1/4|||26/234|protein_coding GT:AD:DP:GQ:PL 1:0,47:47:99:1583,0 1:0,27:27:99:664,0 1:0,28:28:99:974,0 chrX 40510773 . A G 52.63 PASS AC=1;AF=0.5;AN=2;DP=7;FS=0;GQ_MEAN=109;GQ_STDDEV=36.77;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=26.32;SOR=2.303;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000180182|MED14|ENST00000324817|31/31|||-/1454|protein_coding,upstream_gene_variant|||ENSG00000185753|CXorf38|ENST00000327877||||-/319|protein_coding,upstream_gene_variant|||ENSG00000185753|CXorf38|ENST00000378426||||-/200|protein_coding,intron_variant|||ENSG00000180182|MED14|ENST00000416199||||-/155|protein_coding,downstream_gene_variant|||ENSG00000180182|MED14|ENST00000433003||||-/331|protein_coding,upstream_gene_variant|||ENSG00000185753|CXorf38|ENST00000378418||||-/155|protein_coding,upstream_gene_variant|||ENSG00000185753|CXorf38|ENST00000440784||||-/234|protein_coding,upstream_gene_variant|||ENSG00000185753|CXorf38|ENST00000378421||||-/200|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:83:83,0 0:5,0:5:99:0,135 .:0,0:.:.:. chrX 41554814 . T C 1530.64 PASS AC=2;AF=1;AN=2;DP=42;FS=0;GQ_MEAN=779;GQ_STDDEV=207.89;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=29.34;SOR=3.003;set=variant2;CSQ=intron_variant|||ENSG00000147044|CASK|ENST00000378163||||-/926|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000421587||||-/897|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378158||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378166||||-/921|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000442742||||-/898|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378154||||-/590|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000361962||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000318588||||-/921|protein_coding,5_prime_UTR_variant|||ENSG00000171659|GPR34|ENST00000378142|3/3|||-/381|protein_coding,intron_variant|||ENSG00000171659|GPR34|ENST00000378138||||-/381|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:926,0 .:0,0:.:.:. 1:0,16:16:99:632,0 chrX 41556195 . A T 763.64 PASS AC=1;AF=1;AN=1;DP=30;FS=0;GQ_MEAN=791;MLEAC=1;MLEAF=1;MQ=59.81;MQ0=0;NCC=2;QD=26.33;SOR=1.071;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000171659|GPR34|ENST00000378138|3/3|||-/381|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000318588||||-/921|protein_coding,3_prime_UTR_variant|||ENSG00000171659|GPR34|ENST00000378142|3/3|||-/381|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000361962||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378154||||-/590|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000442742||||-/898|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378166||||-/921|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378158||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000421587||||-/897|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378163||||-/926|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,29:29:99:791,0 .:0,0:.:.:. chrX 41587218 . T C 1615.64 PASS AC=3;AF=1;AN=3;DP=48;FS=0;GQ_MEAN=547.67;GQ_STDDEV=493.23;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.66;SOR=1.562;set=variant2;CSQ=intron_variant|||ENSG00000147044|CASK|ENST00000361962||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000318588||||-/921|protein_coding,upstream_gene_variant|||ENSG00000171657|GPR82|ENST00000497180|||||processed_transcript,intron_variant|||ENSG00000147044|CASK|ENST00000378163||||-/926|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000171657|GPR82|ENST00000302548|3/3|||313/336|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000421587||||-/897|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378158||||-/909|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378166||||-/921|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000442742||||-/898|protein_coding,intron_variant|||ENSG00000147044|CASK|ENST00000378154||||-/590|protein_coding GT:AD:DP:GQ:PL 1:0,32:32:99:1063,0 1:0,2:2:80:80,0 1:0,14:14:99:500,0 chrX 43591036 . G T 1151.87 PASS AC=2;AF=0.667;AN=3;DP=39;FS=0;GQ_MEAN=436.67;GQ_STDDEV=287.38;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.88;SOR=0.941;set=variant2;CSQ=downstream_gene_variant|||ENSG00000189221|MAOA|ENST00000497485|||||processed_transcript,synonymous_variant|cgG/cgT|R|ENSG00000189221|MAOA|ENST00000542639|9/16|||164/394|protein_coding,synonymous_variant|cgG/cgT|R|ENSG00000189221|MAOA|ENST00000338702|8/15|||297/527|protein_coding GT:AD:DP:GQ:PL 1:0,20:20:99:693,0 0:5,0:5:99:0,126 1:0,14:14:99:491,0 chrX 43603391 . T C 2033.87 PASS AC=2;AF=0.667;AN=3;DP=63;FS=0;GQ_MEAN=726.67;GQ_STDDEV=538;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.47;SOR=1.034;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000189221|MAOA|ENST00000490604|2/3||||processed_transcript,synonymous_variant|gaT/gaC|D|ENSG00000189221|MAOA|ENST00000338702|14/15|||470/527|protein_coding,synonymous_variant|gaT/gaC|D|ENSG00000189221|MAOA|ENST00000542639|15/16|||337/394|protein_coding GT:AD:DP:GQ:PL 1:0,26:26:99:944,0 0:4,0:4:99:0,114 1:0,33:33:99:1122,0 chrX 44202890 . G GC 1859.64 PASS AC=3;AF=1;AN=3;DP=56;FS=0;GQ_MEAN=629;GQ_STDDEV=289.75;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.46;SOR=1.848;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000183690|EFHC2|ENST00000420999|1/15|||-/749|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:598,0 1:0,25:25:99:933,0 1:0,10:10:99:356,0 chrX 44703935 . T C 124.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=0.747;ClippingRankSum=-0.747;DP=14;FS=0;GQ_MEAN=127.33;GQ_STDDEV=26.08;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;MQRankSum=0.747;NCC=0;QD=15.61;ReadPosRankSum=-0.747;SOR=0.693;set=variant2;CSQ=missense_variant|aTg/aCg|M/T|ENSG00000189037|DUSP21|ENST00000339042|1/1|benign(0)|tolerated(0.39)|186/190|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,117 1:1,7:8:99:157,0 0:3,0:3:99:0,108 chrX 44938563 . G A 1235.87 PASS AC=2;AF=0.667;AN=3;DP=44;FS=0;GQ_MEAN=467.67;GQ_STDDEV=302.43;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.69;SOR=0.743;set=variant2;CSQ=synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000536777|19/28|||992/1356|protein_coding,synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000433797|9/18|||680/1044|protein_coding,synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000377967|20/29|||1037/1401|protein_coding,upstream_gene_variant|||ENSG00000147050|KDM6A|ENST00000485072|||||processed_transcript,synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000543216|18/27|||958/1322|protein_coding,synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000382899|20/29|||1044/1408|protein_coding,upstream_gene_variant|||ENSG00000147050|KDM6A|ENST00000484732|||||processed_transcript,synonymous_variant|caG/caA|Q|ENSG00000147050|KDM6A|ENST00000414389|8/17|||635/999|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:726,0 0:5,0:5:99:0,135 1:0,16:16:99:542,0 chrX 45021592 . A G 187.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=215;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.27;SOR=3.912;set=variant2;CSQ=intron_variant|||ENSG00000147113|CXorf36|ENST00000398000||||-/433|protein_coding,3_prime_UTR_variant|||ENSG00000147113|CXorf36|ENST00000377934|3/3|||-/182|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000147113|CXorf36|ENST00000477281|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:215,0 .:0,0:.:.:. chrX 45023327 . G A 278.87 PASS AC=1;AF=0.333;AN=3;DP=17;FS=0;GQ_MEAN=177;GQ_STDDEV=116.2;MLEAC=1;MLEAF=0.333;MQ=58.34;MQ0=0;NCC=0;QD=25.35;SOR=1.802;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147113|CXorf36|ENST00000377934|3/3|||-/182|protein_coding,intron_variant|||ENSG00000147113|CXorf36|ENST00000398000||||-/433|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000147113|CXorf36|ENST00000477281|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,116 1:0,11:11:99:311,0 0:3,0:3:99:0,104 chrX 45051111 . C T 361.87 PASS AC=1;AF=0.333;AN=3;DP=22;FS=0;GQ_MEAN=206;GQ_STDDEV=162.84;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=22.62;SOR=0.941;set=variant2;CSQ=missense_variant|aGa/aAa|R/K|ENSG00000147113|CXorf36|ENST00000377934|2/3|benign(0.136)|tolerated(0.43)|128/182|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000147113|CXorf36|ENST00000398000|2/5|benign(0.023)|tolerated(0.61)|128/433|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147113|CXorf36|ENST00000477281|1/3||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000229491|RP11-342D14.1|ENST00000438181|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000229491|RP11-342D14.1|ENST00000450527|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147113|CXorf36|ENST00000492138|1/2||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,115 1:0,16:16:99:394,0 0:3,0:3:99:0,109 chrX 46457786 . G A 1243.64 PASS AC=1;AF=1;AN=1;DP=53;FS=0;GQ_MEAN=1271;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.46;SOR=0.808;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147119|CHST7|ENST00000276055|2/2|||-/486|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,53:53:99:1271,0 .:0,0:.:.:. chrX 46472826 . G A 1553.64 PASS AC=3;AF=1;AN=3;DP=49;FS=0;GQ_MEAN=527;GQ_STDDEV=254.21;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.71;SOR=0.733;set=variant2;CSQ=synonymous_variant|taC/taT|Y|ENSG00000065923|SLC9A7|ENST00000328306|16/17|||608/725|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000065923|SLC9A7|ENST00000489574|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000065923|SLC9A7|ENST00000464933|4/6||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000065923|SLC9A7|ENST00000491894|2/4||||processed_transcript GT:AD:DP:GQ:PL 1:0,21:21:99:736,0 1:0,10:10:99:244,0 1:0,18:18:99:601,0 chrX 46618321 . C G 2616.64 PASS AC=3;AF=1;AN=3;DP=89;FS=0;GQ_MEAN=881.33;GQ_STDDEV=372.18;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.4;SOR=0.761;set=variant2;CSQ=synonymous_variant|gcG/gcC|A|ENSG00000065923|SLC9A7|ENST00000328306|1/17|||48/725|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:868,0 1:0,21:21:99:516,0 1:0,40:40:99:1260,0 chrX 46740032 . G A 315.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=343;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.28;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102218|RP2|ENST00000218340|5/5|||-/350|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:343,0 .:0,0:.:.:. chrX 46918916 . C CA 1205.64 PASS AC=1;AF=1;AN=1;DP=31;FS=0;GQ_MEAN=1233;MLEAC=1;MLEAF=1;MQ=60.35;MQ0=0;NCC=2;QD=28.81;SOR=0.892;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000397189|11/11|||-/823|protein_coding,3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000218343|11/11|||-/823|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:1233,0 .:0,0:.:.:. chrX 46918950 . C CA 967.64 PASS AC=1;AF=1;AN=1;DP=24;FS=0;GQ_MEAN=995;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=33.9;SOR=0.776;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000218343|11/11|||-/823|protein_coding,3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000397189|11/11|||-/823|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:995,0 .:0,0:.:.:. chrX 46918957 . C CA 863.64 PASS AC=1;AF=1;AN=1;DP=20;FS=0;GQ_MEAN=891;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000397189|11/11|||-/823|protein_coding,3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000218343|11/11|||-/823|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:891,0 .:0,0:.:.:. chrX 46918974 . C CA 269.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=297;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.96;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000218343|11/11|||-/823|protein_coding,3_prime_UTR_variant|||ENSG00000102221|JADE3|ENST00000397189|11/11|||-/823|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:297,0 .:0,0:.:.:. chrX 47062534 . G A 1044.87 PASS AC=2;AF=0.667;AN=3;DP=37;FS=0;GQ_MEAN=398;GQ_STDDEV=288.26;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.66;SOR=0.88;set=variant2;CSQ=downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000412206||||-/270|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000442035||||-/284|protein_coding,missense_variant&splice_region_variant|cGc/cAc|R/H|ENSG00000130985|UBA1|ENST00000377351|13/26|benign(0.002)|tolerated(0.13)|447/1058|protein_coding,upstream_gene_variant|||ENSG00000224975|INE1|ENST00000456273|||||sense_intronic,splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130985|UBA1|ENST00000490869|3/6||||processed_transcript,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000457753||||-/195|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000427561||||-/173|protein_coding,missense_variant&splice_region_variant|cGc/cAc|R/H|ENSG00000130985|UBA1|ENST00000335972|13/26|benign(0.002)|tolerated(0.13)|447/1058|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000451702||||-/234|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:693,0 0:3,0:3:99:0,117 1:0,12:12:99:384,0 chrX 47065186 . G A 363.64 PASS AC=2;AF=1;AN=2;DP=11;FS=0;GQ_MEAN=195.5;GQ_STDDEV=123.74;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.06;SOR=4.977;set=variant2;CSQ=intron_variant|||ENSG00000130985|UBA1|ENST00000335972||||-/1058|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000451702||||-/234|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000130985|UBA1|ENST00000490869|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224975|INE1|ENST00000456273|1/1||||sense_intronic,upstream_gene_variant|||ENSG00000130985|UBA1|ENST00000377269||||-/506|protein_coding,intron_variant|||ENSG00000130985|UBA1|ENST00000377351||||-/1058|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000442035||||-/284|protein_coding,downstream_gene_variant|||ENSG00000130985|UBA1|ENST00000412206||||-/270|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:108,0 .:0,0:.:.:. 1:0,8:8:99:283,0 chrX 47341885 . C T 80.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=108;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=16.13;SOR=1.022;set=variant2;CSQ=intron_variant|||ENSG00000147124|ZNF41|ENST00000377065||||-/779|protein_coding,upstream_gene_variant|||ENSG00000196741|CXorf24|ENST00000357412||||-/94|protein_coding,5_prime_UTR_variant|||ENSG00000147124|ZNF41|ENST00000397050|1/5|||-/789|protein_coding,5_prime_UTR_variant|||ENSG00000147124|ZNF41|ENST00000313116|1/5|||-/779|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:108,0 .:0,0:.:.:. chrX 47341999 . T TGCGTGCGCGC 477.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=505;MLEAC=1;MLEAF=1;MQ=61.94;MQ0=0;NCC=2;QD=13.03;SOR=0.859;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000147124|ZNF41|ENST00000377065|1/5|||-/779|protein_coding,5_prime_UTR_variant|||ENSG00000147124|ZNF41|ENST00000397050|1/5|||-/789|protein_coding,upstream_gene_variant|||ENSG00000147124|ZNF41|ENST00000313116||||-/779|protein_coding,upstream_gene_variant|||ENSG00000196741|CXorf24|ENST00000357412||||-/94|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:505,0 .:0,0:.:.:. chrX 47444985 . T C 279.87 PASS AC=1;AF=0.333;AN=3;DP=18;FS=0;GQ_MEAN=176.67;GQ_STDDEV=117.55;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=23.32;SOR=0.693;set=variant2;CSQ=intron_variant|||ENSG00000008056|SYN1|ENST00000340666||||-/669|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000102265|TIMP1|ENST00000377017|4/5|||60/143|protein_coding,intron_variant|||ENSG00000008056|SYN1|ENST00000295987||||-/705|protein_coding,upstream_gene_variant|||ENSG00000263858|MIR4769|ENST00000584126|||||miRNA,downstream_gene_variant|||ENSG00000102265|TIMP1|ENST00000441738||||-/95|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000102265|TIMP1|ENST00000218388|5/6|||124/207|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000102265|TIMP1|ENST00000445623|1/2|||82/165|protein_coding,3_prime_UTR_variant|||ENSG00000102265|TIMP1|ENST00000456754|4/4|||-/136|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000102265|TIMP1|ENST00000377018|3/3|||118/261|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,118 1:0,12:12:99:312,0 0:3,0:3:99:0,100 chrX 47466361 . A G 1387.64 PASS AC=3;AF=1;AN=3;DP=46;FS=0;GQ_MEAN=471.67;GQ_STDDEV=141.99;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.17;SOR=2.303;set=variant2;CSQ=synonymous_variant|aaT/aaC|N|ENSG00000008056|SYN1|ENST00000340666|3/13|||170/669|protein_coding,synonymous_variant|aaT/aaC|N|ENSG00000008056|SYN1|ENST00000295987|3/13|||170/705|protein_coding GT:AD:DP:GQ:PL 1:0,17:17:99:603,0 1:0,19:19:99:491,0 1:0,10:10:99:321,0 chrX 47483800 . G A 2238.64 PASS AC=3;AF=1;AN=3;DP=70;FS=0;GQ_MEAN=755.33;GQ_STDDEV=565.91;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.41;SOR=2.483;set=variant2;CSQ=downstream_gene_variant|||ENSG00000126759|CFP|ENST00000377005||||-/415|protein_coding,downstream_gene_variant|||ENSG00000126759|CFP|ENST00000485991|||||retained_intron,synonymous_variant|aaC/aaT|N|ENSG00000126759|CFP|ENST00000396992|9/9|||428/469|protein_coding,downstream_gene_variant|||ENSG00000126759|CFP|ENST00000469388||||-/167|protein_coding,downstream_gene_variant|||ENSG00000126759|CFP|ENST00000480317|||||processed_transcript,synonymous_variant|aaC/aaT|N|ENSG00000126759|CFP|ENST00000247153|10/10|||428/469|protein_coding,upstream_gene_variant|||ENSG00000008056|SYN1|ENST00000295987||||-/705|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000126759|CFP|ENST00000478222|3/3||||retained_intron,upstream_gene_variant|||ENSG00000008056|SYN1|ENST00000340666||||-/669|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1217,0 1:0,5:5:99:124,0 1:0,27:27:99:925,0 chrX 47519504 . C CCCTT 332.87 PASS AC=2;AF=0.667;AN=3;DP=21;FS=0;GQ_MEAN=136.67;GQ_STDDEV=82.25;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=27.74;SOR=2.093;set=variant;CSQ=upstream_gene_variant|||ENSG00000126756|UXT|ENST00000335890||||-/169|protein_coding,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000485641||||-/99|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000267064|UXT-AS1|ENST00000590504|1/1||||antisense,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000376964|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000267064|UXT-AS1|ENST00000591832|2/2||||antisense,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000460840|||||processed_transcript,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000333119||||-/157|protein_coding GT:AD:DP:GQ:PL 1:0,5:5:99:204,0 0:4,0:4:45:0,45 1:0,4:4:99:161,0 chrX 47519533 . TTCTC T 231.64 PASS AC=2;AF=1;AN=2;DP=9;FS=0;GQ_MEAN=129.5;GQ_STDDEV=71.42;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=28.96;SOR=2.303;set=variant;CSQ=upstream_gene_variant|||ENSG00000126756|UXT|ENST00000335890||||-/169|protein_coding,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000376964|||||retained_intron,downstream_gene_variant|||ENSG00000267064|UXT-AS1|ENST00000591832|||||antisense,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000333119||||-/157|protein_coding,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000460840|||||processed_transcript,upstream_gene_variant|||ENSG00000126756|UXT|ENST00000485641||||-/99|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000267064|UXT-AS1|ENST00000590504|1/1||||antisense GT:AD:DP:GQ:PL 1:0,4:4:99:180,0 .:0,0:.:.:. 1:0,2:2:79:79,0 chrX 47834715 . A ACTT 62.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=90;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.32;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000147118|ZNF182|ENST00000396965|7/7|||-/639|protein_coding,intron_variant|||ENSG00000197779|ZNF81|ENST00000376950||||-/103|protein_coding,3_prime_UTR_variant|||ENSG00000147118|ZNF182|ENST00000305127|7/7|||-/639|protein_coding,3_prime_UTR_variant|||ENSG00000147118|ZNF182|ENST00000376943|6/6|||-/620|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. .:0,0:.:.:. 1:0,2:2:90:90,0 chrX 47917686 . G A 1711.64 PASS AC=3;AF=1;AN=3;DP=41;FS=0;GQ_MEAN=579.67;GQ_STDDEV=809.47;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=35.02;SOR=0.843;set=variant2;CSQ=downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000428686||||-/214|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000221994|ZNF630|ENST00000428463||||-/88|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000276054|5/5|||-/533|protein_coding,3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000442455|5/5|||-/643|protein_coding,downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000421903||||-/40|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000238068|ZNF630-AS1|ENST00000436124|||||antisense,3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000409324|5/5|||-/657|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:135,0 1:0,36:36:99:1514,0 1:0,2:2:90:90,0 chrX 47917687 . G T 1711.64 PASS AC=3;AF=1;AN=3;DP=38;FS=0;GQ_MEAN=579.67;GQ_STDDEV=809.47;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.64;SOR=0.798;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000276054|5/5|||-/533|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000221994|ZNF630|ENST00000428463||||-/88|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000442455|5/5|||-/643|protein_coding,downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000428686||||-/214|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000238068|ZNF630-AS1|ENST00000436124|||||antisense,3_prime_UTR_variant|||ENSG00000221994|ZNF630|ENST00000409324|5/5|||-/657|protein_coding,downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000421903||||-/40|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:135,0 1:0,33:33:99:1514,0 1:0,2:2:90:90,0 chrX 47918205 . G A 2136.64 PASS AC=3;AF=1;AN=3;DP=67;FS=0;GQ_MEAN=721.33;GQ_STDDEV=616.22;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.37;SOR=0.754;set=variant2;CSQ=synonymous_variant|ccC/ccT|P|ENSG00000221994|ZNF630|ENST00000442455|5/5|||528/643|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000221994|ZNF630|ENST00000276054|5/5|||418/533|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000221994|ZNF630|ENST00000428463||||-/88|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000428686||||-/214|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000221994|ZNF630|ENST00000409324|5/5|||542/657|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000238068|ZNF630-AS1|ENST00000436124|||||antisense,downstream_gene_variant|||ENSG00000221994|ZNF630|ENST00000421903||||-/40|protein_coding GT:AD:DP:GQ:PL 1:0,39:39:99:1354,0 1:0,5:5:99:123,0 1:0,22:22:99:687,0 chrX 48046032 . T C 1006.64 PASS AC=1;AF=1;AN=1;DP=38;FS=0;GQ_MEAN=1034;MLEAC=1;MLEAF=1;MQ=55.67;MQ0=0;NCC=2;QD=26.49;SOR=0.798;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000165583|SSX5|ENST00000311798|9/9|||-/229|protein_coding,3_prime_UTR_variant|||ENSG00000165583|SSX5|ENST00000376923|7/7|||-/188|protein_coding,downstream_gene_variant|||ENSG00000165583|SSX5|ENST00000403001||||-/128|protein_coding,3_prime_UTR_variant|||ENSG00000165583|SSX5|ENST00000347757|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,38:38:99:1034,0 .:0,0:.:.:. chrX 48049666 . C T 1561.64 PASS AC=3;AF=1;AN=3;DP=57;FS=0;GQ_MEAN=529.67;GQ_STDDEV=363.12;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.4;SOR=1.14;set=variant2;CSQ=synonymous_variant|tcG/tcA|S|ENSG00000165583|SSX5|ENST00000403001|2/4|||63/128|protein_coding,synonymous_variant|tcG/tcA|S|ENSG00000165583|SSX5|ENST00000347757|6/8|||123/188|protein_coding,synonymous_variant|tcG/tcA|S|ENSG00000165583|SSX5|ENST00000376923|5/7|||123/188|protein_coding,synonymous_variant|tcG/tcA|S|ENSG00000165583|SSX5|ENST00000311798|7/9|||164/229|protein_coding GT:AD:DP:GQ:PL 1:0,11:11:99:408,0 1:0,39:39:99:938,0 1:0,7:7:99:243,0 chrX 48054740 . C G 2589.64 PASS AC=3;AF=1;AN=3;DP=79;FS=0;GQ_MEAN=872.33;GQ_STDDEV=314.14;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.78;SOR=1.522;set=variant2;CSQ=upstream_gene_variant|||ENSG00000165583|SSX5|ENST00000403001||||-/128|protein_coding,missense_variant|Gag/Cag|E/Q|ENSG00000165583|SSX5|ENST00000347757|2/8|probably_damaging(0.993)|deleterious(0.04)|19/188|protein_coding,upstream_gene_variant|||ENSG00000234780|RP11-552E4.2|ENST00000437312|||||processed_pseudogene,missense_variant|Gag/Cag|E/Q|ENSG00000165583|SSX5|ENST00000376923|1/7|probably_damaging(0.993)|deleterious(0.04)|19/188|protein_coding,missense_variant|Gag/Cag|E/Q|ENSG00000165583|SSX5|ENST00000311798|2/9|probably_damaging(0.999)|deleterious_low_confidence(0)|19/229|protein_coding GT:AD:DP:GQ:PL 1:0,33:33:99:1153,0 1:0,19:19:99:533,0 1:0,27:27:99:931,0 chrX 48056189 . C G 1494.64 PASS AC=1;AF=1;AN=1;DP=55;FS=0;GQ_MEAN=1522;MLEAC=1;MLEAF=1;MQ=59.95;MQ0=0;NCC=2;QD=27.18;SOR=0.97;set=variant2;CSQ=upstream_gene_variant|||ENSG00000165583|SSX5|ENST00000376923||||-/188|protein_coding,5_prime_UTR_variant|||ENSG00000165583|SSX5|ENST00000311798|1/9|||-/229|protein_coding,5_prime_UTR_variant|||ENSG00000165583|SSX5|ENST00000347757|1/8|||-/188|protein_coding,upstream_gene_variant|||ENSG00000165583|SSX5|ENST00000403001||||-/128|protein_coding,upstream_gene_variant|||ENSG00000234780|RP11-552E4.2|ENST00000437312|||||processed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,55:55:99:1522,0 .:0,0:.:.:. chrX 48125798 . T C 695.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.62;ClippingRankSum=-0.924;DP=31;FS=0;GQ_MEAN=723;MLEAC=1;MLEAF=1;MQ=40.1;MQ0=0;MQRankSum=1.27;NCC=2;QD=23.19;ReadPosRankSum=0.578;SOR=0.314;set=variant2;CSQ=synonymous_variant|agT/agC|S|ENSG00000126752|SSX1|ENST00000376919|7/8|||181/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,29:30:99:723,0 .:0,0:.:.:. chrX 48126414 . G GA 242.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=270;MLEAC=1;MLEAF=1;MQ=50.7;MQ0=0;NCC=2;QD=33.01;SOR=2.303;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000126752|SSX1|ENST00000376919|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:270,0 .:0,0:.:.:. chrX 48126418 . C G 242.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=270;MLEAC=1;MLEAF=1;MQ=47.19;MQ0=0;NCC=2;QD=34.44;SOR=2.303;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000126752|SSX1|ENST00000376919|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:270,0 .:0,0:.:.:. chrX 48126602 . C G 428.64 PASS AC=1;AF=1;AN=1;DP=17;FS=0;GQ_MEAN=456;MLEAC=1;MLEAF=1;MQ=45.51;MQ0=0;NCC=2;QD=25.21;SOR=1.061;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000126752|SSX1|ENST00000376919|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,17:17:99:456,0 .:0,0:.:.:. chrX 48126713 . C CACACACA 219.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=247;MLEAC=1;MLEAF=1;MQ=52.89;MQ0=0;NCC=2;QD=31.38;SOR=1.179;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000126752|SSX1|ENST00000376919|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:99:247,0 .:0,0:.:.:. chrX 48126714 . G GAGAGAGA 219.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=247;MLEAC=1;MLEAF=1;MQ=34.31;MQ0=0;NCC=2;QD=18.83;SOR=1.981;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000126752|SSX1|ENST00000376919|8/8|||-/188|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:247,0 .:0,0:.:.:. chrX 48155051 . C G 91.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=119;MLEAC=1;MLEAF=1;MQ=41.21;MQ0=0;NCC=2;QD=30.55;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000407081|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000376909|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:99:119,0 .:0,0:.:.:. chrX 48155136 . G C 1028.64 PASS AC=1;AF=1;AN=1;DP=40;FS=0;GQ_MEAN=1056;MLEAC=1;MLEAF=1;MQ=48.55;MQ0=0;NCC=2;QD=26.38;SOR=1.236;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000407081|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000376909|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,39:39:99:1056,0 .:0,0:.:.:. chrX 48155262 . A G 711.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.5;ClippingRankSum=0.06;DP=21;FS=0;GQ_MEAN=739;MLEAC=1;MLEAF=1;MQ=44.58;MQ0=0;MQRankSum=-1.977;NCC=2;QD=33.89;ReadPosRankSum=-0.419;SOR=1.292;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000407081|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000376909|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,19:21:99:739,0 .:0,0:.:.:. chrX 48155263 . T C 711.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.74;ClippingRankSum=1.02;DP=21;FS=0;GQ_MEAN=739;MLEAC=1;MLEAF=1;MQ=44.58;MQ0=0;MQRankSum=-1.857;NCC=2;QD=33.89;ReadPosRankSum=0.539;SOR=1.292;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000407081|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000376909|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,19:21:99:739,0 .:0,0:.:.:. chrX 48155343 . A C 954.64 PASS AC=1;AF=1;AN=1;DP=38;FS=0;GQ_MEAN=982;MLEAC=1;MLEAF=1;MQ=49.97;MQ0=0;NCC=2;QD=25.8;SOR=0.984;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000407081|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000376909|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:982,0 .:0,0:.:.:. chrX 48156264 . G A 213.64 my_snp_filter AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=241;MLEAC=1;MLEAF=1;MQ=28.06;MQ0=0;NCC=2;QD=21.36;SOR=0.693;set=FilteredInAll;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000376909|6/6||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000407081|7/7||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000204648|SSX9|ENST00000608568|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:241,0 .:0,0:.:.:. chrX 48161189 . A G 1158.64 PASS AC=1;AF=1;AN=1;DP=46;FS=0;GQ_MEAN=1186;MLEAC=1;MLEAF=1;MQ=55.16;MQ0=0;NCC=2;QD=25.75;SOR=0.829;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000376909|4/6||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000608568|5/5||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000407081|5/7||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,45:45:99:1186,0 .:0,0:.:.:. chrX 48163105 . A G 515.64 PASS AC=3;AF=1;AN=3;DP=22;FS=0;GQ_MEAN=181;GQ_STDDEV=187.01;MLEAC=3;MLEAF=1;MQ=58.79;MQ0=0;NCC=0;QD=23.44;SOR=0.693;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000376909|3/6||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000234391|RP11-344N17.6|ENST00000453735|||||processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000608568|4/5||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000407081|4/7||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,4:4:99:99,0 1:0,16:16:99:395,0 1:0,2:2:49:49,0 chrX 48163717 . C T 1213.64 PASS AC=1;AF=1;AN=1;DP=47;FS=0;GQ_MEAN=1241;MLEAC=1;MLEAF=1;MQ=52.11;MQ0=0;NCC=2;QD=25.82;SOR=0.919;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000376909|2/6||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000234391|RP11-344N17.6|ENST00000453735|||||processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000608568|3/5||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204648|SSX9|ENST00000407081|3/7||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,47:47:99:1241,0 .:0,0:.:.:. chrX 48435928 . C T 756.64 PASS AC=1;AF=1;AN=1;DP=32;FS=0;GQ_MEAN=784;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.41;SOR=0.892;set=variant2;CSQ=missense_variant|cCg/cTg|P/L|ENSG00000102317|RBM3|ENST00000430348|6/6|benign(0)||164/169|protein_coding,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000488216|||||processed_transcript,upstream_gene_variant|||ENSG00000204620|AC115618.1|ENST00000376775||||-/129|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102317|RBM3|ENST00000489344|6/6||||processed_transcript,downstream_gene_variant|||ENSG00000228343|RP11-1148L6.5|ENST00000453810|||||antisense,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000491236|||||processed_transcript,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000485213|||||processed_transcript,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000490127|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102317|RBM3|ENST00000354480|3/3|||-/155|protein_coding,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000472897|||||processed_transcript,downstream_gene_variant|||ENSG00000102317|RBM3|ENST00000491240|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102317|RBM3|ENST00000376759|7/7|||-/157|protein_coding,3_prime_UTR_variant|||ENSG00000102317|RBM3|ENST00000376755|6/6|||-/157|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102317|RBM3|ENST00000466764|8/8||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:784,0 .:0,0:.:.:. chrX 48456223 . G T 1493.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=2.72;ClippingRankSum=1.48;DP=67;FS=11.532;GQ_MEAN=507;GQ_STDDEV=217.54;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.992;NCC=0;QD=22.29;ReadPosRankSum=0.992;SOR=1.205;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000470124|||||processed_transcript,5_prime_UTR_variant|||ENSG00000101940|WDR13|ENST00000218056|1/9|||-/485|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000472440|||||processed_transcript,intron_variant|||ENSG00000101940|WDR13|ENST00000376729||||-/485|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000492715|1/2||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000471334|||||processed_transcript,upstream_gene_variant|||ENSG00000101940|WDR13|ENST00000495575|||||processed_transcript,upstream_gene_variant|||ENSG00000101940|WDR13|ENST00000482760|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000479279|1/8||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000486125|1/4||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000498631|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000497756|||||processed_transcript,upstream_gene_variant|||ENSG00000101940|WDR13|ENST00000466962|||||processed_transcript GT:AD:DP:GQ:PL 1:1,13:14:99:390,0 1:4,38:42:99:758,0 1:0,11:11:99:373,0 chrX 48460314 . A G 3606.64 PASS AC=3;AF=1;AN=3;DP=115;FS=0;GQ_MEAN=1211.33;GQ_STDDEV=842.11;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.92;SOR=1.081;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000495575|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000482760|2/5||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000492715|||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000471334|||||processed_transcript,missense_variant|cAt/cGt|H/R|ENSG00000101940|WDR13|ENST00000376729|7/10|benign(0)||325/485|protein_coding,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000472440|||||processed_transcript,missense_variant|cAt/cGt|H/R|ENSG00000101940|WDR13|ENST00000218056|6/9|benign(0)||325/485|protein_coding,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000470124|||||processed_transcript,upstream_gene_variant|||ENSG00000101940|WDR13|ENST00000492873|||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000466962|||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000497756|||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000498631|||||processed_transcript,downstream_gene_variant|||ENSG00000101940|WDR13|ENST00000486125|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101940|WDR13|ENST00000479279|5/8||||processed_transcript GT:AD:DP:GQ:PL 1:0,57:57:99:1846,0 1:0,9:9:99:256,0 1:0,47:47:99:1532,0 chrX 48819439 . C T 288.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=316;MLEAC=1;MLEAF=1;MQ=58.81;MQ0=0;NCC=2;QD=22.2;SOR=1.179;set=variant2;CSQ=upstream_gene_variant|||ENSG00000068308|OTUD5|ENST00000455452||||-/444|protein_coding,downstream_gene_variant|||ENSG00000102057|KCND1|ENST00000419374||||-/133|protein_coding,upstream_gene_variant|||ENSG00000223309|RNU6-722P|ENST00000411377|||||snRNA,upstream_gene_variant|||ENSG00000068308|OTUD5|ENST00000428668||||-/349|protein_coding,upstream_gene_variant|||ENSG00000068308|OTUD5|ENST00000376488||||-/566|protein_coding,upstream_gene_variant|||ENSG00000068308|OTUD5|ENST00000156084||||-/571|protein_coding,3_prime_UTR_variant|||ENSG00000102057|KCND1|ENST00000218176|6/6|||-/647|protein_coding,upstream_gene_variant|||ENSG00000068308|OTUD5|ENST00000396743||||-/566|protein_coding,3_prime_UTR_variant|||ENSG00000102057|KCND1|ENST00000376477|5/5|||-/270|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:316,0 .:0,0:.:.:. chrX 48847497 . T C 4564.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=0.319;ClippingRankSum=0.365;DP=135;FS=4.582;GQ_MEAN=2296;GQ_STDDEV=354.97;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.501;NCC=1;QD=33.81;ReadPosRankSum=-0.775;SOR=1.344;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000068400|GRIPAP1|ENST00000473581|1/16||||processed_transcript,synonymous_variant|gaA/gaG|E|ENSG00000068400|GRIPAP1|ENST00000376425|7/25|||161/810|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000068400|GRIPAP1|ENST00000376444|5/24|||116/796|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000068400|GRIPAP1|ENST00000376441|7/26|||161/841|protein_coding,synonymous_variant|gaA/gaG|E|ENSG00000068400|GRIPAP1|ENST00000376423|6/20|||108/625|protein_coding,upstream_gene_variant|||ENSG00000068400|GRIPAP1|ENST00000474512|||||processed_transcript GT:AD:DP:GQ:PL 1:1,75:76:99:2547,0 .:0,0:.:.:. 1:0,59:59:99:2045,0 chrX 48888074 . T C 433.64 PASS AC=2;AF=1;AN=2;DP=14;FS=0;GQ_MEAN=230.5;GQ_STDDEV=92.63;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.36;SOR=2.833;set=variant2;CSQ=downstream_gene_variant|||ENSG00000068323|TFE3|ENST00000487451|||||processed_transcript,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000068323|TFE3|ENST00000493583|10/10|||-/109|nonsense_mediated_decay,synonymous_variant|gtA/gtG|V|ENSG00000068323|TFE3|ENST00000315869|10/10|||441/575|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000068323|TFE3|ENST00000495940|2/2||||retained_intron GT:AD:DP:GQ:PL 1:0,4:4:99:165,0 .:0,0:.:.:. 1:0,9:9:99:296,0 chrX 48900900 . T G 354.64 PASS AC=2;AF=1;AN=2;DP=11;FS=0;GQ_MEAN=191;GQ_STDDEV=50.91;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.89;SOR=4.804;set=variant2;CSQ=upstream_gene_variant|||ENSG00000068323|TFE3|ENST00000487451|||||processed_transcript,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000068323|TFE3|ENST00000493583|1/10|||-/109|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000068323|TFE3|ENST00000315869|1/10|||-/575|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:227,0 .:0,0:.:.:. 1:0,4:4:99:155,0 chrX 48932443 . A T 2004.64 PASS AC=3;AF=1;AN=3;DP=65;FS=0;GQ_MEAN=677.33;GQ_STDDEV=440.67;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.32;SOR=1.214;set=variant2;CSQ=downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000419567||||-/190|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000475880||||-/166|protein_coding,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000356463|12/12|||-/361|protein_coding,intron_variant|||ENSG00000250232|AF196779.12|ENST00000376358||||-/292|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000465382||||-/158|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000496803|||||retained_intron,intron_variant|||ENSG00000196998|WDR45|ENST00000553851||||-/292|protein_coding,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000376372|11/11|||-/360|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000465431|||||processed_transcript,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000367375|8/8|||-/287|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000396681||||-/346|protein_coding,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000376368|11/11|||-/361|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000474053||||-/213|protein_coding,downstream_gene_variant|||ENSG00000147144|CCDC120|ENST00000376396||||-/630|protein_coding,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000486337|2/2|||-/81|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000476728||||-/138|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000472654|||||retained_intron,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000480412|||||retained_intron,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000473974|9/9|||-/256|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000196998|WDR45|ENST00000465806|11/11||||retained_intron,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000376357|||||retained_intron,downstream_gene_variant|||ENSG00000147144|CCDC120|ENST00000422185||||-/661|protein_coding,upstream_gene_variant|||ENSG00000243279|PRAF2|ENST00000376386||||-/160|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000471338||||-/142|protein_coding,upstream_gene_variant|||ENSG00000243279|PRAF2|ENST00000376390||||-/178|protein_coding,upstream_gene_variant|||ENSG00000243279|PRAF2|ENST00000491199|||||processed_transcript,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000485908|10/10|||-/325|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000196998|WDR45|ENST00000433252|3/3||||retained_intron,3_prime_UTR_variant|||ENSG00000196998|WDR45|ENST00000322995|11/11|||-/371|protein_coding,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000475977||||-/118|protein_coding,downstream_gene_variant|||ENSG00000147144|CCDC120|ENST00000603745|||||retained_intron,downstream_gene_variant|||ENSG00000196998|WDR45|ENST00000423215||||-/55|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:988,0 1:0,7:7:99:173,0 1:0,27:27:99:871,0 chrX 49021256 . A G 7361.64 PASS AC=3;AF=1;AN=3;DP=231;FS=0;GQ_MEAN=2463;GQ_STDDEV=1098.12;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.01;SOR=1.077;set=variant2;CSQ=missense_variant|cAt/cGt|H/R|ENSG00000017621|MAGIX|ENST00000415364|3/5|benign(0)||81/237|protein_coding,missense_variant|cAt/cGt|H/R|ENSG00000017621|MAGIX|ENST00000425285|3/5|benign(0)||58/214|protein_coding,intron_variant|||ENSG00000017621|MAGIX|ENST00000454342||||-/143|protein_coding,missense_variant|cAt/cGt|H/R|ENSG00000017621|MAGIX|ENST00000376339|2/4|benign(0.001)||53/270|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000017621|MAGIX|ENST00000498742|2/4||||processed_transcript,intron_variant|||ENSG00000017621|MAGIX|ENST00000458388||||-/201|protein_coding,missense_variant|cAt/cGt|H/R|ENSG00000017621|MAGIX|ENST00000376338|2/4|benign(0.001)||53/275|protein_coding,intron_variant|||ENSG00000017621|MAGIX|ENST00000425661||||-/258|protein_coding,missense_variant|cAt/cGt|H/R|ENSG00000017621|MAGIX|ENST00000412696|4/6|benign(0)||112/334|protein_coding GT:AD:DP:GQ:PL 1:0,92:92:99:3100,0 1:0,47:47:99:1195,0 1:0,91:91:99:3094,0 chrX 49021537 . G C 2006.64 PASS AC=3;AF=1;AN=3;DP=64;FS=0;GQ_MEAN=678;GQ_STDDEV=104.1;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.35;SOR=1.044;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000017621|MAGIX|ENST00000498742|3/4||||processed_transcript,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000458388|4/5|benign(0)||103/201|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000376339|3/4|benign(0)||114/270|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000454342|2/3|benign(0)||45/143|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000415364|4/5|benign(0)||142/237|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000425285|4/5|benign(0.001)||119/214|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000425661|4/5|benign(0)||97/258|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000412696|5/6|benign(0.001)||173/334|protein_coding,missense_variant|Gtc/Ctc|V/L|ENSG00000017621|MAGIX|ENST00000376338|3/4|benign(0.002)||114/275|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:732,0 1:0,21:21:99:558,0 1:0,22:22:99:744,0 chrX 49022700 . T C 1832.64 PASS AC=3;AF=1;AN=3;DP=54;FS=0;GQ_MEAN=620;GQ_STDDEV=541.16;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.69;SOR=1.654;set=variant2;CSQ=downstream_gene_variant|||ENSG00000017621|MAGIX|ENST00000415364||||-/237|protein_coding,downstream_gene_variant|||ENSG00000017621|MAGIX|ENST00000425285||||-/214|protein_coding,downstream_gene_variant|||ENSG00000017621|MAGIX|ENST00000454342||||-/143|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000017621|MAGIX|ENST00000376339|4/4|benign(0.001)||259/270|protein_coding,downstream_gene_variant|||ENSG00000017621|MAGIX|ENST00000458388||||-/201|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000017621|MAGIX|ENST00000498742|4/4||||processed_transcript,missense_variant|Ttc/Ctc|F/L|ENSG00000017621|MAGIX|ENST00000376338|4/4|benign(0.001)||264/275|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000017621|MAGIX|ENST00000412696|6/6|benign(0)||323/334|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000017621|MAGIX|ENST00000425661|5/5|benign(0)||247/258|protein_coding GT:AD:DP:GQ:PL 1:0,20:20:99:714,0 1:0,1:1:38:38,0 1:0,32:32:99:1108,0 chrX 49179711 . A T 96.63 PASS AC=1;AF=0.5;AN=2;DP=8;FS=0;GQ_MEAN=154;GQ_STDDEV=38.18;MLEAC=1;MLEAF=0.5;MQ=40;MQ0=0;NCC=1;QD=31.33;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000215274|GAGE10|ENST00000407599||||-/116|protein_coding,missense_variant|agA/agT|R/S|ENSG00000224659|GAGE12J|ENST00000442437|2/5|benign(0.025)||13/117|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 0:6,0:6:99:0,181 1:0,2:2:99:127,0 chrX 49179719 . C G 1310.64 PASS AC=2;AF=1;AN=2;DP=16;FS=0;GQ_MEAN=669;GQ_STDDEV=766.5;MLEAC=2;MLEAF=1;MQ=40;MQ0=0;NCC=1;QD=26.81;SOR=1.244;set=variant2;CSQ=missense_variant|cCc/cGc|P/R|ENSG00000224659|GAGE12J|ENST00000442437|2/5|benign(0)||16/117|protein_coding,downstream_gene_variant|||ENSG00000215274|GAGE10|ENST00000407599||||-/116|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:1211,0 1:0,3:3:99:127,0 chrX 49179755 . G A 221.64 my_snp_filter AC=2;AF=1;AN=2;DP=10;FS=0;GQ_MEAN=124.5;GQ_STDDEV=12.02;MLEAC=2;MLEAF=1;MQ=37.19;MQ0=0;NCC=1;QD=22.16;SOR=0.693;set=FilteredInAll;CSQ=downstream_gene_variant|||ENSG00000215274|GAGE10|ENST00000407599||||-/116|protein_coding,missense_variant&splice_region_variant|cGg/cAg|R/Q|ENSG00000224659|GAGE12J|ENST00000442437|2/5|benign(0.372)||28/117|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:133,0 1:0,4:4:99:116,0 chrX 49369711 . A G 179.64 PASS AC=1;AF=1;AN=1;DP=9;FS=0;GQ_MEAN=207;MLEAC=1;MLEAF=1;MQ=56.34;MQ0=0;NCC=2;QD=19.96;SOR=0.892;set=variant2;CSQ=intron_variant|||ENSG00000205777|GAGE1|ENST00000381700||||-/117|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000205777|GAGE1|ENST00000381709|5/6|||-/139|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,9:9:99:207,0 .:0,0:.:.:. chrX 49767832 . A G 2214.64 PASS AC=3;AF=1;AN=3;DP=53;FS=0;GQ_MEAN=747.33;GQ_STDDEV=274.38;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.14;SOR=2.437;set=variant2;CSQ=intron_variant|||ENSG00000171365|CLCN5|ENST00000482218||||-/64|protein_coding,intron_variant|||ENSG00000171365|CLCN5|ENST00000376088||||-/816|protein_coding,intron_variant|||ENSG00000171365|CLCN5|ENST00000376091||||-/816|protein_coding,upstream_gene_variant|||ENSG00000265152|AF222686.1|ENST00000582167|||||miRNA,upstream_gene_variant|||ENSG00000207768|MIR188|ENST00000385034|||||miRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000207758|MIR532|ENST00000385025|1/1||||miRNA GT:AD:DP:GQ:PL 1:0,13:13:99:566,0 1:0,26:26:99:1063,0 1:0,14:14:99:613,0 chrX 49767835 . A G 1986.64 PASS AC=3;AF=1;AN=3;DP=44;FS=0;GQ_MEAN=671.33;GQ_STDDEV=207.16;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.2;SOR=2.885;set=variant2;CSQ=intron_variant|||ENSG00000171365|CLCN5|ENST00000376088||||-/816|protein_coding,intron_variant|||ENSG00000171365|CLCN5|ENST00000482218||||-/64|protein_coding,intron_variant|||ENSG00000171365|CLCN5|ENST00000376091||||-/816|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000207758|MIR532|ENST00000385025|1/1||||miRNA,upstream_gene_variant|||ENSG00000207768|MIR188|ENST00000385034|||||miRNA,upstream_gene_variant|||ENSG00000265152|AF222686.1|ENST00000582167|||||miRNA GT:AD:DP:GQ:PL 1:0,11:11:99:529,0 1:0,21:21:99:909,0 1:0,12:12:99:576,0 chrX 50121146 . A AG 2078.64 PASS AC=3;AF=1;AN=3;DP=56;FS=0;GQ_MEAN=702;GQ_STDDEV=549.08;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.47;SOR=1.009;set=variant;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000204466|DGKK|ENST00000376025|22/28||||processed_transcript,splice_region_variant&intron_variant&non_coding_transcript_variant|||ENSG00000204466|DGKK|ENST00000546288|||||processed_transcript GT:AD:DP:GQ:PL 1:0,29:29:99:1097,0 1:0,2:2:75:75,0 1:0,25:25:99:934,0 chrX 50336022 . A T 867.64 PASS AC=1;AF=1;AN=1;DP=37;FS=0;GQ_MEAN=895;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.45;SOR=0.859;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000158352|SHROOM4|ENST00000460112|8/8|||-/1377|protein_coding,3_prime_UTR_variant|||ENSG00000158352|SHROOM4|ENST00000376020|9/9|||-/1493|protein_coding,intron_variant|||ENSG00000158352|SHROOM4|ENST00000289292||||-/1493|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000158352|SHROOM4|ENST00000483955|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:895,0 .:0,0:.:.:. chrX 50653775 . C G 2722.64 PASS AC=3;AF=1;AN=3;DP=92;FS=0;GQ_MEAN=916.67;GQ_STDDEV=139.11;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.59;SOR=0.737;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130385|BMP15|ENST00000252677||||-/392|protein_coding,downstream_gene_variant|||ENSG00000226881|H3F3AP5|ENST00000475267|||||processed_pseudogene,downstream_gene_variant|||ENSG00000226881|H3F3AP5|ENST00000414444|||||processed_pseudogene GT:AD:DP:GQ:PL 1:0,30:30:99:953,0 1:0,39:39:99:1034,0 1:0,23:23:99:763,0 chrX 51239295 . ATCCTCGAGGCAGCC A 1345.87 PASS AC=2;AF=0.667;AN=3;DP=46;FS=0;GQ_MEAN=506;GQ_STDDEV=349.39;MLEAC=2;MLEAF=0.667;MQ=51.38;MQ0=0;NCC=0;QD=9.3;SOR=2.093;set=variant;CSQ=coding_sequence_variant&5_prime_UTR_variant|||ENSG00000196368|NUDT11|ENST00000375992|1/2|||?-1/164|protein_coding GT:AD:DP:GQ:PL 1:0,19:19:99:836,0 0:6,0:6:99:0,140 1:0,12:12:99:542,0 chrX 51486659 . C T 2795.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.732;ClippingRankSum=-0.433;DP=98;FS=0;GQ_MEAN=941;GQ_STDDEV=501.54;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.072;NCC=0;QD=29.43;ReadPosRankSum=-0.217;SOR=1.179;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000189369|GSPT2|ENST00000340438|1/1|||-/628|protein_coding GT:AD:DP:GQ:PL 1:1,47:48:99:1439,0 1:0,19:19:99:436,0 1:0,28:28:99:948,0 chrX 52825471 . A G 3902.64 PASS AC=3;AF=1;AN=3;DP=123;FS=0;GQ_MEAN=1310;GQ_STDDEV=465.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.73;SOR=1.274;set=variant2;CSQ=downstream_gene_variant|||ENSG00000229885|RP13-77O11.12|ENST00000452829|||||unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000204363|SPANXN5|ENST00000375511|2/2|||-/72|protein_coding GT:AD:DP:GQ:PL 1:0,54:54:99:1707,0 1:0,28:28:99:798,0 1:0,41:41:99:1425,0 chrX 52825546 . C G 3071.64 PASS AC=3;AF=1;AN=3;DP=98;FS=0;GQ_MEAN=1033;GQ_STDDEV=521.62;MLEAC=3;MLEAF=1;MQ=59.2;MQ0=0;NCC=0;QD=31.34;SOR=1.067;set=variant2;CSQ=synonymous_variant|ctG/ctC|L|ENSG00000204363|SPANXN5|ENST00000375511|2/2|||67/72|protein_coding,downstream_gene_variant|||ENSG00000229885|RP13-77O11.12|ENST00000452829|||||unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,46:46:99:1510,0 1:0,18:18:99:476,0 1:0,34:34:99:1113,0 chrX 52891584 . C T 883.64 PASS AC=3;AF=1;AN=3;DP=32;FS=0;GQ_MEAN=303.67;GQ_STDDEV=275.41;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.61;SOR=0.957;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000171402|XAGE3|ENST00000346279|5/5|||-/111|protein_coding,3_prime_UTR_variant|||ENSG00000171402|XAGE3|ENST00000375491|5/5|||-/111|protein_coding GT:AD:DP:GQ:PL 1:0,5:5:99:163,0 1:0,23:23:99:621,0 1:0,4:4:99:127,0 chrX 53220836 . G T 627.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=655;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.25;SOR=0.765;set=variant2;CSQ=downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000375379||||-/1557|protein_coding,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000404049||||-/1559|protein_coding,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000375383||||-/1516|protein_coding,3_prime_UTR_variant|||ENSG00000126012|KDM5C|ENST00000452825|24/24|||-/1379|protein_coding,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000375401||||-/1560|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,27:27:99:655,0 .:0,0:.:.:. chrX 53222043 . A AC 1472.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.476;ClippingRankSum=-1.605;DP=54;FS=0;GQ_MEAN=500;GQ_STDDEV=333.93;MLEAC=3;MLEAF=1;MQ=60.51;MQ0=0;MQRankSum=1.61;NCC=0;QD=28.88;ReadPosRankSum=-0.706;SOR=0.293;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000126012|KDM5C|ENST00000404049|26/26|||-/1559|protein_coding,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000375379||||-/1557|protein_coding,3_prime_UTR_variant|||ENSG00000126012|KDM5C|ENST00000375401|26/26|||-/1560|protein_coding,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000477109|||||processed_transcript,downstream_gene_variant|||ENSG00000126012|KDM5C|ENST00000375383||||-/1516|protein_coding,intron_variant|||ENSG00000126012|KDM5C|ENST00000452825||||-/1379|protein_coding GT:AD:DP:GQ:PL 1:1,26:27:99:762,0 1:0,4:4:99:124,0 1:0,20:20:99:614,0 chrX 53449568 . G A 3893.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.654;ClippingRankSum=-0.731;DP=121;FS=0;GQ_MEAN=1307;GQ_STDDEV=491.49;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.654;NCC=0;QD=32.18;ReadPosRankSum=1.35;SOR=0.549;set=variant2;CSQ=upstream_gene_variant|||ENSG00000072501|SMC1A|ENST00000428014||||-/262|protein_coding,5_prime_UTR_variant|||ENSG00000072501|SMC1A|ENST00000322213|1/25|||-/1233|protein_coding,upstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000375327||||-/379|protein_coding,upstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000414955||||-/238|protein_coding,5_prime_UTR_variant|||ENSG00000072501|SMC1A|ENST00000375340|1/10|||-/516|protein_coding,upstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000457095||||-/192|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000072501|SMC1A|ENST00000463684|1/4|||-/54|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000329209||||-/181|protein_coding GT:AD:DP:GQ:PL 1:1,44:45:99:1554,0 1:0,28:28:99:741,0 1:0,48:48:99:1626,0 chrX 53457622 . T C 2102.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.383;ClippingRankSum=-0.346;DP=69;FS=11.372;GQ_MEAN=710;GQ_STDDEV=481.96;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.622;NCC=0;QD=30.92;ReadPosRankSum=-0.622;SOR=0.814;set=variant2;CSQ=downstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000457095||||-/192|protein_coding,downstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000329209||||-/181|protein_coding,downstream_gene_variant|||ENSG00000072506|HSD17B10|ENST00000168216||||-/261|protein_coding,downstream_gene_variant|||ENSG00000072506|HSD17B10|ENST00000495986|||||processed_transcript,downstream_gene_variant|||ENSG00000158423|RIBC1|ENST00000490702|||||processed_transcript,synonymous_variant|acT/acC|T|ENSG00000158423|RIBC1|ENST00000375327|7/8|||314/379|protein_coding,downstream_gene_variant|||ENSG00000072506|HSD17B10|ENST00000375298||||-/169|protein_coding,synonymous_variant|acT/acC|T|ENSG00000158423|RIBC1|ENST00000414955|6/6|||199/238|protein_coding,downstream_gene_variant|||ENSG00000233250|RP3-339A18.6|ENST00000418049|||||antisense,downstream_gene_variant|||ENSG00000072506|HSD17B10|ENST00000477706|||||processed_transcript,downstream_gene_variant|||ENSG00000072506|HSD17B10|ENST00000375304||||-/252|protein_coding GT:AD:DP:GQ:PL 1:0,31:31:99:1122,0 1:0,7:7:99:180,0 1:3,27:30:99:828,0 chrX 53563589 . A G 1447.64 PASS AC=2;AF=1;AN=2;DP=44;FS=0;GQ_MEAN=737.5;GQ_STDDEV=48.79;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.9;SOR=1.23;set=variant2;CSQ=synonymous_variant|ggT/ggC|G|ENSG00000086758|HUWE1|ENST00000426907|13/18|||882/1197|protein_coding,synonymous_variant|ggT/ggC|G|ENSG00000086758|HUWE1|ENST00000427052|53/58|||3093/3408|protein_coding,upstream_gene_variant|||ENSG00000086758|HUWE1|ENST00000488459|||||processed_transcript,synonymous_variant|ggT/ggC|G|ENSG00000086758|HUWE1|ENST00000262854|79/84|||4059/4374|protein_coding,downstream_gene_variant|||ENSG00000086758|HUWE1|ENST00000463852|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000086758|HUWE1|ENST00000474971|1/2||||processed_transcript,synonymous_variant|ggT/ggC|G|ENSG00000086758|HUWE1|ENST00000342160|78/83|||4059/4374|protein_coding,downstream_gene_variant|||ENSG00000086758|HUWE1|ENST00000480438|||||processed_transcript GT:AD:DP:GQ:PL 1:0,21:21:99:703,0 .:0,0:.:.:. 1:0,23:23:99:772,0 chrX 53641647 . T C 976.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.751;ClippingRankSum=-0.751;DP=38;FS=0;GQ_MEAN=334.67;GQ_STDDEV=175.19;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.751;NCC=0;QD=25.7;ReadPosRankSum=-0.751;SOR=0.693;set=variant2;CSQ=synonymous_variant|tcA/tcG|S|ENSG00000086758|HUWE1|ENST00000218328|23/41|||703/1672|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000086758|HUWE1|ENST00000342160|22/83|||703/4374|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000086758|HUWE1|ENST00000262854|23/84|||703/4374|protein_coding,downstream_gene_variant|||ENSG00000086758|HUWE1|ENST00000489876|||||processed_transcript GT:AD:DP:GQ:PL 1:1,8:9:99:217,0 1:0,22:22:99:536,0 1:0,7:7:99:251,0 chrX 54095227 . T C 291.64 PASS AC=1;AF=1;AN=1;DP=16;FS=0;GQ_MEAN=319;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.61;SOR=1.179;set=variant2;CSQ=upstream_gene_variant|||ENSG00000252175|U3|ENST00000516366|||||snoRNA,3_prime_UTR_variant|||ENSG00000184083|FAM120C|ENST00000375180|16/16|||-/1096|protein_coding,downstream_gene_variant|||ENSG00000184083|FAM120C|ENST00000328235||||-/895|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:319,0 .:0,0:.:.:. chrX 54095237 . T C 285.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=313;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.9;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000184083|FAM120C|ENST00000328235||||-/895|protein_coding,upstream_gene_variant|||ENSG00000252175|U3|ENST00000516366|||||snoRNA,3_prime_UTR_variant|||ENSG00000184083|FAM120C|ENST00000375180|16/16|||-/1096|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:313,0 .:0,0:.:.:. chrX 54209387 . A G 2172.64 PASS AC=3;AF=1;AN=3;DP=65;FS=0;GQ_MEAN=733.33;GQ_STDDEV=477.78;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.43;SOR=1.162;set=variant2;CSQ=upstream_gene_variant|||ENSG00000184083|FAM120C|ENST00000497680|||||processed_transcript,missense_variant|aTt/aCt|I/T|ENSG00000184083|FAM120C|ENST00000375180|1/16|unknown(0)||82/1096|protein_coding,missense_variant|aTt/aCt|I/T|ENSG00000184083|FAM120C|ENST00000328235|1/14|unknown(0)||82/895|protein_coding,missense_variant|aTt/aCt|I/T|ENSG00000184083|FAM120C|ENST00000477084|1/2|unknown(0)||82/238|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1042,0 1:0,8:8:99:183,0 1:0,27:27:99:975,0 chrX 54781530 . C G 2024.64 PASS AC=3;AF=1;AN=3;DP=67;FS=0;GQ_MEAN=684;GQ_STDDEV=87.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.68;SOR=1.911;set=variant2;CSQ=missense_variant|tGg/tCg|W/S|ENSG00000102313|ITIH6|ENST00000218436|9/13|possibly_damaging(0.656)|tolerated(0.24)|1041/1313|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:710,0 1:0,30:30:99:756,0 1:0,18:18:99:586,0 chrX 54836361 . A G 2559.64 PASS AC=3;AF=1;AN=3;DP=72;FS=0;GQ_MEAN=862.33;GQ_STDDEV=535.83;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=24.74;SOR=0.807;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487482|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000485483|2/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000497484|3/4||||processed_transcript,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000375058|3/13|||84/606|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000375068|3/13|||84/606|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000375053|3/12|||84/606|protein_coding,upstream_gene_variant|||ENSG00000221716|SNORA11|ENST00000408789|||||snoRNA,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000375060|4/15|||46/521|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000463787|||||processed_transcript,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000347546|4/13|||66/588|protein_coding,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487463|||||processed_transcript,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000375062|4/14|||46/521|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000396224|3/12|||84/606|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000102316|MAGED2|ENST00000218439|3/12|||84/606|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1260,0 1:0,7:7:99:253,0 1:0,30:30:99:1074,0 chrX 54836505 . A G 3316.64 PASS AC=3;AF=1;AN=3;DP=101;FS=0;GQ_MEAN=1114.67;GQ_STDDEV=689.62;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.84;SOR=1.081;set=variant2;CSQ=synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000347546|4/13|||114/588|protein_coding,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487463|||||processed_transcript,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000375062|4/14|||94/521|protein_coding,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000396224|3/12|||132/606|protein_coding,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000218439|3/12|||132/606|protein_coding,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000375053|3/12|||132/606|protein_coding,upstream_gene_variant|||ENSG00000221716|SNORA11|ENST00000408789|||||snoRNA,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000375060|4/15|||94/521|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000463787|||||processed_transcript,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487482|||||processed_transcript,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000375068|3/13|||132/606|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000497484|3/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000485483|2/2||||processed_transcript,synonymous_variant|acA/acG|T|ENSG00000102316|MAGED2|ENST00000375058|3/13|||132/606|protein_coding GT:AD:DP:GQ:PL 1:0,47:47:99:1615,0 1:0,13:13:99:328,0 1:0,41:41:99:1401,0 chrX 54837340 . C T 1372.64 PASS AC=3;AF=1;AN=3;DP=44;FS=0;GQ_MEAN=466.67;GQ_STDDEV=207.9;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.92;SOR=1.455;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000485483|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000497484|4/4||||processed_transcript,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000375058|4/13|||208/606|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000375068|4/13|||208/606|protein_coding,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487482|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000463787|4/6||||processed_transcript,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000375053|4/12|||208/606|protein_coding,splice_region_variant&intron_variant|||ENSG00000102316|MAGED2|ENST00000375060||||-/521|protein_coding,upstream_gene_variant|||ENSG00000221716|SNORA11|ENST00000408789|||||snoRNA,splice_region_variant&intron_variant|||ENSG00000102316|MAGED2|ENST00000375062||||-/521|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000218439|4/12|||208/606|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000396224|4/12|||208/606|protein_coding,synonymous_variant|gcC/gcT|A|ENSG00000102316|MAGED2|ENST00000347546|5/13|||190/588|protein_coding,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487463|||||processed_transcript GT:AD:DP:GQ:PL 1:0,17:17:99:637,0 1:0,10:10:99:235,0 1:0,16:16:99:528,0 chrX 54838077 . C T 4361.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.067;ClippingRankSum=0.4;DP=142;FS=3.67;GQ_MEAN=1463;GQ_STDDEV=788.65;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.333;NCC=0;QD=30.72;ReadPosRankSum=1.2;SOR=0.721;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000487482|1/4||||processed_transcript,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000375068|6/13|||327/606|protein_coding,downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000497484|||||processed_transcript,downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000485483|||||processed_transcript,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000375058|6/13|||327/606|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000375053|6/12|||327/606|protein_coding,upstream_gene_variant|||ENSG00000221716|SNORA11|ENST00000408789|||||snoRNA,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000375060|8/15|||242/521|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102316|MAGED2|ENST00000463787|6/6||||processed_transcript,upstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487463|||||processed_transcript,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000347546|7/13|||309/588|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000375062|8/14|||242/521|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000218439|6/12|||327/606|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000102316|MAGED2|ENST00000396224|6/12|||327/606|protein_coding GT:AD:DP:GQ:PL 1:0,49:49:99:1581,0 1:1,25:26:99:622,0 1:0,67:67:99:2186,0 chrX 54841737 . G A 2631.64 PASS AC=3;AF=1;AN=3;DP=82;FS=0;GQ_MEAN=886.33;GQ_STDDEV=642.24;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.49;SOR=1.124;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000463787|||||processed_transcript,downstream_gene_variant|||ENSG00000221716|SNORA11|ENST00000408789|||||snoRNA,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000375060|14/15|||396/521|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000375053|12/12|||481/606|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000218439|12/12|||481/606|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000396224|12/12|||481/606|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000375062|14/14|||396/521|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000347546|13/13|||463/588|protein_coding,downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487463|||||processed_transcript,downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000497484|||||processed_transcript,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000375058|12/13|||481/606|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000102316|MAGED2|ENST00000375068|12/13|||481/606|protein_coding,downstream_gene_variant|||ENSG00000102316|MAGED2|ENST00000487482|||||processed_transcript GT:AD:DP:GQ:PL 1:0,40:40:99:1426,0 1:0,8:8:99:176,0 1:0,33:33:99:1057,0 chrX 55116466 . C G 1214.64 PASS AC=1;AF=1;AN=1;DP=42;FS=0;GQ_MEAN=1242;MLEAC=1;MLEAF=1;MQ=59.45;MQ0=0;NCC=2;QD=29.63;SOR=1.075;set=variant2;CSQ=missense_variant|Cta/Gta|L/V|ENSG00000234068|PAGE2|ENST00000374968|2/5|benign(0.002)|tolerated(1)|5/111|protein_coding,missense_variant|Cta/Gta|L/V|ENSG00000234068|PAGE2|ENST00000374965|2/5|benign(0)|tolerated(1)|5/94|protein_coding,missense_variant|Cta/Gta|L/V|ENSG00000234068|PAGE2|ENST00000449097|2/3|benign(0.002)|tolerated_low_confidence(1)|5/64|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,41:41:99:1242,0 .:0,0:.:.:. chrX 55246965 . C T 2132.64 PASS AC=3;AF=1;AN=3;DP=74;FS=0;GQ_MEAN=720;GQ_STDDEV=202.97;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.21;SOR=0.72;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000158639|PAGE5|ENST00000289619|1/5|||-/130|protein_coding,intron_variant|||ENSG00000158639|PAGE5|ENST00000374955||||-/110|protein_coding,intron_variant|||ENSG00000158639|PAGE5|ENST00000374952||||-/93|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:796,0 1:0,36:36:99:874,0 1:0,14:14:99:490,0 chrX 55247030 . C G 1069.64 PASS AC=2;AF=1;AN=2;DP=34;FS=0;GQ_MEAN=548.5;GQ_STDDEV=231.22;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.41;SOR=0.88;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000158639|PAGE5|ENST00000289619|1/5|||-/130|protein_coding,intron_variant|||ENSG00000158639|PAGE5|ENST00000374955||||-/110|protein_coding,intron_variant|||ENSG00000158639|PAGE5|ENST00000374952||||-/93|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:712,0 .:0,0:.:.:. 1:0,12:12:99:385,0 chrX 55289774 . T C 2072.64 PASS AC=3;AF=1;AN=3;DP=68;FS=0;GQ_MEAN=700;GQ_STDDEV=54.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.48;SOR=1.352;set=variant2;CSQ=missense_variant|Aat/Gat|N/D|ENSG00000204279|PAGE3|ENST00000374951|3/5|benign(0)|tolerated(1)|35/113|protein_coding,missense_variant|Aat/Gat|N/D|ENSG00000204279|PAGE3|ENST00000519203|3/5|benign(0)|tolerated(1)|35/113|protein_coding GT:AD:DP:GQ:PL 1:0,17:17:99:647,0 1:0,30:30:99:756,0 1:0,21:21:99:697,0 chrX 55291168 . G C 530.64 PASS AC=1;AF=1;AN=1;DP=21;FS=0;GQ_MEAN=558;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.53;SOR=0.693;set=variant2;CSQ=upstream_gene_variant|||ENSG00000204279|PAGE3|ENST00000519203||||-/113|protein_coding,5_prime_UTR_variant|||ENSG00000204279|PAGE3|ENST00000374951|1/5|||-/113|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:558,0 .:0,0:.:.:. chrX 55514881 . T C 2661.64 PASS AC=3;AF=1;AN=3;DP=79;FS=0;GQ_MEAN=896.33;GQ_STDDEV=507.18;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.69;SOR=3.174;set=variant2;CSQ=synonymous_variant|agA/agG|R|ENSG00000247746|USP51|ENST00000500968|2/2|||164/711|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000247746|USP51|ENST00000586165|||||processed_transcript GT:AD:DP:GQ:PL 1:0,38:38:99:1290,0 1:0,11:11:99:324,0 1:0,30:30:99:1075,0 chrX 57019862 . G A 1008.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.115;ClippingRankSum=1.12;DP=54;FS=0;GQ_MEAN=1036;MLEAC=1;MLEAF=1;MQ=59.68;MQ0=0;MQRankSum=-0.802;NCC=2;QD=18.68;ReadPosRankSum=-0.023;SOR=0.853;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204271|SPIN3|ENST00000374919||||-/258|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000204271|SPIN3|ENST00000475785||||-/77|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000204271|SPIN3|ENST00000478405||||-/77|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,52:54:99:1036,0 .:0,0:.:.:. chrX 57020115 . C T 471.64 PASS AC=1;AF=1;AN=1;DP=21;FS=0;GQ_MEAN=499;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.58;SOR=0.892;set=variant2;CSQ=intron_variant&NMD_transcript_variant|||ENSG00000204271|SPIN3|ENST00000475785||||-/77|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000204271|SPIN3|ENST00000374919||||-/258|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000204271|SPIN3|ENST00000478405||||-/77|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:499,0 .:0,0:.:.:. chrX 57147944 . G T 43.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=71;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.82;SOR=0.693;set=variant2;CSQ=upstream_gene_variant|||ENSG00000186787|SPIN2B|ENST00000275988||||-/258|protein_coding,upstream_gene_variant|||ENSG00000226310|RP3-323P24.3|ENST00000439622|||||antisense,upstream_gene_variant|||ENSG00000186787|SPIN2B|ENST00000374910||||-/157|protein_coding,5_prime_UTR_variant|||ENSG00000186787|SPIN2B|ENST00000434397|1/2|||-/247|protein_coding,5_prime_UTR_variant|||ENSG00000186787|SPIN2B|ENST00000333933|1/2|||-/258|protein_coding,upstream_gene_variant|||ENSG00000186787|SPIN2B|ENST00000460948|||||processed_transcript,5_prime_UTR_variant|||ENSG00000186787|SPIN2B|ENST00000374912|1/2|||-/258|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. .:0,0:.:.:. 1:0,2:2:71:71,0 chrX 57313357 . T C 1398.64 PASS AC=3;AF=1;AN=3;DP=41;FS=0;GQ_MEAN=475.33;GQ_STDDEV=369.96;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.11;SOR=0.843;set=variant2;CSQ=synonymous_variant|ggT/ggC|G|ENSG00000165591|FAAH2|ENST00000374900|1/11|||33/532|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:665,0 1:0,2:2:49:49,0 1:0,21:21:99:712,0 chrX 57405163 . T C 1433.64 PASS AC=3;AF=1;AN=3;DP=46;FS=0;GQ_MEAN=487;GQ_STDDEV=136.04;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.86;SOR=0.829;set=variant2;CSQ=synonymous_variant|cgT/cgC|R|ENSG00000165591|FAAH2|ENST00000374900|6/11|||274/532|protein_coding GT:AD:DP:GQ:PL 1:0,14:14:99:561,0 1:0,23:23:99:570,0 1:0,8:8:99:330,0 chrX 57619648 . G T 1003.64 PASS AC=3;AF=1;AN=3;DP=37;FS=0;GQ_MEAN=343.67;GQ_STDDEV=204.69;MLEAC=3;MLEAF=1;MQ=51.7;MQ0=0;NCC=0;QD=27.13;SOR=1.27;set=variant2;CSQ=synonymous_variant|ccG/ccT|P|ENSG00000198455|ZXDB|ENST00000374888|1/1|||389/803|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:207,0 1:0,25:25:99:579,0 1:0,6:6:99:245,0 chrX 57622607 . G A 743.64 PASS AC=1;AF=1;AN=1;DP=31;FS=0;GQ_MEAN=771;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.99;SOR=1.044;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000198455|ZXDB|ENST00000374888|1/1|||-/803|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:771,0 .:0,0:.:.:. chrX 63405320 . TC T 84.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=112;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.16;SOR=1.609;set=variant;CSQ=downstream_gene_variant|||ENSG00000184675|AMER1|ENST00000403336||||-/804|protein_coding,3_prime_UTR_variant|||ENSG00000184675|AMER1|ENST00000330258|2/2|||-/1135|protein_coding,3_prime_UTR_variant|||ENSG00000184675|AMER1|ENST00000374869|3/3|||-/804|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:112,0 .:0,0:.:.:. chrX 63413032 . G A 4133.64 PASS AC=2;AF=1;AN=2;DP=113;FS=0;GQ_MEAN=2080.5;GQ_STDDEV=33.23;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=31.56;SOR=1.371;set=variant2;CSQ=synonymous_variant|tcC/tcT|S|ENSG00000184675|AMER1|ENST00000403336|1/2|||45/804|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000184675|AMER1|ENST00000330258|2/2|||45/1135|protein_coding,synonymous_variant|tcC/tcT|S|ENSG00000184675|AMER1|ENST00000374869|2/3|||45/804|protein_coding GT:AD:DP:GQ:PL 1:0,56:56:99:2057,0 .:0,0:.:.:. 1:0,56:56:99:2104,0 chrX 65241726 . G A 131.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=159;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.94;SOR=1.329;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000155659|VSIG4|ENST00000427538|7/7|||-/274|protein_coding,3_prime_UTR_variant|||ENSG00000155659|VSIG4|ENST00000412866|7/7|||-/305|protein_coding,3_prime_UTR_variant|||ENSG00000155659|VSIG4|ENST00000455586|7/7|||-/321|protein_coding,3_prime_UTR_variant|||ENSG00000155659|VSIG4|ENST00000374737|8/8|||-/399|protein_coding,downstream_gene_variant|||ENSG00000207939|MIR223|ENST00000385204|||||miRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:159,0 .:0,0:.:.:. chrX 65382685 . T C 3593.64 PASS AC=3;AF=1;AN=3;DP=124;FS=0;GQ_MEAN=1207;GQ_STDDEV=273.1;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.98;SOR=1.107;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000089472|HEPH|ENST00000374727|1/21|||-/1161|protein_coding,missense_variant|gTg/gCg|V/A|ENSG00000089472|HEPH|ENST00000519389|1/21|benign(0)|tolerated_low_confidence(1)|39/1212|protein_coding,upstream_gene_variant|||ENSG00000089472|HEPH|ENST00000336279||||-/891|protein_coding,upstream_gene_variant|||ENSG00000089472|HEPH|ENST00000458621||||-/208|protein_coding,upstream_gene_variant|||ENSG00000089472|HEPH|ENST00000419594||||-/969|protein_coding,upstream_gene_variant|||ENSG00000089472|HEPH|ENST00000429547||||-/63|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000089472|HEPH|ENST00000441993||||-/1160|protein_coding GT:AD:DP:GQ:PL 1:0,39:39:99:1307,0 1:0,39:39:99:898,0 1:0,46:46:99:1416,0 chrX 65815591 . T C 592.64 PASS AC=1;AF=1;AN=1;DP=22;FS=0;GQ_MEAN=620;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.94;SOR=0.874;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000131080|EDA2R|ENST00000396050|6/6|||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000456230||||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000253392||||-/318|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000451436||||-/173|protein_coding,3_prime_UTR_variant|||ENSG00000131080|EDA2R|ENST00000374719|7/7|||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000450752||||-/318|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,22:22:99:620,0 .:0,0:.:.:. chrX 65815817 . G A 393.64 PASS AC=1;AF=1;AN=1;DP=20;FS=0;GQ_MEAN=421;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.72;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000131080|EDA2R|ENST00000396050|6/6|||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000456230||||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000253392||||-/318|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000451436||||-/173|protein_coding,3_prime_UTR_variant|||ENSG00000131080|EDA2R|ENST00000374719|7/7|||-/297|protein_coding,downstream_gene_variant|||ENSG00000131080|EDA2R|ENST00000450752||||-/318|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:421,0 .:0,0:.:.:. chrX 65824986 . C T 2147.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.622;ClippingRankSum=0.183;DP=69;FS=2.604;GQ_MEAN=725;GQ_STDDEV=367.8;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.256;NCC=0;QD=31.13;ReadPosRankSum=1.13;SOR=0.33;set=variant2;CSQ=missense_variant|aGa/aAa|R/K|ENSG00000131080|EDA2R|ENST00000374719|3/7|benign(0.224)|tolerated(0.6)|57/297|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000131080|EDA2R|ENST00000450752|3/7|benign(0.008)|tolerated(0.84)|57/318|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000131080|EDA2R|ENST00000396050|2/6|benign(0.224)|tolerated(0.6)|57/297|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000131080|EDA2R|ENST00000456230|3/6|benign(0.224)|tolerated(0.6)|57/297|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000131080|EDA2R|ENST00000253392|2/6|benign(0.008)|tolerated(0.84)|57/318|protein_coding,intron_variant|||ENSG00000131080|EDA2R|ENST00000451436||||-/173|protein_coding GT:AD:DP:GQ:PL 1:2,32:34:99:1070,0 1:0,13:13:99:338,0 1:0,22:22:99:767,0 chrX 66765158 . TGCAGCA T 206.87 PASS AC=1;AF=0.333;AN=3;DP=30;FS=0;GQ_MEAN=152.33;GQ_STDDEV=75.12;MLEAC=1;MLEAF=0.333;MQ=57.33;MQ0=0;NCC=0;QD=14.78;SOR=1.022;set=variant;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000169083|AR|ENST00000513847|1/4||||processed_transcript,inframe_deletion&NMD_transcript_variant|ctGCAGCAg/ctg|LQQ/L|ENSG00000169083|AR|ENST00000514029|1/5|||57-59/600|nonsense_mediated_decay,inframe_deletion|ctGCAGCAg/ctg|LQQ/L|ENSG00000169083|AR|ENST00000396044|1/5|||57-59/734|protein_coding,inframe_deletion|ctGCAGCAg/ctg|LQQ/L|ENSG00000169083|AR|ENST00000374690|1/8|||57-59/920|protein_coding,inframe_deletion|ctGCAGCAg/ctg|LQQ/L|ENSG00000169083|AR|ENST00000504326|1/4|||57-59/644|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,106 0:3,0:3:99:0,112 1:0,2,5:7:99:239,0 chrX 66766356 . T TGGC 165.64 PASS AC=2;AF=1;AN=2;DP=12;FS=0;GQ_MEAN=96.5;GQ_STDDEV=27.58;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.13;SOR=1.022;set=variant;CSQ=inframe_insertion|-/GGC|-/G|ENSG00000169083|AR|ENST00000396044|1/5|||456-457/734|protein_coding,inframe_insertion|-/GGC|-/G|ENSG00000169083|AR|ENST00000504326|1/4|||456-457/644|protein_coding,inframe_insertion|-/GGC|-/G|ENSG00000169083|AR|ENST00000374690|1/8|||456-457/920|protein_coding,inframe_insertion&NMD_transcript_variant|-/GGC|-/G|ENSG00000169083|AR|ENST00000514029|1/5|||456-457/600|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000169083|AR|ENST00000513847|1/4||||processed_transcript GT:AD:DP:GQ:PL 1:0,3:3:99:116,0 .:0,0:.:.:. 1:0,2:2:77:77,0 chrX 68381264 . C A 2973.64 PASS AC=3;AF=1;AN=3;DP=95;FS=0;GQ_MEAN=1000.33;GQ_STDDEV=479.17;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.97;SOR=0.714;set=variant2;CSQ=intron_variant|||ENSG00000181191|PJA1|ENST00000471141||||-/67|protein_coding,downstream_gene_variant|||ENSG00000181191|PJA1|ENST00000590146||||-/144|protein_coding,missense_variant|gaG/gaT|E/D|ENSG00000181191|PJA1|ENST00000374571|2/2|benign(0.405)|tolerated(0.39)|551/588|protein_coding,missense_variant|gaG/gaT|E/D|ENSG00000181191|PJA1|ENST00000361478|2/2|benign(0.405)|tolerated(0.39)|606/643|protein_coding,missense_variant|gaG/gaT|E/D|ENSG00000181191|PJA1|ENST00000374583|1/1|benign(0.405)|tolerated(0.39)|606/643|protein_coding,downstream_gene_variant|||ENSG00000181191|PJA1|ENST00000477231|||||processed_transcript,missense_variant|gaG/gaT|E/D|ENSG00000181191|PJA1|ENST00000374584|3/3|benign(0.307)|tolerated(0.23)|418/455|protein_coding GT:AD:DP:GQ:PL 1:0,41:41:99:1354,0 1:0,18:18:99:455,0 1:0,34:34:99:1192,0 chrX 68381787 . C T 3418.64 PASS AC=3;AF=1;AN=3;DP=103;FS=0;GQ_MEAN=1148.67;GQ_STDDEV=631.82;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.19;SOR=1.679;set=variant2;CSQ=missense_variant|aGt/aAt|S/N|ENSG00000181191|PJA1|ENST00000374584|3/3|benign(0.208)|tolerated(0.25)|244/455|protein_coding,downstream_gene_variant|||ENSG00000181191|PJA1|ENST00000477231|||||processed_transcript,downstream_gene_variant|||ENSG00000181191|PJA1|ENST00000590146||||-/144|protein_coding,missense_variant|aGt/aAt|S/N|ENSG00000181191|PJA1|ENST00000361478|2/2|benign(0.07)|tolerated(0.37)|432/643|protein_coding,missense_variant|aGt/aAt|S/N|ENSG00000181191|PJA1|ENST00000374571|2/2|benign(0.07)|tolerated(0.31)|377/588|protein_coding,intron_variant|||ENSG00000181191|PJA1|ENST00000471141||||-/67|protein_coding,missense_variant|aGt/aAt|S/N|ENSG00000181191|PJA1|ENST00000374583|1/1|benign(0.07)|tolerated(0.37)|432/643|protein_coding GT:AD:DP:GQ:PL 1:0,45:45:99:1633,0 1:0,19:19:99:434,0 1:0,39:39:99:1379,0 chrX 68382836 . G A 4622.64 PASS AC=3;AF=1;AN=3;DP=148;FS=0;GQ_MEAN=1550;GQ_STDDEV=881.27;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.23;SOR=0.806;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000181191|PJA1|ENST00000477231|2/2||||processed_transcript,synonymous_variant|agC/agT|S|ENSG00000181191|PJA1|ENST00000374584|2/3|||82/455|protein_coding,upstream_gene_variant|||ENSG00000181191|PJA1|ENST00000471141||||-/67|protein_coding,synonymous_variant|agC/agT|S|ENSG00000181191|PJA1|ENST00000374571|2/2|||27/588|protein_coding,synonymous_variant|agC/agT|S|ENSG00000181191|PJA1|ENST00000590146|2/2|||82/144|protein_coding,synonymous_variant|agC/agT|S|ENSG00000181191|PJA1|ENST00000361478|2/2|||82/643|protein_coding,synonymous_variant|agC/agT|S|ENSG00000181191|PJA1|ENST00000374583|1/1|||82/643|protein_coding GT:AD:DP:GQ:PL 1:0,68:68:99:2255,0 1:0,24:24:99:562,0 1:0,56:56:99:1833,0 chrX 69257972 . G C 92.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=120;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.16;SOR=1.609;set=variant2;CSQ=downstream_gene_variant|||ENSG00000158813|EDA|ENST00000503592||||-/136|protein_coding,downstream_gene_variant|||ENSG00000158813|EDA|ENST00000524573||||-/386|protein_coding,3_prime_UTR_variant|||ENSG00000158813|EDA|ENST00000374553|8/8|||-/389|protein_coding,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000440401||||-/166|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000276101||||-/333|protein_coding,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000443056|||||retained_intron,3_prime_UTR_variant|||ENSG00000158813|EDA|ENST00000374552|8/8|||-/391|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:120,0 .:0,0:.:.:. chrX 69258515 . T G 331.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=359;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.51;SOR=0.836;set=variant2;CSQ=downstream_gene_variant|||ENSG00000158813|EDA|ENST00000524573||||-/386|protein_coding,3_prime_UTR_variant|||ENSG00000158813|EDA|ENST00000374553|8/8|||-/389|protein_coding,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000440401||||-/166|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000276101||||-/333|protein_coding,downstream_gene_variant|||ENSG00000147160|AWAT2|ENST00000443056|||||retained_intron,3_prime_UTR_variant|||ENSG00000158813|EDA|ENST00000374552|8/8|||-/391|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:359,0 .:0,0:.:.:. chrX 69510335 . C T 1993.64 PASS AC=3;AF=1;AN=3;DP=57;FS=0;GQ_MEAN=673.67;GQ_STDDEV=324.66;MLEAC=3;MLEAF=1;MQ=48.01;MQ0=0;NCC=0;QD=34.98;SOR=1.692;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000090889|KIF4A|ENST00000485406|2/4||||processed_transcript,synonymous_variant|ccC/ccT|P|ENSG00000090889|KIF4A|ENST00000374388|2/29|||9/1127|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000120509|PDZD11|ENST00000486461|1/5||||processed_transcript,synonymous_variant|ccC/ccT|P|ENSG00000090889|KIF4A|ENST00000374403|2/31|||9/1232|protein_coding,upstream_gene_variant|||ENSG00000120509|PDZD11|ENST00000473667|||||processed_transcript,upstream_gene_variant|||ENSG00000120509|PDZD11|ENST00000374454||||-/140|protein_coding,upstream_gene_variant|||ENSG00000120509|PDZD11|ENST00000239666||||-/140|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:850,0 1:0,11:11:99:299,0 1:0,23:23:99:872,0 chrX 69774517 . A T 2172.64 PASS AC=3;AF=1;AN=3;DP=70;FS=0;GQ_MEAN=733.33;GQ_STDDEV=440.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.04;SOR=1.712;set=variant2;CSQ=synonymous_variant|acT/acA|T|ENSG00000120498|TEX11|ENST00000395889|27/31|||773/940|protein_coding,synonymous_variant|acT/acA|T|ENSG00000120498|TEX11|ENST00000374320|15/19|||448/615|protein_coding,synonymous_variant|acT/acA|T|ENSG00000120498|TEX11|ENST00000344304|25/29|||773/940|protein_coding,synonymous_variant|acT/acA|T|ENSG00000120498|TEX11|ENST00000374333|26/30|||758/925|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1242,0 1:0,19:19:99:473,0 1:0,15:15:99:485,0 chrX 70146398 . A G 2241.64 PASS AC=3;AF=1;AN=3;DP=71;FS=0;GQ_MEAN=756.33;GQ_STDDEV=415.29;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.57;SOR=1.117;set=variant2;CSQ=synonymous_variant|agT/agC|S|ENSG00000165349|SLC7A3|ENST00000374299|10/12|||533/619|protein_coding,synonymous_variant|agT/agC|S|ENSG00000165349|SLC7A3|ENST00000298085|10/12|||533/619|protein_coding GT:AD:DP:GQ:PL 1:0,37:37:99:1231,0 1:0,18:18:99:460,0 1:0,16:16:99:578,0 chrX 71348837 . G A 1181.64 PASS AC=2;AF=1;AN=2;DP=47;FS=0;GQ_MEAN=604.5;GQ_STDDEV=726.2;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25.14;SOR=0.735;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000545866|1/2|||-/569|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,3_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000609883|1/1|||-/569|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000242732|RGAG4|ENST00000479991|1/2|||-/569|nonsense_mediated_decay,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,44:44:99:1118,0 1:0,3:3:91:91,0 chrX 71349143 . A C 517.64 PASS AC=1;AF=1;AN=1;DP=20;FS=0;GQ_MEAN=545;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.88;SOR=1.127;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000609883|1/1|||-/569|protein_coding,3_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000545866|1/2|||-/569|protein_coding,upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000242732|RGAG4|ENST00000479991|1/2|||-/569|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,20:20:99:545,0 .:0,0:.:.:. chrX 71349753 . G A 4308.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.69;ClippingRankSum=-1.642;DP=133;FS=0;GQ_MEAN=1445.33;GQ_STDDEV=1241;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.64;NCC=0;QD=32.4;ReadPosRankSum=0.877;SOR=0.589;set=variant2;CSQ=upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,synonymous_variant|cgC/cgT|R|ENSG00000242732|RGAG4|ENST00000609883|1/1|||546/569|protein_coding,synonymous_variant|cgC/cgT|R|ENSG00000242732|RGAG4|ENST00000545866|1/2|||546/569|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,synonymous_variant&NMD_transcript_variant|cgC/cgT|R|ENSG00000242732|RGAG4|ENST00000479991|1/2|||546/569|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding GT:AD:DP:GQ:PL 1:0,53:53:99:1788,0 1:0,3:3:69:69,0 1:1,76:77:99:2479,0 chrX 71349774 . T C 4879.64 PASS AC=3;AF=1;AN=3;DP=145;FS=0;GQ_MEAN=1635.67;GQ_STDDEV=1350.92;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.65;SOR=1.292;set=variant2;CSQ=upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,synonymous_variant|ggA/ggG|G|ENSG00000242732|RGAG4|ENST00000545866|1/2|||539/569|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000242732|RGAG4|ENST00000609883|1/1|||539/569|protein_coding,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,synonymous_variant&NMD_transcript_variant|ggA/ggG|G|ENSG00000242732|RGAG4|ENST00000479991|1/2|||539/569|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding GT:AD:DP:GQ:PL 1:0,59:59:99:2070,0 1:0,4:4:99:121,0 1:0,82:82:99:2716,0 chrX 71351443 . A G 2280.64 PASS AC=3;AF=1;AN=3;DP=66;FS=0;GQ_MEAN=769.33;GQ_STDDEV=345.08;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.56;SOR=1.911;set=variant2;CSQ=upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000609883|1/1|||-/569|protein_coding,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000545866|1/2|||-/569|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000242732|RGAG4|ENST00000479991|1/2|||-/569|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:994,0 1:0,13:13:99:372,0 1:0,25:25:99:942,0 chrX 71351519 . C A 694.64 PASS AC=3;AF=1;AN=3;DP=24;FS=0;GQ_MEAN=240.67;GQ_STDDEV=90.52;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.94;SOR=2.494;set=variant2;CSQ=5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000242732|RGAG4|ENST00000479991|1/2|||-/569|nonsense_mediated_decay,intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000545866|1/2|||-/569|protein_coding,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000609883|1/1|||-/569|protein_coding GT:AD:DP:GQ:PL 1:0,9:9:99:309,0 1:0,7:7:99:138,0 1:0,8:8:99:275,0 chrX 71351646 . C T 207.64 PASS AC=2;AF=1;AN=2;DP=6;FS=0;GQ_MEAN=117.5;GQ_STDDEV=53.03;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.61;SOR=0.693;set=variant2;CSQ=intron_variant|||ENSG00000204131|NHSL2|ENST00000540800||||-/1225|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000242732|RGAG4|ENST00000479991|1/2|||-/569|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding,upstream_gene_variant|||ENSG00000248345|RP11-262D11.1|ENST00000513469|||||unprocessed_pseudogene,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000545866|1/2|||-/569|protein_coding,5_prime_UTR_variant|||ENSG00000242732|RGAG4|ENST00000609883|1/1|||-/569|protein_coding GT:AD:DP:GQ:PL 1:0,4:4:99:155,0 .:0,0:.:.:. 1:0,2:2:80:80,0 chrX 71363415 . C T 2460.64 PASS AC=3;AF=1;AN=3;DP=77;FS=0;GQ_MEAN=829.33;GQ_STDDEV=652.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.96;SOR=1.55;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000535692||||-/709|protein_coding,downstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000373677||||-/709|protein_coding,upstream_gene_variant|||ENSG00000225471|RP11-262D11.2|ENST00000456343|||||processed_pseudogene,downstream_gene_variant|||ENSG00000204131|NHSL2|ENST00000510661||||-/844|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000204131|NHSL2|ENST00000540800|8/8|||1223/1225|protein_coding GT:AD:DP:GQ:PL 1:0,37:37:99:1242,0 1:0,5:5:77:77,0 1:0,35:35:99:1169,0 chrX 71379702 . T C 3686.64 PASS AC=2;AF=1;AN=2;DP=112;FS=0;GQ_MEAN=1857;GQ_STDDEV=456.79;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.21;SOR=1.189;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000432517|1/1||||processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000456343|2/2||||processed_pseudogene GT:AD:DP:GQ:PL 1:0,64:64:99:2180,0 .:0,0:.:.:. 1:0,47:47:99:1534,0 chrX 71379853 . C T 3305.64 PASS AC=3;AF=1;AN=3;DP=108;FS=0;GQ_MEAN=1111;GQ_STDDEV=174.98;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.61;SOR=0.769;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000456343|2/2||||processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000432517|1/1||||processed_pseudogene GT:AD:DP:GQ:PL 1:0,25:25:99:909,0 1:0,48:48:99:1208,0 1:0,35:35:99:1216,0 chrX 71380152 . C T 285.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=313;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.97;SOR=1.179;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000432517|1/1||||processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000225471|RP11-262D11.2|ENST00000456343|2/2||||processed_pseudogene GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:313,0 .:0,0:.:.:. chrX 71401607 . G A 3010.64 PASS AC=3;AF=1;AN=3;DP=66;FS=0;GQ_MEAN=1012.67;GQ_STDDEV=240.59;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=26.88;SOR=0.886;set=variant2;CSQ=missense_variant|cGg/cAg|R/Q|ENSG00000102309|PIN4|ENST00000423432|1/4|benign(0)|tolerated_low_confidence(0.27)|16/133|protein_coding,upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000446576||||-/116|protein_coding,upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000496835||||-/115|protein_coding,upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000439980||||-/91|nonsense_mediated_decay,missense_variant|cGg/cAg|R/Q|ENSG00000102309|PIN4|ENST00000373669|1/4|benign(0)|tolerated_low_confidence(0.47)|16/156|protein_coding,missense_variant|cGg/cAg|R/Q|ENSG00000102309|PIN4|ENST00000218432|1/3|benign(0)|tolerated_low_confidence(0.25)|16/111|protein_coding,missense_variant&NMD_transcript_variant|cGg/cAg|R/Q|ENSG00000102309|PIN4|ENST00000373662|1/3|unknown(0)|tolerated_low_confidence(0.24)|16/106|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,30:30:99:1290,0 1:0,16:16:99:888,0 1:0,20:20:99:860,0 chrX 71401614 . C A 2993.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.6;ClippingRankSum=-1.333;DP=72;FS=3.388;GQ_MEAN=1007;GQ_STDDEV=243.98;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.6;NCC=0;QD=31.6;ReadPosRankSum=0.8;SOR=0.542;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000439980||||-/91|nonsense_mediated_decay,missense_variant|agC/agA|S/R|ENSG00000102309|PIN4|ENST00000373669|1/4|benign(0)|tolerated_low_confidence(0.61)|18/156|protein_coding,missense_variant|agC/agA|S/R|ENSG00000102309|PIN4|ENST00000218432|1/3|benign(0)|tolerated_low_confidence(0.32)|18/111|protein_coding,missense_variant&NMD_transcript_variant|agC/agA|S/R|ENSG00000102309|PIN4|ENST00000373662|1/3|unknown(0)|tolerated_low_confidence(0.56)|18/106|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000446576||||-/116|protein_coding,missense_variant|agC/agA|S/R|ENSG00000102309|PIN4|ENST00000423432|1/4|benign(0)|tolerated_low_confidence(0.34)|18/133|protein_coding,upstream_gene_variant|||ENSG00000102309|PIN4|ENST00000496835||||-/115|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:1284,0 1:1,25:26:99:913,0 1:0,18:18:99:824,0 chrX 71493691 . C T 733.64 PASS AC=3;AF=1;AN=3;DP=23;FS=0;GQ_MEAN=253.67;GQ_STDDEV=177.57;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.9;SOR=2.4;set=variant2;CSQ=downstream_gene_variant|||ENSG00000198034|RPS4X|ENST00000373626||||-/122|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000198034|RPS4X|ENST00000486733|3/5||||processed_transcript,intron_variant&NMD_transcript_variant|||ENSG00000102309|PIN4|ENST00000439980||||-/91|nonsense_mediated_decay,synonymous_variant|ttG/ttA|L|ENSG00000198034|RPS4X|ENST00000316084|5/7|||164/263|protein_coding,upstream_gene_variant|||ENSG00000198034|RPS4X|ENST00000492695|||||processed_transcript,upstream_gene_variant|||ENSG00000198034|RPS4X|ENST00000470671|||||processed_transcript GT:AD:DP:GQ:PL 1:0,6:6:99:210,0 1:0,5:5:99:102,0 1:0,12:12:99:449,0 chrX 71521867 . G C 2267.64 PASS AC=3;AF=1;AN=3;DP=65;FS=0;GQ_MEAN=765;GQ_STDDEV=550.37;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.89;SOR=0.723;set=variant2;CSQ=missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000431381|4/4|benign(0.001)|tolerated(1)|122/219|protein_coding,downstream_gene_variant|||ENSG00000125931|CITED1|ENST00000450875||||-/109|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000102309|PIN4|ENST00000439980||||-/91|nonsense_mediated_decay,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000417400|3/3|||96/140|protein_coding,intron_variant|||ENSG00000125931|CITED1|ENST00000429794||||-/106|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000373619|3/3|benign(0)|tolerated(1)|96/193|protein_coding,downstream_gene_variant|||ENSG00000125931|CITED1|ENST00000454225||||-/59|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000246139|3/3|benign(0)|tolerated(1)|96/193|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000445983|3/3|benign(0)|tolerated(1)|96/193|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000427412|3/3|benign(0)|tolerated_low_confidence(1)|122/138|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000125931|CITED1|ENST00000453707|5/5|benign(0.001)|tolerated(1)|122/219|protein_coding GT:AD:DP:GQ:PL 1:0,33:33:99:1146,0 1:0,5:5:99:134,0 1:0,27:27:99:1015,0 chrX 71549512 . G C 4262.64 PASS AC=3;AF=1;AN=3;DP=139;FS=0;GQ_MEAN=1430;GQ_STDDEV=109.66;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.11;SOR=0.831;set=variant2;CSQ=downstream_gene_variant|||ENSG00000147099|HDAC8|ENST00000429103||||-/182|protein_coding,downstream_gene_variant|||ENSG00000147099|HDAC8|ENST00000470998|||||processed_transcript,3_prime_UTR_variant|||ENSG00000147099|HDAC8|ENST00000373573|11/11|||-/377|protein_coding,3_prime_UTR_variant|||ENSG00000147099|HDAC8|ENST00000373589|9/9|||-/286|protein_coding,3_prime_UTR_variant|||ENSG00000147099|HDAC8|ENST00000373583|3/3|||-/64|protein_coding GT:AD:DP:GQ:PL 1:0,43:43:99:1510,0 1:0,50:50:99:1305,0 1:0,44:44:99:1475,0 chrX 72223371 . A G 96.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=124;MLEAC=1;MLEAF=1;MQ=59.34;MQ0=0;NCC=2;QD=32.21;SOR=2.833;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000184388|PABPC1L2B|ENST00000373521|1/1|||-/200|protein_coding,upstream_gene_variant|||ENSG00000184388|PABPC1L2B|ENST00000538388||||-/200|protein_coding,upstream_gene_variant|||ENSG00000226725|RP11-493K23.1|ENST00000416989|||||antisense GT:AD:DP:GQ:PL 1:0,3:3:99:124,0 .:0,0:.:.:. .:0,0:.:.:. chrX 72297417 . T C 375.64 PASS AC=2;AF=1;AN=2;DP=12;FS=0;GQ_MEAN=201.5;GQ_STDDEV=215.67;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=31.3;SOR=1.981;set=variant2;CSQ=downstream_gene_variant|||ENSG00000186288|PABPC1L2A|ENST00000453389||||-/200|protein_coding,upstream_gene_variant|||ENSG00000231963|RP11-493K23.4|ENST00000454388|||||antisense,3_prime_UTR_variant|||ENSG00000186288|PABPC1L2A|ENST00000373519|1/1|||-/200|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:49:49,0 1:0,10:10:99:354,0 .:0,0:.:.:. chrX 72297541 . T C 404.64 PASS AC=1;AF=1;AN=1;DP=15;FS=0;GQ_MEAN=432;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.9;SOR=0.976;set=variant2;CSQ=downstream_gene_variant|||ENSG00000186288|PABPC1L2A|ENST00000453389||||-/200|protein_coding,upstream_gene_variant|||ENSG00000231963|RP11-493K23.4|ENST00000454388|||||antisense,3_prime_UTR_variant|||ENSG00000186288|PABPC1L2A|ENST00000373519|1/1|||-/200|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,14:14:99:432,0 .:0,0:.:.:. chrX 72745977 . T G 547.64 PASS AC=2;AF=1;AN=2;DP=21;FS=0;GQ_MEAN=287.5;GQ_STDDEV=279.31;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=30.42;SOR=1.179;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000269904|MAP2K4P1|ENST00000438453|1/1||||transcribed_processed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000269904|MAP2K4P1|ENST00000602584|2/2||||processed_transcript GT:AD:DP:GQ:PL 1:0,3:3:90:90,0 1:0,15:15:99:485,0 .:0,0:.:.:. chrX 72904584 . G A 333.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=361;MLEAC=1;MLEAF=1;MQ=58.98;MQ0=0;NCC=2;QD=27.8;SOR=1.022;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204116|CHIC1|ENST00000373502||||-/224|protein_coding,downstream_gene_variant|||ENSG00000204116|CHIC1|ENST00000498318||||-/64|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000204116|CHIC1|ENST00000498407||||-/217|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000204116|CHIC1|ENST00000373504|5/5|||-/204|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:361,0 .:0,0:.:.:. chrX 73063911 . T C 2129.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.385;ClippingRankSum=1.16;DP=63;FS=3.68;GQ_MEAN=719;GQ_STDDEV=473.97;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0;NCC=0;QD=33.8;ReadPosRankSum=0.193;SOR=0.755;set=variant2;CSQ=upstream_gene_variant|||ENSG00000229807|XIST|ENST00000602863|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000229807|XIST|ENST00000429829|1/6||||lincRNA GT:AD:DP:GQ:PL 1:0,34:34:99:1248,0 1:0,11:11:99:333,0 1:1,17:18:99:576,0 chrX 73501562 . T C 912.64 PASS AC=1;AF=1;AN=1;DP=38;FS=0;GQ_MEAN=940;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.67;SOR=0.984;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000429124|2/4||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000430772|2/6||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000602576|2/5||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000423992|3/4||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000418855|2/4||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000602812|2/7||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000455395|2/4||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000602776|2/5||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000602420|2/5||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000230590|FTX|ENST00000603672|2/6||||lincRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:940,0 .:0,0:.:.:. chrX 73958629 . G A 357.64 PASS AC=1;AF=1;AN=1;DP=16;FS=0;GQ_MEAN=385;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.55;SOR=1.329;set=variant2;CSQ=intron_variant|||ENSG00000050030|KIAA2022|ENST00000424929||||-/118|protein_coding,3_prime_UTR_variant|||ENSG00000050030|KIAA2022|ENST00000055682|4/4|||-/1516|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,14:14:99:385,0 .:0,0:.:.:. chrX 74494470 . T G 2139.64 PASS AC=2;AF=1;AN=2;DP=64;FS=0;GQ_MEAN=1083.5;GQ_STDDEV=665.39;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.96;SOR=1.685;set=variant2;CSQ=upstream_gene_variant|||ENSG00000094841|UPRT|ENST00000530743||||-/173|protein_coding,synonymous_variant&NMD_transcript_variant|cgT/cgG|R|ENSG00000094841|UPRT|ENST00000373373|1/3|||127/142|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000094841|UPRT|ENST00000531704|1/4||||processed_transcript,synonymous_variant&NMD_transcript_variant|cgT/cgG|R|ENSG00000094841|UPRT|ENST00000462237|1/8|||127/176|nonsense_mediated_decay,synonymous_variant|cgT/cgG|R|ENSG00000094841|UPRT|ENST00000373383|1/7|||127/309|protein_coding,synonymous_variant|cgT/cgG|R|ENSG00000094841|UPRT|ENST00000373379|1/7|||127/281|protein_coding GT:AD:DP:GQ:PL 1:0,45:45:99:1554,0 .:0,0:.:.:. 1:0,18:18:99:613,0 chrX 74523367 . A G 1234.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=420.67;GQ_STDDEV=375.24;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.3;SOR=1.061;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373379|7/7|||-/281|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000094841|UPRT|ENST00000474175|5/5||||processed_transcript,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000462237||||-/176|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000094841|UPRT|ENST00000526850|8/8||||processed_transcript,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373383|7/7|||-/309|protein_coding,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000530743|7/7|||-/173|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:844,0 1:0,5:5:99:129,0 1:0,7:7:99:289,0 chrX 74523871 . G A 437.64 PASS AC=1;AF=1;AN=1;DP=17;FS=0;GQ_MEAN=465;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.74;SOR=1.371;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000530743|7/7|||-/173|protein_coding,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000526850|||||processed_transcript,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373383|7/7|||-/309|protein_coding,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000462237||||-/176|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373379|7/7|||-/281|protein_coding,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000474175|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,17:17:99:465,0 .:0,0:.:.:. chrX 74524280 . C A 139.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=167;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=17.46;SOR=1.179;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000530743|7/7|||-/173|protein_coding,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000474175|||||processed_transcript,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373379|7/7|||-/281|protein_coding,3_prime_UTR_variant|||ENSG00000094841|UPRT|ENST00000373383|7/7|||-/309|protein_coding,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000526850|||||processed_transcript,downstream_gene_variant|||ENSG00000094841|UPRT|ENST00000462237||||-/176|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:167,0 .:0,0:.:.:. chrX 74589117 . C T 859.64 PASS AC=1;AF=1;AN=1;DP=40;FS=0;GQ_MEAN=887;MLEAC=1;MLEAF=1;MQ=59.77;MQ0=0;NCC=2;QD=22.04;SOR=0.743;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000373367|12/12|||-/337|protein_coding,3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|11/11|||-/328|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,39:39:99:887,0 .:0,0:.:.:. chrX 74590136 . G C 987.64 PASS AC=1;AF=1;AN=1;DP=36;FS=0;GQ_MEAN=1015;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.43;SOR=1.371;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000373367|12/12|||-/337|protein_coding,3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|11/11|||-/328|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,36:36:99:1015,0 .:0,0:.:.:. chrX 74590180 . G A 636.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=664;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.58;SOR=0.922;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|11/11|||-/328|protein_coding,3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000373367|12/12|||-/337|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,27:27:99:664,0 .:0,0:.:.:. chrX 74590258 . G T 585.64 PASS AC=1;AF=1;AN=1;DP=26;FS=0;GQ_MEAN=613;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.52;SOR=1.22;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|11/11|||-/328|protein_coding,3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000373367|12/12|||-/337|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:613,0 .:0,0:.:.:. chrX 74591706 . T C 931.64 PASS AC=1;AF=1;AN=1;DP=36;FS=0;GQ_MEAN=959;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.88;SOR=1.061;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000373367|12/12|||-/337|protein_coding,3_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|11/11|||-/328|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,36:36:99:959,0 .:0,0:.:.:. chrX 74743194 . C G 48.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=76;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.32;SOR=2.303;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102383|ZDHHC15|ENST00000482827|||||processed_transcript,upstream_gene_variant|||ENSG00000102383|ZDHHC15|ENST00000373367||||-/337|protein_coding,upstream_gene_variant|||ENSG00000102383|ZDHHC15|ENST00000373361||||-/187|protein_coding,5_prime_UTR_variant|||ENSG00000102383|ZDHHC15|ENST00000541184|1/11|||-/328|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:76:76,0 .:0,0:.:.:. chrX 76937963 . G C 2245.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.04;ClippingRankSum=0.069;DP=65;FS=0;GQ_MEAN=757.67;GQ_STDDEV=304.67;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.179;NCC=0;QD=34.55;ReadPosRankSum=-0.208;SOR=0.249;set=variant2;CSQ=missense_variant|Cag/Gag|Q/E|ENSG00000085224|ATRX|ENST00000395603|8/34|benign(0)||891/2454|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000085224|ATRX|ENST00000480283|10/36||||processed_transcript,upstream_gene_variant|||ENSG00000085224|ATRX|ENST00000493470|||||processed_transcript,missense_variant|Cag/Gag|Q/E|ENSG00000085224|ATRX|ENST00000373344|9/35|benign(0)||929/2492|protein_coding GT:AD:DP:GQ:PL 1:1,24:25:99:899,0 1:0,13:13:99:408,0 1:0,27:27:99:966,0 chrX 77086362 . A C 1799.64 PASS AC=3;AF=1;AN=3;DP=60;FS=0;GQ_MEAN=609;GQ_STDDEV=263.74;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.99;SOR=0.76;set=variant2;CSQ=missense_variant|gTa/gGa|V/G|ENSG00000102158|MAGT1|ENST00000358075|9/10|benign(0.003)|deleterious(0)|343/367|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:492,0 1:0,32:32:99:911,0 1:0,12:12:99:424,0 chrX 77268502 . G C 2711.64 PASS AC=3;AF=1;AN=3;DP=78;FS=0;GQ_MEAN=913;GQ_STDDEV=397.04;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.76;SOR=0.976;set=variant2;CSQ=intron_variant|||ENSG00000165240|ATP7A|ENST00000350425||||-/503|protein_coding,missense_variant|Gtt/Ctt|V/L|ENSG00000165240|ATP7A|ENST00000341514|10/23|probably_damaging(0.997)||767/1500|protein_coding,intron_variant|||ENSG00000165240|ATP7A|ENST00000343533||||-/1422|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1358,0 1:0,22:22:99:595,0 1:0,20:20:99:786,0 chrX 77298857 . G A 1686.64 PASS AC=3;AF=1;AN=3;DP=57;FS=0;GQ_MEAN=571.33;GQ_STDDEV=318.22;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.59;SOR=1.238;set=variant2;CSQ=missense_variant|Gag/Aag|E/K|ENSG00000165240|ATP7A|ENST00000341514|21/23|benign(0)||1350/1500|protein_coding,missense_variant|Gag/Aag|E/K|ENSG00000165240|ATP7A|ENST00000350425|8/10|benign(0)||353/503|protein_coding,missense_variant|Gag/Aag|E/K|ENSG00000165240|ATP7A|ENST00000343533|20/22|benign(0)||1272/1422|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:763,0 1:0,30:30:99:747,0 1:0,6:6:99:204,0 chrX 77385748 . C T 174.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=202;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=29.11;SOR=3.912;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000187325|TAF9B|ENST00000341864|7/7|||-/251|protein_coding,downstream_gene_variant|||ENSG00000187325|TAF9B|ENST00000480681|||||retained_intron,downstream_gene_variant|||ENSG00000102144|PGK1|ENST00000442431||||-/281|protein_coding,downstream_gene_variant|||ENSG00000102144|PGK1|ENST00000373316||||-/417|protein_coding,downstream_gene_variant|||ENSG00000102144|PGK1|ENST00000537456||||-/389|protein_coding,downstream_gene_variant|||ENSG00000102144|PGK1|ENST00000476531|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:202,0 .:0,0:.:.:. chrX 78011737 . T C 457.64 PASS AC=3;AF=1;AN=3;DP=18;FS=0;GQ_MEAN=161.67;GQ_STDDEV=137.99;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.6;SOR=2.049;set=variant2;CSQ=downstream_gene_variant|||ENSG00000147145|LPAR4|ENST00000514744||||-/45|protein_coding,3_prime_UTR_variant|||ENSG00000147145|LPAR4|ENST00000435339|2/2|||-/370|protein_coding,downstream_gene_variant|||ENSG00000147145|LPAR4|ENST00000610214|||||processed_transcript,downstream_gene_variant|||ENSG00000147145|LPAR4|ENST00000607964|||||processed_transcript GT:AD:DP:GQ:PL 1:0,2:2:82:82,0 1:0,12:12:99:321,0 1:0,2:2:82:82,0 chrX 78426471 . C T 442.64 PASS AC=3;AF=1;AN=3;DP=13;FS=0;GQ_MEAN=156.67;GQ_STDDEV=90;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.05;SOR=3.767;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000147138|GPR174|ENST00000276077|1/1|||-/333|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:247,0 1:0,2:2:67:67,0 1:0,4:4:99:156,0 chrX 78426488 . T C 543.64 PASS AC=3;AF=1;AN=3;DP=16;FS=0;GQ_MEAN=190.33;GQ_STDDEV=50;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.98;SOR=1.244;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000147138|GPR174|ENST00000276077|1/1|||-/333|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:248,0 1:0,5:5:99:159,0 1:0,4:4:99:164,0 chrX 78426988 . T C 3572.64 PASS AC=3;AF=1;AN=3;DP=109;FS=0;GQ_MEAN=1200;GQ_STDDEV=889.41;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.08;SOR=1.077;set=variant2;CSQ=missense_variant|Tct/Cct|S/P|ENSG00000147138|GPR174|ENST00000276077|1/1|benign(0.001)|tolerated(0.37)|162/333|protein_coding GT:AD:DP:GQ:PL 1:0,52:52:99:1712,0 1:0,6:6:99:173,0 1:0,50:50:99:1715,0 chrX 78616214 . C G 379.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=407;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.12;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000462038|||||processed_transcript,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000469541|||||processed_transcript,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000434584|5/5|||-/219|protein_coding,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000373298|6/6|||-/263|protein_coding,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000482194|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,14:14:99:407,0 .:0,0:.:.:. chrX 78616371 . T G 230.64 PASS AC=2;AF=1;AN=2;DP=7;FS=0;GQ_MEAN=129;GQ_STDDEV=83.44;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.95;SOR=1.609;set=variant2;CSQ=downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000462038|||||processed_transcript,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000469541|||||processed_transcript,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000434584|5/5|||-/219|protein_coding,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000373298|6/6|||-/263|protein_coding,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000482194|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:188,0 1:0,2:2:70:70,0 chrX 78616443 . G GT 294.65 PASS AC=3;AF=1;AN=3;DP=15;FS=0;GQ_MEAN=107.33;GQ_STDDEV=28.57;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=21.05;SOR=4.977;set=variant;CSQ=downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000462038|||||processed_transcript,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000469541|||||processed_transcript,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000434584|5/5|||-/219|protein_coding,3_prime_UTR_variant|||ENSG00000078596|ITM2A|ENST00000373298|6/6|||-/263|protein_coding,downstream_gene_variant|||ENSG00000078596|ITM2A|ENST00000482194|||||processed_transcript GT:AD:DP:GQ:PL 1:0,3,0:3:80:80,0 1:0,4,3:7:99:137,0 1:0,4,0:4:99:105,0 chrX 79698593 . C G 3227.04 PASS AC=3;AF=1;AN=3;DP=90;FS=0;GQ_MEAN=1084.67;GQ_STDDEV=504.57;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.34;SOR=1.295;set=variant2;CSQ=missense_variant|gaC/gaG|D/E|ENSG00000174016|FAM46D|ENST00000538312|5/5|benign(0.02)|tolerated(1)|185/389|protein_coding,missense_variant|gaC/gaG|D/E|ENSG00000174016|FAM46D|ENST00000308293|3/3|benign(0.02)|tolerated(1)|185/389|protein_coding GT:AD:DP:GQ:PL 1:0,40:40:99:1445,0 1:0,16:16:99:508,0 1:0,34:34:99:1301,0 chrX 79931831 . CGTGT C 390.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=418;MLEAC=1;MLEAF=1;MQ=62.28;MQ0=0;NCC=2;QD=29.3;SOR=1.085;set=variant;CSQ=downstream_gene_variant|||ENSG00000165288|BRWD3|ENST00000473691|||||processed_transcript,3_prime_UTR_variant|||ENSG00000165288|BRWD3|ENST00000373275|41/41|||-/1802|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:418,0 .:0,0:.:.:. chrX 79943569 . T C 1974.64 PASS AC=3;AF=1;AN=3;DP=59;FS=0;GQ_MEAN=667.33;GQ_STDDEV=408.52;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.47;SOR=1.532;set=variant2;CSQ=splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165288|BRWD3|ENST00000473691|18/25||||processed_transcript,missense_variant&splice_region_variant|aAg/aGg|K/R|ENSG00000165288|BRWD3|ENST00000373275|34/41|benign(0.001)|tolerated(1)|1288/1802|protein_coding GT:AD:DP:GQ:PL 1:0,28:28:99:943,0 1:0,7:7:99:198,0 1:0,24:24:99:861,0 chrX 80369834 . G T 708.64 PASS AC=1;AF=1;AN=1;DP=30;FS=0;GQ_MEAN=736;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.62;SOR=0.826;set=variant2;CSQ=downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000451455||||-/89|protein_coding,downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000447319||||-/201|protein_coding,downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000436386||||-/102|protein_coding,downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000373250||||-/161|protein_coding,downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000430960||||-/148|protein_coding,3_prime_UTR_variant|||ENSG00000198157|HMGN5|ENST00000358130|7/7|||-/282|protein_coding,downstream_gene_variant|||ENSG00000198157|HMGN5|ENST00000491275|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,30:30:99:736,0 .:0,0:.:.:. chrX 80553229 . C T 653.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=681;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.42;SOR=0.963;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000131171|SH3BGRL|ENST00000373212|4/4|||-/114|protein_coding,downstream_gene_variant|||ENSG00000131171|SH3BGRL|ENST00000463546|||||processed_transcript,downstream_gene_variant|||ENSG00000131171|SH3BGRL|ENST00000474113|||||processed_transcript,downstream_gene_variant|||ENSG00000131171|SH3BGRL|ENST00000481106|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:681,0 .:0,0:.:.:. chrX 82764040 . A G 5105.64 PASS AC=3;AF=1;AN=3;DP=111;FS=0;GQ_MEAN=1711;GQ_STDDEV=613.09;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.17;SOR=0.748;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000272066|RP3-326L13.2|ENST00000607095|1/1||||antisense,upstream_gene_variant|||ENSG00000272294|RP3-326L13.3|ENST00000607789|||||lincRNA,synonymous_variant|gaA/gaG|E|ENSG00000196767|POU3F4|ENST00000373200|1/1|||236/361|protein_coding GT:AD:DP:GQ:PL 1:0,51:51:99:2330,0 1:0,24:24:99:1104,0 1:0,36:36:99:1699,0 chrX 82764042 . G C 5105.64 PASS AC=3;AF=1;AN=3;DP=115;FS=0;GQ_MEAN=1711;GQ_STDDEV=613.09;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.55;SOR=0.746;set=variant2;CSQ=missense_variant|gGc/gCc|G/A|ENSG00000196767|POU3F4|ENST00000373200|1/1|benign(0)||237/361|protein_coding,upstream_gene_variant|||ENSG00000272294|RP3-326L13.3|ENST00000607789|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000272066|RP3-326L13.2|ENST00000607095|1/1||||antisense GT:AD:DP:GQ:PL 1:0,52:52:99:2330,0 1:0,25:25:99:1104,0 1:0,38:38:99:1699,0 chrX 83591866 . C T 1169.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=399;GQ_STDDEV=67.95;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.49;SOR=0.693;set=variant2;CSQ=synonymous_variant|ccG/ccA|P|ENSG00000165259|HDX|ENST00000373177|8/11|||561/690|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000165259|HDX|ENST00000297977|7/10|||561/690|protein_coding,synonymous_variant|ccG/ccA|P|ENSG00000165259|HDX|ENST00000506585|7/10|||503/632|protein_coding GT:AD:DP:GQ:PL 1:0,13:13:99:462,0 1:0,12:12:99:327,0 1:0,11:11:99:408,0 chrX 84189813 . A G 4382.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.214;ClippingRankSum=-1.258;DP=132;FS=4.674;GQ_MEAN=1470;GQ_STDDEV=992.31;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.593;NCC=0;QD=33.2;ReadPosRankSum=-1.495;SOR=1.405;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000229547|UBE2DNL|ENST00000451386|2/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000229547|UBE2DNL|ENST00000442533|2/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000229547|UBE2DNL|ENST00000602536|1/1||||processed_transcript,downstream_gene_variant|||ENSG00000229547|UBE2DNL|ENST00000474922|||||transcribed_processed_pseudogene GT:AD:DP:GQ:PL 1:1,72:73:99:2380,0 1:0,14:14:99:412,0 1:0,45:45:99:1618,0 chrX 84533652 . C A 150.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=178;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.11;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000124429|POF1B|ENST00000262753|17/17|||-/589|protein_coding,downstream_gene_variant|||ENSG00000124429|POF1B|ENST00000373145||||-/595|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:178,0 .:0,0:.:.:. chrX 84534383 . A C 1781.64 PASS AC=3;AF=1;AN=3;DP=66;FS=0;GQ_MEAN=603;GQ_STDDEV=155.54;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.26;SOR=1.14;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000124429|POF1B|ENST00000262753|17/17|||-/589|protein_coding,downstream_gene_variant|||ENSG00000124429|POF1B|ENST00000373145||||-/595|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:546,0 1:0,27:27:99:779,0 1:0,15:15:99:484,0 chrX 85116895 . T C 869.64 PASS AC=1;AF=1;AN=1;DP=32;FS=0;GQ_MEAN=897;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.05;SOR=0.756;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000188419|CHM|ENST00000467744|3/3||||processed_transcript,3_prime_UTR_variant|||ENSG00000188419|CHM|ENST00000357749|15/15|||-/653|protein_coding,downstream_gene_variant|||ENSG00000188419|CHM|ENST00000537751||||-/505|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,31:31:99:897,0 .:0,0:.:.:. chrX 85219021 . T C 2696.64 PASS AC=3;AF=1;AN=3;DP=90;FS=0;GQ_MEAN=908;GQ_STDDEV=139.95;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.96;SOR=0.935;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000188419|CHM|ENST00000467744|||||processed_transcript,synonymous_variant|gcA/gcG|A|ENSG00000188419|CHM|ENST00000357749|5/15|||117/653|protein_coding,5_prime_UTR_variant|||ENSG00000188419|CHM|ENST00000537751|2/12|||-/505|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1054,0 1:0,33:33:99:775,0 1:0,27:27:99:895,0 chrX 85224107 . G A 451.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-1.734;ClippingRankSum=1.26;DP=22;FS=0;GQ_MEAN=479;MLEAC=1;MLEAF=1;MQ=60.27;MQ0=0;MQRankSum=0.63;NCC=2;QD=20.53;ReadPosRankSum=-0.63;SOR=0.365;set=variant2;CSQ=intron_variant|||ENSG00000188419|CHM|ENST00000537751||||-/505|protein_coding,intron_variant|||ENSG00000188419|CHM|ENST00000357749||||-/653|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000188419|CHM|ENST00000467744|||||processed_transcript,3_prime_UTR_variant|||ENSG00000188419|CHM|ENST00000358786|5/5|||-/110|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,21:22:99:479,0 .:0,0:.:.:. chrX 85224121 . A AT 549.64 PASS AC=1;AF=1;AN=1;DP=20;FS=0;GQ_MEAN=577;MLEAC=1;MLEAF=1;MQ=60.3;MQ0=0;NCC=2;QD=30.54;SOR=1.179;set=variant;CSQ=intron_variant|||ENSG00000188419|CHM|ENST00000537751||||-/505|protein_coding,intron_variant|||ENSG00000188419|CHM|ENST00000357749||||-/653|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000188419|CHM|ENST00000467744|||||processed_transcript,3_prime_UTR_variant|||ENSG00000188419|CHM|ENST00000358786|5/5|||-/110|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,18:18:99:577,0 .:0,0:.:.:. chrX 85224213 . C T 499.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-1.589;ClippingRankSum=1.01;DP=24;FS=0;GQ_MEAN=527;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.144;NCC=2;QD=20.82;ReadPosRankSum=-0.722;SOR=0.257;set=variant2;CSQ=intron_variant|||ENSG00000188419|CHM|ENST00000357749||||-/653|protein_coding,intron_variant|||ENSG00000188419|CHM|ENST00000537751||||-/505|protein_coding,3_prime_UTR_variant|||ENSG00000188419|CHM|ENST00000358786|5/5|||-/110|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000188419|CHM|ENST00000467744|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,23:24:99:527,0 .:0,0:.:.:. chrX 86087385 . A T 337.64 PASS AC=1;AF=1;AN=1;DP=14;FS=0;GQ_MEAN=365;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.14;SOR=1.445;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000126733|DACH2|ENST00000510272|11/11|||-/380|protein_coding,3_prime_UTR_variant|||ENSG00000126733|DACH2|ENST00000373131|12/12|||-/571|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126733|DACH2|ENST00000461604|13/13|||-/440|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000126733|DACH2|ENST00000484479|7/7|||-/249|protein_coding,3_prime_UTR_variant|||ENSG00000126733|DACH2|ENST00000373125|12/12|||-/599|protein_coding,downstream_gene_variant|||ENSG00000126733|DACH2|ENST00000506327||||-/175|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000126733|DACH2|ENST00000508860|12/12|||-/432|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:365,0 .:0,0:.:.:. chrX 86877348 . G T 1179.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.6;ClippingRankSum=-0.667;DP=52;FS=3.274;GQ_MEAN=402.33;GQ_STDDEV=315.98;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.6;NCC=0;QD=23.13;ReadPosRankSum=-0.4;SOR=0.477;set=variant2;CSQ=synonymous_variant|ggG/ggT|G|ENSG00000102271|KLHL4|ENST00000373119|5/11|||354/718|protein_coding,synonymous_variant|ggG/ggT|G|ENSG00000102271|KLHL4|ENST00000373114|5/11|||354/720|protein_coding GT:AD:DP:GQ:PL 1:0,22:22:99:703,0 1:1,25:26:99:431,0 1:0,3:3:73:73,0 chrX 86887244 . C T 2003.64 PASS AC=3;AF=1;AN=3;DP=62;FS=0;GQ_MEAN=677;GQ_STDDEV=392.48;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.32;SOR=1.647;set=variant2;CSQ=synonymous_variant|acC/acT|T|ENSG00000102271|KLHL4|ENST00000373119|7/11|||453/718|protein_coding,synonymous_variant|acC/acT|T|ENSG00000102271|KLHL4|ENST00000373114|7/11|||453/720|protein_coding GT:AD:DP:GQ:PL 1:0,26:26:99:892,0 1:0,9:9:99:224,0 1:0,27:27:99:915,0 chrX 86922086 . A G 380.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.347;ClippingRankSum=-1.042;DP=15;FS=0;GQ_MEAN=408;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.81;NCC=2;QD=25.38;ReadPosRankSum=0.116;SOR=0.793;set=variant2;CSQ=intron_variant|||ENSG00000102271|KLHL4|ENST00000373114||||-/720|protein_coding,3_prime_UTR_variant|||ENSG00000102271|KLHL4|ENST00000373119|11/11|||-/718|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,14:15:99:408,0 .:0,0:.:.:. chrX 86922089 . T TA 405.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.224;ClippingRankSum=-0.075;DP=17;FS=0;GQ_MEAN=433;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.82;NCC=2;QD=23.86;ReadPosRankSum=0.969;SOR=1.473;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102271|KLHL4|ENST00000373119|11/11|||-/718|protein_coding,intron_variant|||ENSG00000102271|KLHL4|ENST00000373114||||-/720|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,15:17:99:433,0 .:0,0:.:.:. chrX 88008423 . A C 1878.64 PASS AC=3;AF=1;AN=3;DP=57;FS=0;GQ_MEAN=635.33;GQ_STDDEV=204.41;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.96;SOR=1.961;set=variant2;CSQ=missense_variant|tAt/tCt|Y/S|ENSG00000147183|CPXCR1|ENST00000276127|3/3|benign(0)|tolerated(1)|3/301|protein_coding,missense_variant|tAt/tCt|Y/S|ENSG00000147183|CPXCR1|ENST00000373111|3/3|benign(0)|tolerated(1)|3/301|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:777,0 1:0,14:14:99:401,0 1:0,20:20:99:728,0 chrX 88009322 . A G 1376.64 PASS AC=3;AF=1;AN=3;DP=45;FS=0;GQ_MEAN=468;GQ_STDDEV=50.27;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.29;SOR=1.662;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147183|CPXCR1|ENST00000276127|3/3|||-/301|protein_coding,3_prime_UTR_variant|||ENSG00000147183|CPXCR1|ENST00000373111|3/3|||-/301|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:421,0 1:0,19:19:99:521,0 1:0,13:13:99:462,0 chrX 89177673 . G A 8342.64 PASS AC=3;AF=1;AN=3;DP=270;FS=0;GQ_MEAN=2790;GQ_STDDEV=1962.23;MLEAC=3;MLEAF=1;MQ=56.17;MQ0=0;NCC=0;QD=31.13;SOR=0.887;set=variant2;CSQ=missense_variant|Gtc/Atc|V/I|ENSG00000153779|TGIF2LX|ENST00000561129|1/1|benign(0)|tolerated(0.25)|197/241|protein_coding,missense_variant|Gtc/Atc|V/I|ENSG00000153779|TGIF2LX|ENST00000283891|2/2|benign(0)|tolerated(0.25)|197/241|protein_coding GT:AD:DP:GQ:PL 1:0,145:145:99:4684,0 1:0,31:31:99:766,0 1:0,92:92:99:2920,0 chrX 90689704 . G A 1074.64 PASS AC=1;AF=1;AN=1;DP=44;FS=0;GQ_MEAN=1102;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.42;SOR=0.784;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000234161|PABPC5-AS1|ENST00000456187|||||antisense,upstream_gene_variant|||ENSG00000174740|PABPC5|ENST00000312600||||-/382|protein_coding,5_prime_UTR_variant|||ENSG00000174740|PABPC5|ENST00000373105|1/2|||-/218|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,44:44:99:1102,0 .:0,0:.:.:. chrX 91874217 . C G 1123.64 my_snp_filter AC=1;AF=1;AN=1;DP=41;FS=0;GQ_MEAN=1151;MLEAC=1;MLEAF=1;MQ=37.16;MQ0=0;NCC=2;QD=27.41;SOR=0.741;set=FilteredInAll;CSQ=downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000298274||||-/1310|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000373088||||-/1310|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000406881||||-/1339|protein_coding,3_prime_UTR_variant|||ENSG00000102290|PCDH11X|ENST00000373097|6/6|||-/1337|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000504220||||-/1065|protein_coding,3_prime_UTR_variant|||ENSG00000102290|PCDH11X|ENST00000373094|7/7|||-/1347|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000361655||||-/1329|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,41:41:99:1151,0 .:0,0:.:.:. chrX 91874474 . G A 1042.64 PASS AC=1;AF=1;AN=1;DP=39;FS=0;GQ_MEAN=1070;MLEAC=1;MLEAF=1;MQ=43.22;MQ0=0;NCC=2;QD=26.73;SOR=1.73;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102290|PCDH11X|ENST00000373097|6/6|||-/1337|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000504220||||-/1065|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000373088||||-/1310|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000298274||||-/1310|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000406881||||-/1339|protein_coding,downstream_gene_variant|||ENSG00000102290|PCDH11X|ENST00000361655||||-/1329|protein_coding,3_prime_UTR_variant|||ENSG00000102290|PCDH11X|ENST00000373094|7/7|||-/1347|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,39:39:99:1070,0 .:0,0:.:.:. chrX 92927634 . G C 1066.87 PASS AC=2;AF=0.667;AN=3;DP=36;FS=0;GQ_MEAN=402.33;GQ_STDDEV=506.34;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.34;SOR=0.818;set=variant2;CSQ=missense_variant|Cct/Gct|P/A|ENSG00000186310|NAP1L3|ENST00000373079|1/1|possibly_damaging(0.822)|tolerated_low_confidence(0.53)|224/506|protein_coding,missense_variant|Cct/Gct|P/A|ENSG00000186310|NAP1L3|ENST00000475430|2/2|possibly_damaging(0.822)|tolerated_low_confidence(0.44)|217/499|protein_coding,upstream_gene_variant|||ENSG00000179083|FAM133A|ENST00000332647||||-/248|protein_coding,upstream_gene_variant|||ENSG00000179083|FAM133A|ENST00000322139||||-/248|protein_coding,upstream_gene_variant|||ENSG00000179083|FAM133A|ENST00000538690||||-/248|protein_coding,upstream_gene_variant|||ENSG00000179083|FAM133A|ENST00000355813||||-/248|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,108 1:0,3:3:99:112,0 1:0,29:29:99:987,0 chrX 92964617 . G A 519.63 PASS AC=1;AF=0.5;AN=2;DP=20;FS=0;GQ_MEAN=329.5;GQ_STDDEV=311.83;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=32.48;SOR=1.244;set=variant2;CSQ=missense_variant|Gaa/Aaa|E/K|ENSG00000179083|FAM133A|ENST00000322139|3/3|probably_damaging(0.936)|deleterious_low_confidence(0.03)|67/248|protein_coding,missense_variant|Gaa/Aaa|E/K|ENSG00000179083|FAM133A|ENST00000332647|4/4|probably_damaging(0.936)|deleterious_low_confidence(0.03)|67/248|protein_coding,missense_variant|Gaa/Aaa|E/K|ENSG00000179083|FAM133A|ENST00000355813|4/4|probably_damaging(0.936)|deleterious_low_confidence(0.03)|67/248|protein_coding,missense_variant|Gaa/Aaa|E/K|ENSG00000179083|FAM133A|ENST00000538690|5/5|probably_damaging(0.936)|deleterious_low_confidence(0.03)|67/248|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 .:0,0:.:.:. 1:0,16:16:99:550,0 chrX 96139406 . G A 3822.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.543;ClippingRankSum=0.031;DP=120;FS=3.513;GQ_MEAN=1283.33;GQ_STDDEV=986.89;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.291;NCC=0;QD=32.12;ReadPosRankSum=-0.976;SOR=0.614;set=variant2;CSQ=intron_variant|||ENSG00000147202|DIAPH2|ENST00000373061||||-/1101|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000373049||||-/1096|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000355827||||-/1096|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000373054||||-/1097|protein_coding,missense_variant|Gct/Act|A/T|ENSG00000204086|RPA4|ENST00000373040|1/1|benign(0.025)|tolerated(0.3)|33/261|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000324765||||-/1101|protein_coding GT:AD:DP:GQ:PL 1:1,54:55:99:1766,0 1:0,6:6:99:148,0 1:0,58:58:99:1936,0 chrX 96139459 . T C 4421.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=-1.732;ClippingRankSum=-1.049;DP=138;FS=0;GQ_MEAN=2224.5;GQ_STDDEV=68.59;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.952;NCC=1;QD=32.27;ReadPosRankSum=1.1;SOR=0.223;set=variant2;CSQ=intron_variant|||ENSG00000147202|DIAPH2|ENST00000324765||||-/1101|protein_coding,synonymous_variant|aaT/aaC|N|ENSG00000204086|RPA4|ENST00000373040|1/1|||50/261|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000355827||||-/1096|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000373054||||-/1097|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000373061||||-/1101|protein_coding,intron_variant|||ENSG00000147202|DIAPH2|ENST00000373049||||-/1096|protein_coding GT:AD:DP:GQ:PL 1:0,66:66:99:2176,0 .:0,0:.:.:. 1:1,70:71:99:2273,0 chrX 99664018 . G A 414.64 PASS AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=442;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.04;SOR=0.693;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000165194|PCDH19|ENST00000255531|1/5|||-/1101|protein_coding,5_prime_UTR_variant|||ENSG00000165194|PCDH19|ENST00000373034|1/6|||-/1148|protein_coding,upstream_gene_variant|||ENSG00000165194|PCDH19|ENST00000420881||||-/1100|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,18:18:99:442,0 .:0,0:.:.:. chrX 99664299 . C A 60.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=88;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.21;SOR=2.833;set=variant2;CSQ=upstream_gene_variant|||ENSG00000165194|PCDH19|ENST00000420881||||-/1100|protein_coding,5_prime_UTR_variant|||ENSG00000165194|PCDH19|ENST00000373034|1/6|||-/1148|protein_coding,5_prime_UTR_variant|||ENSG00000165194|PCDH19|ENST00000255531|1/5|||-/1101|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:88:88,0 .:0,0:.:.:. chrX 99926122 . G A 1384.64 PASS AC=3;AF=1;AN=3;DP=40;FS=0;GQ_MEAN=470.67;GQ_STDDEV=262.71;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.62;SOR=2.948;set=variant2;CSQ=upstream_gene_variant|||ENSG00000261295|RP11-524D16__A.3|ENST00000568809|||||antisense,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000263033||||-/671|protein_coding,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000276141||||-/671|protein_coding,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000491602|||||processed_transcript,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000372989||||-/671|protein_coding,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000455616||||-/671|protein_coding,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000454200||||-/673|protein_coding,3_prime_UTR_variant|||ENSG00000102359|SRPX2|ENST00000373004|11/11|||-/465|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:666,0 1:0,7:7:99:172,0 1:0,15:15:99:574,0 chrX 99930886 . T TAC 62.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=90;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.32;SOR=2.303;set=variant;CSQ=downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000263033||||-/671|protein_coding,downstream_gene_variant|||ENSG00000261295|RP11-524D16__A.3|ENST00000568809|||||antisense,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000372989|19/19|||-/671|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102362|SYTL4|ENST00000491602|2/2||||processed_transcript,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000276141|17/17|||-/671|protein_coding,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000454200|17/17|||-/673|protein_coding,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000455616|18/18|||-/671|protein_coding,downstream_gene_variant|||ENSG00000102359|SRPX2|ENST00000373004||||-/465|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. .:0,0:.:.:. 1:0,2:2:90:90,0 chrX 99930892 . T C 648.64 PASS AC=3;AF=1;AN=3;DP=22;FS=0;GQ_MEAN=225.33;GQ_STDDEV=241.37;MLEAC=3;MLEAF=1;MQ=69.48;MQ0=0;NCC=0;QD=29.48;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000372989|19/19|||-/671|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102362|SYTL4|ENST00000491602|2/2||||processed_transcript,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000276141|17/17|||-/671|protein_coding,downstream_gene_variant|||ENSG00000102362|SYTL4|ENST00000263033||||-/671|protein_coding,downstream_gene_variant|||ENSG00000261295|RP11-524D16__A.3|ENST00000568809|||||antisense,downstream_gene_variant|||ENSG00000102359|SRPX2|ENST00000373004||||-/465|protein_coding,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000454200|17/17|||-/673|protein_coding,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000455616|18/18|||-/671|protein_coding GT:AD:DP:GQ:PL 1:0,2,0:2:82:82,0 1:0,18,0:18:99:504,0 1:0,2,0:2:90:90,0 chrX 99941705 . T C 4246.64 PASS AC=3;AF=1;AN=3;DP=131;FS=0;GQ_MEAN=1424.67;GQ_STDDEV=323.19;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.42;SOR=1.022;set=variant2;CSQ=missense_variant|Att/Gtt|I/V|ENSG00000102362|SYTL4|ENST00000276141|12/17|benign(0.004)|tolerated(0.57)|420/671|protein_coding,3_prime_UTR_variant|||ENSG00000102362|SYTL4|ENST00000372981|10/10|||-/349|protein_coding,missense_variant|Att/Gtt|I/V|ENSG00000102362|SYTL4|ENST00000372989|14/19|benign(0.004)|tolerated(0.57)|420/671|protein_coding,missense_variant|Att/Gtt|I/V|ENSG00000102362|SYTL4|ENST00000455616|13/18|benign(0.004)|tolerated(0.57)|420/671|protein_coding,missense_variant|Att/Gtt|I/V|ENSG00000102362|SYTL4|ENST00000263033|12/17|benign(0.004)|tolerated(0.57)|420/671|protein_coding,missense_variant|Att/Gtt|I/V|ENSG00000102362|SYTL4|ENST00000454200|12/17|benign(0.005)||422/673|protein_coding GT:AD:DP:GQ:PL 1:0,40:40:99:1522,0 1:0,63:63:99:1688,0 1:0,28:28:99:1064,0 chrX 100098355 . TAAG T 551.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.747;ClippingRankSum=0.747;DP=16;FS=5.051;GQ_MEAN=193;GQ_STDDEV=62.39;MLEAC=3;MLEAF=1;MQ=61.34;MQ0=0;MQRankSum=0.747;NCC=0;QD=34.48;ReadPosRankSum=0.747;SOR=1.793;set=variant;CSQ=downstream_gene_variant|||ENSG00000101811|CSTF2|ENST00000415585||||-/597|protein_coding,3_prime_UTR_variant|||ENSG00000007952|NOX1|ENST00000372966|13/13|||-/564|protein_coding,downstream_gene_variant|||ENSG00000007952|NOX1|ENST00000372960||||-/527|protein_coding,downstream_gene_variant|||ENSG00000007952|NOX1|ENST00000427768||||-/175|protein_coding,inframe_deletion|ttCTTa/tta|FL/L|ENSG00000007952|NOX1|ENST00000372964|6/6|||185-186/192|protein_coding,downstream_gene_variant|||ENSG00000101811|CSTF2|ENST00000475126||||-/438|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000101811|CSTF2|ENST00000372972||||-/577|protein_coding,downstream_gene_variant|||ENSG00000007952|NOX1|ENST00000217885||||-/515|protein_coding GT:AD:DP:GQ:PL 1:1,7:8:99:259,0 1:0,5:5:99:185,0 1:0,3:3:99:135,0 chrX 100243459 . G T 2807.64 PASS AC=3;AF=1;AN=3;DP=89;FS=0;GQ_MEAN=945;GQ_STDDEV=248.95;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.55;SOR=1.636;set=variant2;CSQ=intron_variant|||ENSG00000174225|ARL13A|ENST00000450049||||-/256|protein_coding,intron_variant|||ENSG00000174225|ARL13A|ENST00000372953||||-/163|protein_coding,missense_variant&NMD_transcript_variant|atG/atT|M/I|ENSG00000174225|ARL13A|ENST00000494863|3/4|benign(0)|tolerated(0.15)|113/124|nonsense_mediated_decay,missense_variant&NMD_transcript_variant|atG/atT|M/I|ENSG00000174225|ARL13A|ENST00000450457|8/9|benign(0)|tolerated_low_confidence(0.12)|279/290|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,32:32:99:1120,0 1:0,28:28:99:660,0 1:0,29:29:99:1055,0 chrX 100245606 . A G 1356.87 PASS AC=2;AF=0.667;AN=3;DP=45;FS=0;GQ_MEAN=500.33;GQ_STDDEV=557.39;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.31;SOR=1.402;set=variant2;CSQ=synonymous_variant|ccA/ccG|P|ENSG00000174225|ARL13A|ENST00000372953|6/6|||143/163|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000174225|ARL13A|ENST00000450457|9/9|||-/290|nonsense_mediated_decay,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000174225|ARL13A|ENST00000494863|4/4|||-/124|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000174225|ARL13A|ENST00000450049|8/8|||-/256|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,112 1:0,10:10:99:250,0 1:0,32:32:99:1139,0 chrX 100350683 . TA T 1443.64 PASS AC=1;AF=1;AN=1;DP=39;FS=0;GQ_MEAN=1471;MLEAC=1;MLEAF=1;MQ=60.28;MQ0=0;NCC=2;QD=30.18;SOR=1.27;set=variant;CSQ=upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000372927||||-/756|protein_coding,3_prime_UTR_variant|||ENSG00000126950|TMEM35|ENST00000372930|2/2|||-/167|protein_coding,upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000435570||||-/45|protein_coding,downstream_gene_variant|||ENSG00000126950|TMEM35|ENST00000478351|||||processed_transcript,upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000403304||||-/75|protein_coding,upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000218507||||-/742|protein_coding,upstream_gene_variant|||ENSG00000225839|TRMT2B-AS1|ENST00000443801|||||sense_overlapping,upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000423383||||-/756|protein_coding,upstream_gene_variant|||ENSG00000102384|CENPI|ENST00000372926||||-/522|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:1471,0 .:0,0:.:.:. chrX 100490933 . G C 951.87 PASS AC=2;AF=0.667;AN=3;DP=34;FS=0;GQ_MEAN=367.67;GQ_STDDEV=228.37;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.71;SOR=1.402;set=variant2;CSQ=missense_variant|Gtt/Ctt|V/L|ENSG00000102385|DRP2|ENST00000395209|4/24|benign(0.097)|tolerated_low_confidence(0.32)|68/957|protein_coding,missense_variant|Gtt/Ctt|V/L|ENSG00000102385|DRP2|ENST00000538510|2/22|benign(0.097)|tolerated_low_confidence(0.32)|68/957|protein_coding,missense_variant&NMD_transcript_variant|Gtt/Ctt|V/L|ENSG00000102385|DRP2|ENST00000372916|4/16|benign(0.001)|tolerated_low_confidence(0.22)|68/353|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|2/22|||-/879|protein_coding,missense_variant|Gtt/Ctt|V/L|ENSG00000102385|DRP2|ENST00000402866|4/24|benign(0.097)|tolerated_low_confidence(0.32)|68/957|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,119 1:0,15:15:99:416,0 1:0,16:16:99:568,0 chrX 100515792 . A G 846.87 PASS AC=2;AF=0.667;AN=3;DP=27;FS=0;GQ_MEAN=329.33;GQ_STDDEV=253.9;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=35.84;SOR=1.708;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 1:0,7:7:99:272,0 1:0,16:16:99:607,0 chrX 100516325 . A ATT 565.64 PASS AC=1;AF=1;AN=1;DP=18;FS=0;GQ_MEAN=593;MLEAC=1;MLEAF=1;MQ=61.19;MQ0=0;NCC=2;QD=31.42;SOR=0.941;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2,16:18:99:593,0 .:0,0:.:.:. chrX 100516507 . A G 62.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=90;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.32;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:90:90,0 .:0,0:.:.:. chrX 100516510 . G T 62.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=90;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.32;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:90:90,0 .:0,0:.:.:. chrX 100517057 . C T 451.64 PASS AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=479;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.77;SOR=0.793;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,19:19:99:479,0 .:0,0:.:.:. chrX 100517135 . T C 1485.64 PASS AC=2;AF=1;AN=2;DP=58;FS=0;GQ_MEAN=756.5;GQ_STDDEV=1000.56;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.06;SOR=0.8;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,55:55:99:1464,0 1:0,2:2:49:49,0 chrX 100517416 . T C 188.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=216;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.95;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:216,0 .:0,0:.:.:. chrX 100517837 . CT C 400.64 PASS AC=2;AF=1;AN=2;DP=12;FS=0;GQ_MEAN=214;GQ_STDDEV=202.23;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.39;SOR=1.022;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:71:71,0 1:0,10:10:99:357,0 .:0,0:.:.:. chrX 100518165 . T C 707.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.61;ClippingRankSum=0.06;DP=30;FS=3.163;GQ_MEAN=389;GQ_STDDEV=493.56;MLEAC=1;MLEAF=0.5;MQ=59.49;MQ0=0;MQRankSum=-0.896;NCC=1;QD=24.4;ReadPosRankSum=0.538;SOR=0.442;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding GT:AD:DP:GQ:PL 0:1,0:1:40:0,40 1:1,28:29:99:738,0 .:0,0:.:.:. chrX 100518448 . G C 559.63 PASS AC=1;AF=0.5;AN=2;DP=22;FS=0;GQ_MEAN=319.5;GQ_STDDEV=382.54;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=27.98;SOR=0.892;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102387|TAF7L|ENST00000324762||||-/302|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000538510|22/22|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000402866|24/24|||-/957|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000541709|22/22|||-/879|protein_coding,downstream_gene_variant|||ENSG00000102387|TAF7L|ENST00000372907||||-/462|protein_coding,3_prime_UTR_variant|||ENSG00000102385|DRP2|ENST00000395209|24/24|||-/957|protein_coding,downstream_gene_variant|||ENSG00000102387|TAF7L|ENST00000372905||||-/302|protein_coding GT:AD:DP:GQ:PL 0:2,0:2:49:0,49 1:0,20:20:99:590,0 .:0,0:.:.:. chrX 100547853 . C T 792.87 PASS AC=1;AF=0.333;AN=3;DP=32;FS=0;GQ_MEAN=347;GQ_STDDEV=414.06;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=30.49;SOR=1.22;set=variant2;CSQ=missense_variant|Gag/Aag|E/K|ENSG00000102387|TAF7L|ENST00000372907|1/13|benign(0.003)|tolerated(0.57)|61/462|protein_coding,upstream_gene_variant|||ENSG00000222203|Y_RNA|ENST00000410271|||||misc_RNA,upstream_gene_variant|||ENSG00000102387|TAF7L|ENST00000356784||||-/376|protein_coding,5_prime_UTR_variant|||ENSG00000102387|TAF7L|ENST00000372905|1/12|||-/302|protein_coding GT:AD:DP:GQ:PL 1:0,26:26:99:825,0 0:3,0:3:99:0,99 0:3,0:3:99:0,117 chrX 100547933 . A G 4547.64 PASS AC=3;AF=1;AN=3;DP=155;FS=0;GQ_MEAN=1525;GQ_STDDEV=781.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.53;SOR=0.92;set=variant2;CSQ=upstream_gene_variant|||ENSG00000222203|Y_RNA|ENST00000410271|||||misc_RNA,missense_variant|cTt/cCt|L/P|ENSG00000102387|TAF7L|ENST00000372907|1/13|benign(0)|tolerated(0.52)|34/462|protein_coding,upstream_gene_variant|||ENSG00000102387|TAF7L|ENST00000356784||||-/376|protein_coding,5_prime_UTR_variant|||ENSG00000102387|TAF7L|ENST00000372905|1/12|||-/302|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1148,0 1:0,89:89:99:2424,0 1:0,30:30:99:1003,0 chrX 100604757 . T G 1543.64 PASS AC=3;AF=1;AN=3;DP=51;FS=0;GQ_MEAN=523.67;GQ_STDDEV=273.54;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.27;SOR=1.436;set=variant2;CSQ=downstream_gene_variant|||ENSG00000010671|BTK|ENST00000488970|||||processed_transcript,3_prime_UTR_variant|||ENSG00000010671|BTK|ENST00000308731|19/19|||-/659|protein_coding,upstream_gene_variant|||ENSG00000126953|TIMM8A|ENST00000480575|||||processed_transcript,3_prime_UTR_variant|||ENSG00000010671|BTK|ENST00000372880|17/17|||-/483|protein_coding,downstream_gene_variant|||ENSG00000010671|BTK|ENST00000470069|||||processed_transcript,upstream_gene_variant|||ENSG00000126953|TIMM8A|ENST00000372902||||-/97|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:253,0 1:0,28:28:99:800,0 1:0,16:16:99:518,0 chrX 100743037 . C T 3500.64 PASS AC=3;AF=1;AN=3;DP=112;FS=0;GQ_MEAN=1176;GQ_STDDEV=449.84;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.26;SOR=0.844;set=variant2;CSQ=synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000442270|5/13|||27/51|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000455331|5/8|||27/348|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000452188|5/13|||39/360|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000445416|5/11|||27/51|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000354842|5/13|||27/348|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000196440|ARMCX4|ENST00000423738|1/2|||-/2290|protein_coding,synonymous_variant&NMD_transcript_variant|taC/taT|Y|ENSG00000196440|ARMCX4|ENST00000433011|8/16|||39/360|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,40:40:99:1391,0 1:0,27:27:99:659,0 1:0,45:45:99:1478,0 chrX 100743826 . A G 4457.64 PASS AC=3;AF=1;AN=3;DP=142;FS=0;GQ_MEAN=1495;GQ_STDDEV=221.21;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.39;SOR=0.811;set=variant2;CSQ=missense_variant&NMD_transcript_variant|Agg/Ggg|R/G|ENSG00000196440|ARMCX4|ENST00000455331|6/8|benign(0)||176/348|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000196440|ARMCX4|ENST00000442270||||-/51|nonsense_mediated_decay,missense_variant&NMD_transcript_variant|Agg/Ggg|R/G|ENSG00000196440|ARMCX4|ENST00000452188|6/13|benign(0)|tolerated(1)|188/360|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000196440|ARMCX4|ENST00000445416||||-/51|nonsense_mediated_decay,missense_variant&NMD_transcript_variant|Agg/Ggg|R/G|ENSG00000196440|ARMCX4|ENST00000354842|6/13|benign(0)||176/348|nonsense_mediated_decay,missense_variant|Agg/Ggg|R/G|ENSG00000196440|ARMCX4|ENST00000423738|2/2|benign(0)||84/2290|protein_coding,missense_variant&NMD_transcript_variant|Agg/Ggg|R/G|ENSG00000196440|ARMCX4|ENST00000433011|9/16|benign(0)|tolerated(1)|188/360|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,50:50:99:1732,0 1:0,55:55:99:1459,0 1:0,37:37:99:1294,0 chrX 100880857 . G A 417.87 PASS AC=1;AF=0.333;AN=3;DP=18;FS=0;GQ_MEAN=222.33;GQ_STDDEV=197.31;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.82;SOR=1.022;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102401|ARMCX3|ENST00000477980|||||processed_transcript,synonymous_variant|aaG/aaA|K|ENSG00000102401|ARMCX3|ENST00000537169|5/5|||296/379|protein_coding,downstream_gene_variant|||ENSG00000102401|ARMCX3|ENST00000479298||||-/63|protein_coding,downstream_gene_variant|||ENSG00000102401|ARMCX3|ENST00000491568||||-/94|protein_coding,upstream_gene_variant|||ENSG00000228275|ARMCX3-AS1|ENST00000454228|||||antisense,downstream_gene_variant|||ENSG00000102401|ARMCX3|ENST00000467808|||||processed_transcript,synonymous_variant|aaG/aaA|K|ENSG00000102401|ARMCX3|ENST00000341189|5/5|||296/379|protein_coding,upstream_gene_variant|||ENSG00000261101|RP4-545K15.5|ENST00000564612|||||sense_overlapping,synonymous_variant|aaG/aaA|K|ENSG00000102401|ARMCX3|ENST00000471229|5/5|||296/379|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:450,0 0:3,0:3:99:0,101 0:3,0:3:99:0,116 chrX 100911066 . C T 1128.64 PASS AC=3;AF=1;AN=3;DP=36;FS=0;GQ_MEAN=385.33;GQ_STDDEV=181.39;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.35;SOR=2.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000496581|||||processed_transcript,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000458024||||-/92|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000413506||||-/167|protein_coding,synonymous_variant|caG/caA|Q|ENSG00000184867|ARMCX2|ENST00000328766|5/5|||503/632|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000433318||||-/165|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000467416|||||processed_transcript,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000431597||||-/62|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000488982|||||processed_transcript,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000475854|||||processed_transcript,synonymous_variant|caG/caA|Q|ENSG00000184867|ARMCX2|ENST00000330154|3/3|||503/632|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000440675||||-/104|protein_coding,synonymous_variant|caG/caA|Q|ENSG00000184867|ARMCX2|ENST00000356824|6/6|||503/632|protein_coding,downstream_gene_variant|||ENSG00000184867|ARMCX2|ENST00000479333|||||processed_transcript GT:AD:DP:GQ:PL 1:0,13:13:99:484,0 1:0,9:9:99:176,0 1:0,14:14:99:496,0 chrX 101091164 . T C 1044.87 PASS AC=2;AF=0.667;AN=3;DP=33;FS=0;GQ_MEAN=392.67;GQ_STDDEV=492.25;MLEAC=2;MLEAF=0.667;MQ=58.52;MQ0=0;NCC=0;QD=34.83;SOR=1.765;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000372803|17/19|||-/368|nonsense_mediated_decay,intron_variant|||ENSG00000126952|NXF5|ENST00000473265||||-/365|protein_coding,synonymous_variant&NMD_transcript_variant|tcA/tcG|S|ENSG00000126952|NXF5|ENST00000263032|17/19|||397/397|nonsense_mediated_decay,synonymous_variant|tcA/tcG|S|ENSG00000126952|NXF5|ENST00000361708|17/17|||397/397|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000493509|17/19|||-/168|nonsense_mediated_decay,intron_variant|||ENSG00000126952|NXF5|ENST00000537026||||-/365|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000361330|15/17|||-/305|nonsense_mediated_decay,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000332614|15/17|||-/302|nonsense_mediated_decay GT:AD:DP:GQ:PL 0:3,0:3:99:0,101 1:0,4:4:99:116,0 1:0,26:26:99:961,0 chrX 101095482 . A G 35.64 my_snp_filter AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=63;MLEAC=1;MLEAF=1;MQ=29.27;MQ0=0;NCC=2;QD=17.82;SOR=2.303;set=FilteredInAll;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000493509|10/19|||-/168|nonsense_mediated_decay,synonymous_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000361708|10/17|||229/397|protein_coding,synonymous_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000473265|9/15|||229/365|protein_coding,synonymous_variant&NMD_transcript_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000263032|10/19|||229/397|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000372803|10/19|||229/368|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000332614|8/17|||166/302|nonsense_mediated_decay,synonymous_variant&NMD_transcript_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000361330|8/17|||166/305|nonsense_mediated_decay,synonymous_variant|tcT/tcC|S|ENSG00000126952|NXF5|ENST00000537026|10/16|||229/365|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:63:63,0 .:0,0:.:.:. chrX 101096930 . T C 675.87 PASS AC=2;AF=0.667;AN=3;DP=22;FS=0;GQ_MEAN=272.33;GQ_STDDEV=193.47;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.9;SOR=1.022;set=variant2;CSQ=missense_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000537026|4/16|probably_damaging(0.937)|deleterious(0)|23/365|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000361330||||-/305|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000126952|NXF5|ENST00000332614||||-/302|nonsense_mediated_decay,missense_variant&NMD_transcript_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000372803|4/19|possibly_damaging(0.836)|deleterious(0)|23/368|nonsense_mediated_decay,missense_variant&NMD_transcript_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000263032|4/19|possibly_damaging(0.723)|deleterious(0)|23/397|nonsense_mediated_decay,missense_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000473265|3/15|probably_damaging(0.937)|deleterious(0)|23/365|protein_coding,missense_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000361708|4/17|possibly_damaging(0.723)|deleterious(0)|23/397|protein_coding,missense_variant&NMD_transcript_variant|Aag/Gag|K/E|ENSG00000126952|NXF5|ENST00000493509|4/19|possibly_damaging(0.807)|deleterious(0)|23/168|nonsense_mediated_decay GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 1:0,7:7:99:222,0 1:0,12:12:99:486,0 chrX 101137682 . A C 317.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=345;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.76;SOR=1.609;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000540921||||-/638|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000458570||||-/467|protein_coding,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000372782|7/7|||-/638|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000488347|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:345,0 .:0,0:.:.:. chrX 101137796 . G A 103.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=131;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.91;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000488347|||||processed_transcript,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000372782|7/7|||-/638|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000458570||||-/467|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000540921||||-/638|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:131,0 .:0,0:.:.:. chrX 101138282 . CT C 298.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=326;MLEAC=1;MLEAF=1;MQ=61.07;MQ0=0;NCC=2;QD=29.86;SOR=1.085;set=variant;CSQ=downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000488347|||||processed_transcript,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000458570|9/9|||-/467|protein_coding,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000372782|7/7|||-/638|protein_coding,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000540921|6/6|||-/638|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:326,0 .:0,0:.:.:. chrX 101138438 . GT G 235.87 PASS AC=1;AF=0.333;AN=3;DP=20;FS=0;GQ_MEAN=169.67;GQ_STDDEV=86.38;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=23.59;SOR=4.804;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000540921|6/6|||-/638|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000488347|||||processed_transcript,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000372782|7/7|||-/638|protein_coding,3_prime_UTR_variant|||ENSG00000166432|ZMAT1|ENST00000458570|9/9|||-/467|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript GT:AD:DP:GQ:PL 1:0,10:10:99:268,0 0:5,0:5:99:0,106 0:4,0:4:99:0,135 chrX 101138792 . T C 2135.64 PASS AC=3;AF=1;AN=3;DP=64;FS=0;GQ_MEAN=721;GQ_STDDEV=583.27;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.37;SOR=0.966;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript,missense_variant|cAg/cGg|Q/R|ENSG00000166432|ZMAT1|ENST00000540921|6/6|benign(0.001)||536/638|protein_coding,downstream_gene_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript,missense_variant|cAg/cGg|Q/R|ENSG00000166432|ZMAT1|ENST00000372782|7/7|benign(0.001)||536/638|protein_coding,missense_variant|cAg/cGg|Q/R|ENSG00000166432|ZMAT1|ENST00000458570|9/9|benign(0.001)||365/467|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000488347|10/10||||processed_transcript GT:AD:DP:GQ:PL 1:0,29:29:99:1018,0 1:0,2:2:49:49,0 1:0,33:33:99:1096,0 chrX 101139758 . C T 1075.87 PASS AC=1;AF=0.333;AN=3;DP=41;FS=0;GQ_MEAN=447.33;GQ_STDDEV=572.44;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.71;SOR=2.694;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|2/2||||processed_transcript,missense_variant|aGg/aAg|R/K|ENSG00000166432|ZMAT1|ENST00000540921|6/6|benign(0)||214/638|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000490757|3/3||||processed_transcript,missense_variant|aGg/aAg|R/K|ENSG00000166432|ZMAT1|ENST00000458570|9/9|benign(0)||43/467|protein_coding,missense_variant|aGg/aAg|R/K|ENSG00000166432|ZMAT1|ENST00000372782|7/7|benign(0)||214/638|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000488347|10/10||||processed_transcript GT:AD:DP:GQ:PL 1:0,31:31:99:1108,0 0:3,0:3:99:0,99 0:7,0:7:99:0,135 chrX 101141776 . AC A 231.64 PASS AC=2;AF=1;AN=2;DP=9;FS=0;GQ_MEAN=129.5;GQ_STDDEV=78.49;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.09;SOR=4.174;set=variant;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000494068|1/2||||processed_transcript,intron_variant|||ENSG00000166432|ZMAT1|ENST00000540921||||-/638|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000490757|||||processed_transcript,intron_variant|||ENSG00000166432|ZMAT1|ENST00000458570||||-/467|protein_coding,intron_variant|||ENSG00000166432|ZMAT1|ENST00000372782||||-/638|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000166432|ZMAT1|ENST00000488347|||||processed_transcript GT:AD:DP:GQ:PL 1:0,5:5:99:185,0 .:0,0:.:.:. 1:0,2:2:74:74,0 chrX 101382005 . G C 850.63 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;GQ_MEAN=495;GQ_STDDEV=545.89;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=31.22;SOR=0.963;set=variant2;CSQ=downstream_gene_variant|||ENSG00000184905|TCEAL2|ENST00000476749|||||processed_transcript,missense_variant|gGa/gCa|G/A|ENSG00000184905|TCEAL2|ENST00000372780|3/3|probably_damaging(0.939)|tolerated(0.24)|68/227|protein_coding,missense_variant|gGa/gCa|G/A|ENSG00000184905|TCEAL2|ENST00000329035|3/3|probably_damaging(0.939)|tolerated(0.24)|68/227|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 .:0,0:.:.:. 1:0,23:23:99:881,0 chrX 101382411 . T C 1103.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.16;ClippingRankSum=0.385;DP=35;FS=0;GQ_MEAN=415;GQ_STDDEV=287.31;MLEAC=2;MLEAF=0.667;MQ=58.62;MQ0=0;MQRankSum=-0.964;NCC=0;QD=34.5;ReadPosRankSum=-1.735;SOR=0.379;set=variant2;CSQ=downstream_gene_variant|||ENSG00000184905|TCEAL2|ENST00000476749|||||processed_transcript,synonymous_variant|taT/taC|Y|ENSG00000184905|TCEAL2|ENST00000329035|3/3|||203/227|protein_coding,synonymous_variant|taT/taC|Y|ENSG00000184905|TCEAL2|ENST00000372780|3/3|||203/227|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 1:0,14:14:99:457,0 1:1,17:18:99:679,0 chrX 101382417 . G A 763.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-0.306;ClippingRankSum=1.53;DP=25;FS=0;GQ_MEAN=301.67;GQ_STDDEV=320.81;MLEAC=2;MLEAF=0.667;MQ=57.86;MQ0=0;MQRankSum=-1.123;NCC=0;QD=34.72;ReadPosRankSum=0.102;SOR=0.365;set=variant2;CSQ=synonymous_variant|agG/agA|R|ENSG00000184905|TCEAL2|ENST00000329035|3/3|||205/227|protein_coding,synonymous_variant|agG/agA|R|ENSG00000184905|TCEAL2|ENST00000372780|3/3|||205/227|protein_coding,downstream_gene_variant|||ENSG00000184905|TCEAL2|ENST00000476749|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 1:0,5:5:99:124,0 1:1,16:17:99:672,0 chrX 101395780 . T TG 293.64 PASS AC=3;AF=1;AN=3;DP=11;FS=0;GQ_MEAN=107;GQ_STDDEV=43.31;MLEAC=3;MLEAF=1;MQ=41.73;MQ0=0;NCC=0;QD=29.36;SOR=3.258;set=variant;CSQ=frameshift_variant|caa/cCaa|Q/PX|ENSG00000204071|TCEAL6|ENST00000372773|3/3|||175/183|protein_coding,frameshift_variant|caa/cCaa|Q/PX|ENSG00000204071|TCEAL6|ENST00000372774|3/3|||175/183|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:101,0 1:0,5:5:99:153,0 1:0,2:2:67:67,0 chrX 101823022 . C G 102.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=130;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.66;SOR=1.609;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000196970|NXF4|ENST00000416098|||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000196970|NXF4|ENST00000360035|15/17||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:130,0 .:0,0:.:.:. chrX 101823177 . G A 469.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.47;ClippingRankSum=-0.261;DP=25;FS=0;GQ_MEAN=268;GQ_STDDEV=328.1;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-0.052;NCC=1;QD=19.57;ReadPosRankSum=-1.306;SOR=0.874;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000196970|NXF4|ENST00000416098|||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000196970|NXF4|ENST00000360035|15/17||||processed_transcript GT:AD:DP:GQ:PL 0:1,0:1:36:0,36 1:2,22:24:99:500,0 .:0,0:.:.:. chrX 101969605 . T C 499.87 PASS AC=2;AF=0.667;AN=3;DP=19;FS=0;GQ_MEAN=189.67;GQ_STDDEV=260.97;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.4;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000271147|RP4-769N13.6|ENST00000602463|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000158301|GPRASP2|ENST00000483720|5/5||||processed_transcript,downstream_gene_variant|||ENSG00000271147|RP4-769N13.6|ENST00000602366|||||processed_transcript,5_prime_UTR_variant|||ENSG00000158301|GPRASP2|ENST00000535209|4/4|||-/838|protein_coding,5_prime_UTR_variant|||ENSG00000158301|GPRASP2|ENST00000332262|4/4|||-/838|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000158301|GPRASP2|ENST00000486814|5/5||||processed_transcript,5_prime_UTR_variant|||ENSG00000158301|GPRASP2|ENST00000543253|5/5|||-/838|protein_coding,downstream_gene_variant|||ENSG00000271147|RP4-769N13.6|ENST00000486740|||||processed_transcript GT:AD:DP:GQ:PL 0:1,0:1:37:0,37 1:0,17:17:99:491,0 1:0,1:1:41:41,0 chrX 102585902 . G C 581.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=609;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.44;SOR=1.329;set=variant2;CSQ=splice_region_variant&intron_variant|||ENSG00000182916|TCEAL7|ENST00000372666||||-/100|protein_coding,5_prime_UTR_variant|||ENSG00000182916|TCEAL7|ENST00000332431|2/3|||-/100|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,22:22:99:609,0 .:0,0:.:.:. chrX 102755551 . T A 2801.87 PASS AC=2;AF=0.667;AN=3;DP=92;FS=0;GQ_MEAN=983;GQ_STDDEV=816.6;MLEAC=2;MLEAF=0.667;MQ=59.2;MQ0=0;NCC=0;QD=31.48;SOR=1.022;set=variant2;CSQ=downstream_gene_variant|||ENSG00000234405|LL0XNC01-250H12.3|ENST00000445990|||||antisense,missense_variant|cAt/cTt|H/L|ENSG00000172476|RAB40A|ENST00000304236|3/3|benign(0.04)|tolerated(0.54)|45/277|protein_coding,missense_variant|cAt/cTt|H/L|ENSG00000172476|RAB40A|ENST00000372633|1/1|benign(0.04)|tolerated(0.54)|45/277|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,115 1:0,41:41:99:1098,0 1:0,48:48:99:1736,0 chrX 102840421 . G T 331.87 PASS AC=2;AF=0.667;AN=3;DP=13;FS=0;GQ_MEAN=148.33;GQ_STDDEV=101.44;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.17;SOR=3.442;set=variant2;CSQ=upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000494801||||-/215|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000459722||||-/91|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000472745||||-/215|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000481555|||||retained_intron,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000415568||||-/215|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000472484||||-/215|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000425011||||-/58|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000490644||||-/76|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000434216||||-/50|protein_coding,upstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000469586||||-/129|protein_coding,intron_variant|||ENSG00000133142|TCEAL4|ENST00000372629||||-/358|protein_coding,5_prime_UTR_variant|||ENSG00000133142|TCEAL4|ENST00000468024|1/3|||-/215|protein_coding GT:AD:DP:GQ:PL 0:2,0:2:81:0,81 1:0,4:4:99:99,0 1:0,7:7:99:265,0 chrX 102842041 . T C 1326.87 PASS AC=2;AF=0.667;AN=3;DP=45;FS=0;GQ_MEAN=492.67;GQ_STDDEV=445.72;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.59;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000481555|||||retained_intron,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000472745|3/3|||146/215|protein_coding,downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000459722||||-/91|protein_coding,downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000425011||||-/58|protein_coding,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000472484|3/3|||146/215|protein_coding,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000415568|2/2|||146/215|protein_coding,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000494801|3/3|||146/215|protein_coding,downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000434216||||-/50|protein_coding,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000372629|5/5|||289/358|protein_coding,synonymous_variant|caT/caC|H|ENSG00000133142|TCEAL4|ENST00000468024|3/3|||146/215|protein_coding,downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000469586||||-/129|protein_coding,downstream_gene_variant|||ENSG00000133142|TCEAL4|ENST00000490644||||-/76|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,119 1:0,13:13:99:373,0 1:0,29:29:99:986,0 chrX 102930960 . A G 252.87 PASS AC=1;AF=0.333;AN=3;DP=12;FS=0;GQ_MEAN=141.67;GQ_STDDEV=128.7;MLEAC=1;MLEAF=0.333;MQ=59.51;MQ0=0;NCC=0;QD=31.61;SOR=2.833;set=variant2;CSQ=downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000418819||||-/177|protein_coding,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000422355||||-/67|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000423833|3/3|||-/288|protein_coding,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000498064|||||processed_transcript,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000492116|||||processed_transcript,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000442614||||-/158|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000441076|4/4|||-/288|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000422154|5/5|||-/288|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000451301|3/3|||-/288|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000433176|5/5|||-/288|protein_coding,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000434230||||-/177|protein_coding,3_prime_UTR_variant|||ENSG00000123562|MORF4L2|ENST00000360458|4/4|||-/288|protein_coding,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000474653|||||processed_transcript,downstream_gene_variant|||ENSG00000123562|MORF4L2|ENST00000467755|||||processed_transcript GT:AD:DP:GQ:PL 1:0,8:8:99:285,0 0:1,0:1:36:0,36 0:3,0:3:99:0,104 chrX 102978806 . G C 2729.64 PASS AC=3;AF=1;AN=3;DP=87;FS=0;GQ_MEAN=919;GQ_STDDEV=167.39;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.38;SOR=1.664;set=variant2;CSQ=upstream_gene_variant|||ENSG00000188828|GLRA4|ENST00000469567|||||processed_transcript,synonymous_variant|acC/acG|T|ENSG00000188828|GLRA4|ENST00000372617|5/9|||185/417|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000188828|GLRA4|ENST00000480725|5/7||||retained_intron,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000188828|GLRA4|ENST00000436213|5/8|||-/44|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,25:25:99:948,0 1:0,42:42:99:1070,0 1:0,20:20:99:739,0 chrX 102979486 . T C 3485.64 PASS AC=3;AF=1;AN=3;DP=125;FS=0;GQ_MEAN=1171;GQ_STDDEV=244.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.34;SOR=1.004;set=variant2;CSQ=upstream_gene_variant|||ENSG00000188828|GLRA4|ENST00000469567|||||processed_transcript,missense_variant|Atc/Gtc|I/V|ENSG00000188828|GLRA4|ENST00000372617|3/9|benign(0.002)|tolerated(0.4)|85/417|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000188828|GLRA4|ENST00000480725|3/7||||retained_intron,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000188828|GLRA4|ENST00000436213|4/8|||-/44|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,38:38:99:1250,0 1:0,56:56:99:1366,0 1:0,29:29:99:897,0 chrX 103046417 . C T 81.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=109;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.41;SOR=3.258;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000303958|7/7|||-/277|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000476160|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000434483||||-/122|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000443502||||-/111|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000466486|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000494475|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000478642|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000485688|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000433491||||-/100|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000479569|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000422393||||-/127|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000455268||||-/136|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000461231|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000494119|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000465975|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000485931|||||processed_transcript,3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000418604|8/8|||-/277|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000429977||||-/136|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000464776|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000495678|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000496836|||||retained_intron,3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000361621|7/7|||-/242|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:109,0 .:0,0:.:.:. chrX 103046526 . TG T 462.64 PASS AC=2;AF=1;AN=2;DP=16;FS=0;GQ_MEAN=245;GQ_STDDEV=254.56;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=30.84;SOR=1.112;set=variant;CSQ=downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000496836|||||retained_intron,3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000418604|8/8|||-/277|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000429977||||-/136|protein_coding,3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000361621|7/7|||-/242|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000479569|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000466486|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000494475|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000476160|||||processed_transcript,3_prime_UTR_variant|||ENSG00000123560|PLP1|ENST00000303958|7/7|||-/277|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000443502||||-/111|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000434483||||-/122|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000485688|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000478642|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000494119|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000465975|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000485931|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000422393||||-/127|protein_coding,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000461231|||||processed_transcript,downstream_gene_variant|||ENSG00000123560|PLP1|ENST00000455268||||-/136|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:425,0 1:0,2:2:65:65,0 chrX 103267865 . C T 1894.87 PASS AC=2;AF=0.667;AN=3;DP=78;FS=0;GQ_MEAN=679.33;GQ_STDDEV=682.28;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=25.26;SOR=0.832;set=variant2;CSQ=upstream_gene_variant|||ENSG00000101812|H2BFM|ENST00000243297||||-/257|protein_coding,missense_variant|cGc/cAc|R/H|ENSG00000123569|H2BFWT|ENST00000217926|1/3|benign(0.005)||123/175|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,111 1:0,61:61:99:1436,0 1:0,14:14:99:491,0 chrX 103268241 . G A 820.63 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;GQ_MEAN=481;GQ_STDDEV=523.26;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=31.56;SOR=1.697;set=variant2;CSQ=upstream_gene_variant|||ENSG00000101812|H2BFM|ENST00000243297||||-/257|protein_coding,5_prime_UTR_variant|||ENSG00000123569|H2BFWT|ENST00000217926|1/3|||-/175|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,111 .:0,0:.:.:. 1:0,26:26:99:851,0 chrX 103294760 . C T 837.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=0.579;ClippingRankSum=-1.273;DP=32;FS=3.163;GQ_MEAN=328.33;GQ_STDDEV=189.47;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-0.347;NCC=0;QD=28.89;ReadPosRankSum=0.579;SOR=0.442;set=variant2;CSQ=stop_gained|Cag/Tag|Q/*|ENSG00000101812|H2BFM|ENST00000243297|3/5|||176/257|protein_coding,stop_gained|Cag/Tag|Q/*|ENSG00000101812|H2BFM|ENST00000355016|1/3|||73/154|protein_coding,upstream_gene_variant|||ENSG00000101812|H2BFM|ENST00000417637||||-/52|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,115 1:1,14:15:99:393,0 1:0,14:14:99:477,0 chrX 103348230 . C T 638.64 PASS AC=1;AF=1;AN=1;DP=30;FS=0;GQ_MEAN=666;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.81;SOR=0.836;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000176274|SLC25A53|ENST00000357421|2/2|||-/307|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,28:28:99:666,0 .:0,0:.:.:. chrX 103348397 . G GC 1532.64 PASS AC=1;AF=1;AN=1;DP=42;FS=0;GQ_MEAN=1560;MLEAC=1;MLEAF=1;MQ=59.1;MQ0=0;NCC=2;QD=32.65;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000176274|SLC25A53|ENST00000357421|2/2|||-/307|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,42:42:99:1560,0 .:0,0:.:.:. chrX 104464276 . CA C 7145.64 PASS AC=3;AF=1;AN=3;DP=155;FS=0;GQ_MEAN=2391;GQ_STDDEV=379.08;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.44;SOR=0.859;set=variant;CSQ=intron_variant|||ENSG00000189108|IL1RAPL2|ENST00000372582||||-/686|protein_coding,intron_variant|||ENSG00000189108|IL1RAPL2|ENST00000344799||||-/686|protein_coding,splice_acceptor_variant&frameshift_variant|gtT/gt|V/X|ENSG00000133149|TEX13A|ENST00000413579|4/5|||200/409|protein_coding,frameshift_variant|Tgg/gg|W/X|ENSG00000133149|TEX13A|ENST00000372575|3/3|||201/352|protein_coding,frameshift_variant|Tgg/gg|W/X|ENSG00000133149|TEX13A|ENST00000372578|3/3|||201/352|protein_coding GT:AD:DP:GQ:PL 1:0,53:53:99:2505,0 1:0,41:41:99:1968,0 1:0,60:60:99:2700,0 chrX 104464281 . TC T 7310.64 PASS AC=3;AF=1;AN=3;DP=167;FS=0;GQ_MEAN=2446;GQ_STDDEV=354.2;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.95;SOR=0.859;set=variant;CSQ=intron_variant|||ENSG00000189108|IL1RAPL2|ENST00000372582||||-/686|protein_coding,splice_donor_variant&frameshift_variant|Gat/at|D/X|ENSG00000133149|TEX13A|ENST00000413579|4/5|||199/409|protein_coding,intron_variant|||ENSG00000189108|IL1RAPL2|ENST00000344799||||-/686|protein_coding,frameshift_variant|gGa/ga|G/X|ENSG00000133149|TEX13A|ENST00000372575|3/3|||199/352|protein_coding,frameshift_variant|gGa/ga|G/X|ENSG00000133149|TEX13A|ENST00000372578|3/3|||199/352|protein_coding GT:AD:DP:GQ:PL 1:0,56:56:99:2505,0 1:0,49:49:99:2066,0 1:0,62:62:99:2767,0 chrX 105152282 . G A 403.87 PASS AC=2;AF=0.667;AN=3;DP=18;FS=0;GQ_MEAN=181;GQ_STDDEV=69.16;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.92;SOR=0.818;set=variant2;CSQ=missense_variant|Gtg/Atg|V/M|ENSG00000123572|NRK|ENST00000243300|12/29|benign(0.001)|tolerated(1)|358/1582|protein_coding,missense_variant|Gtg/Atg|V/M|ENSG00000123572|NRK|ENST00000428173|12/29|benign(0.001)||359/1583|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,107 1:0,10:10:99:244,0 1:0,5:5:99:192,0 chrX 105153001 . A G 3014.64 PASS AC=3;AF=1;AN=3;DP=89;FS=0;GQ_MEAN=1014;GQ_STDDEV=548.25;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.87;SOR=0.715;set=variant2;CSQ=synonymous_variant|aaA/aaG|K|ENSG00000123572|NRK|ENST00000428173|13/29|||457/1583|protein_coding,synonymous_variant|aaA/aaG|K|ENSG00000123572|NRK|ENST00000243300|13/29|||456/1582|protein_coding GT:AD:DP:GQ:PL 1:0,42:42:99:1431,0 1:0,15:15:99:393,0 1:0,32:32:99:1218,0 chrX 105200690 . G T 155.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=183;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.23;SOR=2.584;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000123572|NRK|ENST00000428173|29/29|||-/1583|protein_coding,3_prime_UTR_variant|||ENSG00000123572|NRK|ENST00000243300|29/29|||-/1582|protein_coding,downstream_gene_variant|||ENSG00000123572|NRK|ENST00000540278||||-/163|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:183,0 .:0,0:.:.:. chrX 105201635 . A G 169.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=197;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.21;SOR=0.693;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000123572|NRK|ENST00000428173|29/29|||-/1583|protein_coding,3_prime_UTR_variant|||ENSG00000123572|NRK|ENST00000243300|29/29|||-/1582|protein_coding,downstream_gene_variant|||ENSG00000123572|NRK|ENST00000540278||||-/163|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:197,0 .:0,0:.:.:. chrX 105278361 . C A 602.87 PASS AC=1;AF=0.333;AN=3;DP=24;FS=0;GQ_MEAN=264;GQ_STDDEV=323.04;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=31.73;SOR=1.292;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000123561|SERPINA7|ENST00000487487|2/3||||processed_transcript,missense_variant|ttG/ttT|L/F|ENSG00000123561|SERPINA7|ENST00000372563|4/5|possibly_damaging(0.804)|deleterious(0)|303/415|protein_coding,missense_variant|ttG/ttT|L/F|ENSG00000123561|SERPINA7|ENST00000327674|3/4|possibly_damaging(0.804)|deleterious(0)|303/415|protein_coding GT:AD:DP:GQ:PL 1:0,19:19:99:635,0 0:2,0:2:45:0,45 0:3,0:3:99:0,112 chrX 105449971 . G A 1037.87 PASS AC=1;AF=0.333;AN=3;DP=34;FS=0;GQ_MEAN=406.33;GQ_STDDEV=575.79;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.6;SOR=0.693;set=variant2;CSQ=synonymous_variant|gtG/gtA|V|ENSG00000157502|MUM1L1|ENST00000337685|5/5|||182/696|protein_coding,synonymous_variant|gtG/gtA|V|ENSG00000157502|MUM1L1|ENST00000372552|3/3|||182/696|protein_coding,synonymous_variant|gtG/gtA|V|ENSG00000157502|MUM1L1|ENST00000357175|4/4|||182/696|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1070,0 0:1,0:1:40:0,40 0:3,0:3:99:0,109 chrX 106118819 . G T 84.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=112;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.16;SOR=3.258;set=variant2;CSQ=downstream_gene_variant|||ENSG00000133138|TBC1D8B|ENST00000276175||||-/1114|protein_coding,3_prime_UTR_variant|||ENSG00000133138|TBC1D8B|ENST00000357242|21/21|||-/1120|protein_coding,intron_variant|||ENSG00000133131|MORC4|ENST00000604604||||-/38|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:112,0 .:0,0:.:.:. chrX 106200202 . G A 796.87 PASS AC=1;AF=0.333;AN=3;DP=33;FS=0;GQ_MEAN=366.33;GQ_STDDEV=400.68;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.2;SOR=2.124;set=variant2;CSQ=missense_variant|aCt/aTt|T/I|ENSG00000133131|MORC4|ENST00000355610|12/17|benign(0)|tolerated(0.22)|473/937|protein_coding,missense_variant|aCt/aTt|T/I|ENSG00000133131|MORC4|ENST00000535534|11/16|benign(0.001)||221/648|protein_coding,missense_variant|aCt/aTt|T/I|ENSG00000133131|MORC4|ENST00000255495|12/17|benign(0.001)|tolerated(0.24)|473/900|protein_coding,intron_variant|||ENSG00000133131|MORC4|ENST00000604604||||-/38|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:829,0 0:5,0:5:99:0,135 0:4,0:4:99:0,135 chrX 107084075 . A C 1769.87 PASS AC=2;AF=0.667;AN=3;DP=53;FS=0;GQ_MEAN=660.67;GQ_STDDEV=916.93;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=35.29;SOR=0.693;set=variant2;CSQ=synonymous_variant|tcA/tcC|S|ENSG00000080561|MID2|ENST00000262843|2/10|||60/735|protein_coding,synonymous_variant|tcA/tcC|S|ENSG00000080561|MID2|ENST00000443968|2/10|||60/705|protein_coding,synonymous_variant|tcA/tcC|S|ENSG00000080561|MID2|ENST00000451923|2/2|||40/218|protein_coding GT:AD:DP:GQ:PL 0:5,0:5:99:0,180 1:0,3:3:84:84,0 1:0,45:45:99:1718,0 chrX 107172944 . C G 39.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.727;ClippingRankSum=-0.727;DP=4;FS=6.021;GQ_MEAN=67;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.727;NCC=2;QD=9.91;ReadPosRankSum=0.727;SOR=2.788;set=variant2;CSQ=downstream_gene_variant|||ENSG00000080561|MID2|ENST00000443968||||-/705|protein_coding,downstream_gene_variant|||ENSG00000080561|MID2|ENST00000262843||||-/735|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000236064|RP6-191P20.4|ENST00000430140|||||antisense,downstream_gene_variant|||ENSG00000080561|MID2|ENST00000474517|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,3:4:67:67,0 .:0,0:.:.:. chrX 107174169 . T A 55.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=83;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=11.13;SOR=1.981;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000236064|RP6-191P20.4|ENST00000430140|||||antisense,downstream_gene_variant|||ENSG00000080561|MID2|ENST00000262843||||-/735|protein_coding,downstream_gene_variant|||ENSG00000080561|MID2|ENST00000443968||||-/705|protein_coding,downstream_gene_variant|||ENSG00000080561|MID2|ENST00000474517|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:83:83,0 .:0,0:.:.:. chrX 107417730 . G A 897.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.52;ClippingRankSum=0.434;DP=36;FS=3.424;GQ_MEAN=349.33;GQ_STDDEV=204.1;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=0.434;NCC=0;QD=27.21;ReadPosRankSum=0.434;SOR=0.618;set=variant2;CSQ=synonymous_variant|ggC/ggT|G|ENSG00000197565|COL4A6|ENST00000334504|31/45|||1026/1690|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000197565|COL4A6|ENST00000538570|31/43|||1026/1633|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000197565|COL4A6|ENST00000394872|31/45|||1027/1691|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000197565|COL4A6|ENST00000545689|31/44|||1026/1666|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000197565|COL4A6|ENST00000372216|31/45|||1027/1691|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,118 1:0,17:17:99:426,0 1:1,15:16:99:504,0 chrX 107418906 . A G 815.64 PASS AC=3;AF=1;AN=3;DP=26;FS=0;GQ_MEAN=281;GQ_STDDEV=157.65;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.37;SOR=3.098;set=variant2;CSQ=synonymous_variant|cgT/cgC|R|ENSG00000197565|COL4A6|ENST00000334504|29/45|||936/1690|protein_coding,synonymous_variant|cgT/cgC|R|ENSG00000197565|COL4A6|ENST00000538570|29/43|||936/1633|protein_coding,synonymous_variant|cgT/cgC|R|ENSG00000197565|COL4A6|ENST00000545689|29/44|||936/1666|protein_coding,synonymous_variant|cgT/cgC|R|ENSG00000197565|COL4A6|ENST00000394872|29/45|||937/1691|protein_coding,synonymous_variant|cgT/cgC|R|ENSG00000197565|COL4A6|ENST00000372216|29/45|||937/1691|protein_coding GT:AD:DP:GQ:PL 1:0,11:11:99:403,0 1:0,12:12:99:337,0 1:0,3:3:99:103,0 chrX 107433688 . A G 512.87 PASS AC=1;AF=0.333;AN=3;DP=22;FS=0;GQ_MEAN=254;GQ_STDDEV=252.05;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.19;SOR=2.448;set=variant2;CSQ=missense_variant|Tca/Cca|S/P|ENSG00000197565|COL4A6|ENST00000372216|20/45|benign(0)||455/1691|protein_coding,missense_variant|Tca/Cca|S/P|ENSG00000197565|COL4A6|ENST00000538570|20/43|unknown(0)|tolerated(1)|454/1633|protein_coding,missense_variant|Tca/Cca|S/P|ENSG00000197565|COL4A6|ENST00000394872|20/45|benign(0)||455/1691|protein_coding,missense_variant|Tca/Cca|S/P|ENSG00000197565|COL4A6|ENST00000545689|20/44|unknown(0)||454/1666|protein_coding,missense_variant|Tca/Cca|S/P|ENSG00000197565|COL4A6|ENST00000334504|20/45|benign(0)||454/1690|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:545,0 0:4,0:4:99:0,113 0:3,0:3:99:0,104 chrX 108708516 . C T 3394.64 PASS AC=3;AF=1;AN=3;DP=96;FS=0;GQ_MEAN=1140.67;GQ_STDDEV=896.06;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.25;SOR=0.735;set=variant2;CSQ=missense_variant|cGg/cAg|R/Q|ENSG00000101890|GUCY2F|ENST00000218006|3/20|benign(0)|tolerated(0.62)|296/1108|protein_coding GT:AD:DP:GQ:PL 1:0,45:45:99:1654,0 1:0,3:3:99:106,0 1:0,48:48:99:1662,0 chrX 108708552 . A G 1480.87 PASS AC=1;AF=0.333;AN=3;DP=57;FS=0;GQ_MEAN=592.67;GQ_STDDEV=797.04;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.66;SOR=0.784;set=variant2;CSQ=missense_variant|cTg/cCg|L/P|ENSG00000101890|GUCY2F|ENST00000218006|3/20|possibly_damaging(0.886)|deleterious(0)|284/1108|protein_coding GT:AD:DP:GQ:PL 1:0,44:44:99:1513,0 0:5,0:5:99:0,130 0:8,0:8:99:0,135 chrX 108786876 . T C 1224.64 PASS AC=1;AF=1;AN=1;DP=49;FS=0;GQ_MEAN=1252;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.51;SOR=0.963;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101888|NXT2|ENST00000372103||||-/114|protein_coding,3_prime_UTR_variant|||ENSG00000101888|NXT2|ENST00000372106|4/4|||-/142|protein_coding,downstream_gene_variant|||ENSG00000101888|NXT2|ENST00000372107||||-/114|protein_coding,3_prime_UTR_variant|||ENSG00000101888|NXT2|ENST00000218004|5/5|||-/197|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,48:48:99:1252,0 .:0,0:.:.:. chrX 108868153 . G A 828.63 PASS AC=1;AF=0.5;AN=2;DP=30;FS=0;GQ_MEAN=494.5;GQ_STDDEV=515.48;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=34.58;SOR=1.179;set=variant2;CSQ=missense_variant|Cct/Tct|P/S|ENSG00000176076|KCNE1L|ENST00000372101|1/1|benign(0.001)|tolerated_low_confidence(0.58)|33/142|protein_coding,downstream_gene_variant|||ENSG00000068366|ACSL4|ENST00000505075|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000068366|ACSL4|ENST00000439581|||||processed_transcript GT:AD:DP:GQ:PL 0:4,0:4:99:0,130 .:0,0:.:.:. 1:0,23:23:99:859,0 chrX 109439634 . T G 281.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=309;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.16;SOR=3.258;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101935|AMMECR1|ENST00000372057||||-/210|protein_coding,3_prime_UTR_variant|||ENSG00000101935|AMMECR1|ENST00000262844|6/6|||-/333|protein_coding,3_prime_UTR_variant|||ENSG00000101935|AMMECR1|ENST00000372059|5/5|||-/296|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:309,0 .:0,0:.:.:. chrX 110039256 . C T 115.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=143;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=16.52;SOR=0.941;set=variant2;CSQ=upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000218054||||-/456|protein_coding,upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000444321||||-/457|protein_coding,5_prime_UTR_variant|||ENSG00000101938|CHRDL1|ENST00000434224|1/10|||-/377|protein_coding,upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000394797||||-/456|protein_coding,upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000372042||||-/458|protein_coding,upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000482160||||-/378|protein_coding,upstream_gene_variant|||ENSG00000101938|CHRDL1|ENST00000372045||||-/450|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:143,0 .:0,0:.:.:. chrX 110489520 . A G 157.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=185;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.52;SOR=0.941;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000077274|CAPN6|ENST00000324068|13/13|||-/641|protein_coding,downstream_gene_variant|||ENSG00000077274|CAPN6|ENST00000541758||||-/386|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:185,0 .:0,0:.:.:. chrX 111090573 . G A 1335.87 PASS AC=1;AF=0.333;AN=3;DP=47;FS=0;GQ_MEAN=520.67;GQ_STDDEV=733.97;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=32.58;SOR=0.741;set=variant2;CSQ=missense_variant|tCg/tTg|S/L|ENSG00000072315|TRPC5|ENST00000262839|6/11|probably_damaging(0.914)|deleterious(0.04)|490/973|protein_coding GT:AD:DP:GQ:PL 1:0,41:41:99:1368,0 0:3,0:3:82:0,82 0:3,0:3:99:0,112 chrX 112058599 . G C 728.87 PASS AC=2;AF=0.667;AN=3;DP=24;FS=0;GQ_MEAN=290.33;GQ_STDDEV=271.84;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.71;SOR=3.16;set=variant2;CSQ=missense_variant|gCa/gGa|A/G|ENSG00000126016|AMOT|ENST00000304758|3/12|unknown(0)||51/675|protein_coding,missense_variant|gCa/gGa|A/G|ENSG00000126016|AMOT|ENST00000371959|2/11|unknown(0)||460/1084|protein_coding,missense_variant|gCa/gGa|A/G|ENSG00000126016|AMOT|ENST00000371958|2/9|benign(0.006)|tolerated(0.56)|228/597|protein_coding,missense_variant|gCa/gGa|A/G|ENSG00000126016|AMOT|ENST00000371962|2/11|unknown(0)||228/852|protein_coding,missense_variant|gCa/gGa|A/G|ENSG00000126016|AMOT|ENST00000524145|3/12|unknown(0)||460/1084|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,110 1:0,4:4:99:158,0 1:0,17:17:99:603,0 chrX 114142704 . T G 128.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=156;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=32.16;SOR=3.258;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147246|HTR2C|ENST00000276198|6/6|||-/458|protein_coding,3_prime_UTR_variant|||ENSG00000147246|HTR2C|ENST00000371950|6/6|||-/248|protein_coding,3_prime_UTR_variant|||ENSG00000147246|HTR2C|ENST00000371951|7/7|||-/458|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:156,0 .:0,0:.:.:. chrX 114425181 . A AGAGGCCGCTCGCCCAACGCCCACAGCG 6341.65 PASS AC=2;AF=0.667;AN=3;DP=142;FS=0;GQ_MEAN=2124;GQ_STDDEV=1849.21;MLEAC=3;MLEAF=1;MQ=66.25;MQ0=0;NCC=0;QD=5.73;SOR=1.285;set=variant;CSQ=inframe_insertion|aga/aGAGGCCGCTCGCCCAACGCCCACAGCGga|R/RGRSPNAHSG|ENSG00000175718|RBMXL3|ENST00000424776|1/1|||393/1067|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding GT:AD:DP:GQ:PL 1:0,2,52:54:99:2971,0 0:4,0:4:3:0,3 1:0,0,69:69:99:3398,0 chrX 114425400 . G A 2667.87 PASS AC=2;AF=0.667;AN=3;DP=146;FS=0;GQ_MEAN=979.67;GQ_STDDEV=854.13;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.32;SOR=0.76;set=variant2;CSQ=intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,missense_variant|Gga/Aga|G/R|ENSG00000175718|RBMXL3|ENST00000424776|1/1|benign(0.003)|tolerated_low_confidence(0.59)|466/1067|protein_coding GT:AD:DP:GQ:PL 0:55,0:55:99:0,239 1:0,34:34:99:786,0 1:0,57:57:99:1914,0 chrX 114426171 . C T 6383.64 PASS AC=3;AF=1;AN=3;DP=185;FS=0;GQ_MEAN=2137;GQ_STDDEV=1691.91;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.69;SOR=1.042;set=variant2;CSQ=missense_variant|Cgc/Tgc|R/C|ENSG00000175718|RBMXL3|ENST00000424776|1/1|benign(0)|tolerated_low_confidence(0.24)|723/1067|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding GT:AD:DP:GQ:PL 1:0,91:91:99:3157,0 1:0,9:9:99:184,0 1:0,84:84:99:3070,0 chrX 114426765 . C T 2575.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=0.112;ClippingRankSum=0.832;DP=126;FS=3.813;GQ_MEAN=1381.33;GQ_STDDEV=1227.5;MLEAC=1;MLEAF=0.333;MQ=59.86;MQ0=0;MQRankSum=-1.012;NCC=0;QD=33.45;ReadPosRankSum=1.46;SOR=0.84;set=variant2;CSQ=intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,missense_variant|Ccc/Tcc|P/S|ENSG00000175718|RBMXL3|ENST00000424776|1/1|possibly_damaging(0.641)|tolerated_low_confidence(0.19)|921/1067|protein_coding GT:AD:DP:GQ:PL 1:1,76:77:99:2608,0 0:6,0:6:99:0,153 0:43,0:43:99:0,1383 chrX 114426917 . C T 3063.87 PASS AC=2;AF=0.667;AN=3;DP=122;FS=0;GQ_MEAN=1347;GQ_STDDEV=1381.58;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.67;SOR=0.76;set=variant2;CSQ=intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,synonymous_variant|taC/taT|Y|ENSG00000175718|RBMXL3|ENST00000424776|1/1|||971/1067|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding GT:AD:DP:GQ:PL 0:29,0:29:99:0,945 1:0,9:9:99:211,0 1:0,82:82:99:2885,0 chrX 114427149 . A G 1002.87 PASS AC=1;AF=0.333;AN=3;DP=38;FS=0;GQ_MEAN=424;GQ_STDDEV=529.17;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.43;SOR=1.329;set=variant2;CSQ=intron_variant|||ENSG00000130224|LRCH2|ENST00000538422||||-/748|protein_coding,missense_variant|Agg/Ggg|R/G|ENSG00000175718|RBMXL3|ENST00000424776|1/1|unknown(0)|deleterious_low_confidence(0.01)|1049/1067|protein_coding,intron_variant|||ENSG00000130224|LRCH2|ENST00000317135||||-/765|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1035,0 0:5,0:5:99:0,124 0:3,0:3:99:0,113 chrX 114541027 . A G 744.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=1.89;ClippingRankSum=-0.733;DP=32;FS=2.634;GQ_MEAN=316.33;GQ_STDDEV=399.35;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;MQRankSum=1.5;NCC=0;QD=27.59;ReadPosRankSum=-0.193;SOR=1.781;set=variant2;CSQ=synonymous_variant|caA/caG|Q|ENSG00000102021|LUZP4|ENST00000451986|3/3|||118/231|protein_coding,3_prime_UTR_variant|||ENSG00000102021|LUZP4|ENST00000371921|3/3|||-/78|protein_coding,synonymous_variant|caA/caG|Q|ENSG00000102021|LUZP4|ENST00000371920|4/4|||200/313|protein_coding GT:AD:DP:GQ:PL 1:3,24:27:99:777,0 0:2,0:2:68:0,68 0:3,0:3:99:0,104 chrX 114795541 . C G 1075.63 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;GQ_MEAN=570;GQ_STDDEV=758.02;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=25.61;SOR=0.892;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000271826|RP1-93I3.1|ENST00000607680|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000271826|RP1-93I3.1|ENST00000606397|||||antisense,upstream_gene_variant|||ENSG00000102024|PLS3|ENST00000289290||||-/594|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102024|PLS3|ENST00000489283|1/6|||-/42|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000102024|PLS3|ENST00000355899|1/16|||-/630|protein_coding,upstream_gene_variant|||ENSG00000102024|PLS3|ENST00000537301||||-/617|protein_coding GT:AD:DP:GQ:PL 0:1,0:1:34:0,34 1:0,42:42:99:1106,0 .:0,0:.:.:. chrX 115590299 . C G 734.64 PASS AC=3;AF=1;AN=3;DP=22;FS=0;GQ_MEAN=254;GQ_STDDEV=48.28;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.39;SOR=3.258;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204019|CT83|ENST00000371894||||-/113|protein_coding,3_prime_UTR_variant|||ENSG00000087916|SLC6A14|ENST00000371900|14/14|||-/642|protein_coding,downstream_gene_variant|||ENSG00000087916|SLC6A14|ENST00000463626|||||processed_transcript GT:AD:DP:GQ:PL 1:0,7:7:99:269,0 1:0,10:10:99:293,0 1:0,5:5:99:200,0 chrX 115590829 . C T 296.64 PASS AC=1;AF=1;AN=1;DP=17;FS=0;GQ_MEAN=324;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=18.54;SOR=1.609;set=variant2;CSQ=downstream_gene_variant|||ENSG00000204019|CT83|ENST00000371894||||-/113|protein_coding,3_prime_UTR_variant|||ENSG00000087916|SLC6A14|ENST00000371900|14/14|||-/642|protein_coding,downstream_gene_variant|||ENSG00000087916|SLC6A14|ENST00000463626|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,16:16:99:324,0 .:0,0:.:.:. chrX 118281538 . C A 372.64 PASS AC=3;AF=1;AN=3;DP=15;FS=0;GQ_MEAN=133.33;GQ_STDDEV=83.03;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=26.62;SOR=1.765;set=variant2;CSQ=missense_variant|gGc/gTc|G/V|ENSG00000250423|KIAA1210|ENST00000402510|2/14|benign(0)|tolerated(0.36)|103/1709|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:215,0 1:0,2:2:49:49,0 1:0,5:5:99:136,0 chrX 118533299 . A G 148.64 PASS AC=2;AF=1;AN=2;DP=7;FS=0;GQ_MEAN=88;GQ_STDDEV=48.08;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=21.23;SOR=2.584;set=variant2;CSQ=upstream_gene_variant|||ENSG00000077713|SLC25A43|ENST00000488158|||||processed_transcript,upstream_gene_variant|||ENSG00000077713|SLC25A43|ENST00000336249||||-/226|protein_coding,upstream_gene_variant|||ENSG00000077713|SLC25A43|ENST00000493093|||||processed_transcript,5_prime_UTR_variant|||ENSG00000077713|SLC25A43|ENST00000217909|1/5|||-/341|protein_coding GT:AD:DP:GQ:PL 1:0,5:5:99:122,0 .:0,0:.:.:. 1:0,2:2:54:54,0 chrX 118533423 . T C 1378.64 PASS AC=3;AF=1;AN=3;DP=46;FS=0;GQ_MEAN=468.67;GQ_STDDEV=287.23;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.97;SOR=0.976;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000077713|SLC25A43|ENST00000493093|1/4||||processed_transcript,synonymous_variant|gcT/gcC|A|ENSG00000077713|SLC25A43|ENST00000217909|1/5|||19/341|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000077713|SLC25A43|ENST00000488158|1/6||||processed_transcript,synonymous_variant|gcT/gcC|A|ENSG00000077713|SLC25A43|ENST00000336249|1/4|||19/226|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:770,0 1:0,8:8:99:198,0 1:0,14:14:99:438,0 chrX 118602222 . G C 98.64 PASS AC=2;AF=1;AN=2;DP=5;FS=0;GQ_MEAN=63;GQ_STDDEV=19.8;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=24.66;SOR=1.609;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000395539|1/1||||retained_intron,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000317881||||-/298|protein_coding,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000460013|||||processed_transcript,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000463551|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000609227|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000446986|1/2||||lincRNA,intron_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000445759|||||lincRNA,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000475354|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:49:49,0 1:0,2:2:77:77,0 chrX 118602886 . C G 997.64 PASS AC=2;AF=1;AN=2;DP=39;FS=0;GQ_MEAN=512.5;GQ_STDDEV=614.48;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25.58;SOR=0.85;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000395539|1/1||||retained_intron,intron_variant|||ENSG00000005022|SLC25A5|ENST00000317881||||-/298|protein_coding,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000460013|||||processed_transcript,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000463551|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000609227|||||lincRNA,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000446986|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000445759|1/2||||lincRNA,intron_variant&non_coding_transcript_variant|||ENSG00000005022|SLC25A5|ENST00000475354|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:947,0 1:0,2:2:78:78,0 chrX 118603844 . T G 1468.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=0.065;ClippingRankSum=0.49;DP=64;FS=0;GQ_MEAN=748;GQ_STDDEV=316.78;MLEAC=2;MLEAF=1;MQ=58.57;MQ0=0;MQRankSum=3.25;NCC=1;QD=22.95;ReadPosRankSum=0.294;SOR=0.522;set=variant2;CSQ=upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000446986|||||lincRNA,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000445759|||||lincRNA,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000609227|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000005022|SLC25A5|ENST00000475354|2/2||||processed_transcript,missense_variant|cTc/cGc|L/R|ENSG00000005022|SLC25A5|ENST00000317881|2/4|benign(0)|tolerated(1)|111/298|protein_coding,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000395539|||||retained_intron,upstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000463551|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000005022|SLC25A5|ENST00000460013|2/4||||processed_transcript GT:AD:DP:GQ:PL 1:2,36:38:99:972,0 .:0,0:.:.:. 1:5,21:26:99:524,0 chrX 118604436 . T C 3601.64 PASS AC=3;AF=1;AN=3;DP=127;FS=0;GQ_MEAN=1209.67;GQ_STDDEV=95.77;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.81;SOR=1.198;set=variant2;CSQ=downstream_gene_variant|||ENSG00000005022|SLC25A5|ENST00000475354|||||processed_transcript,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000609227|||||lincRNA,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000446986|||||lincRNA,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000445759|||||lincRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000005022|SLC25A5|ENST00000460013|3/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000005022|SLC25A5|ENST00000463551|1/2||||processed_transcript,upstream_gene_variant|||ENSG00000224281|SLC25A5-AS1|ENST00000395539|||||retained_intron,synonymous_variant|acT/acC|T|ENSG00000005022|SLC25A5|ENST00000317881|3/4|||233/298|protein_coding GT:AD:DP:GQ:PL 1:0,32,0:32:99:1148,0 1:0,46,6:52:99:1161,0 1:0,41,0:41:99:1320,0 chrX 118678364 . G A 1816.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=2.19;ClippingRankSum=-0.465;DP=62;FS=0;GQ_MEAN=614.67;GQ_STDDEV=331.78;MLEAC=3;MLEAF=1;MQ=58.81;MQ0=0;MQRankSum=-0.996;NCC=0;QD=29.3;ReadPosRankSum=1.13;SOR=1.46;set=variant2;CSQ=synonymous_variant|ggC/ggT|G|ENSG00000018610|CXorf56|ENST00000320339|4/7|||76/173|protein_coding,upstream_gene_variant|||ENSG00000018610|CXorf56|ENST00000469448|||||processed_transcript,synonymous_variant|ggC/ggT|G|ENSG00000018610|CXorf56|ENST00000371594|4/7|||125/222|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000018610|CXorf56|ENST00000536133|3/6|||111/208|protein_coding GT:AD:DP:GQ:PL 1:2,17:19:99:599,0 1:0,13:13:99:291,0 1:0,30:30:99:954,0 chrX 118699320 . A G 3394.64 PASS AC=3;AF=1;AN=3;DP=110;FS=0;GQ_MEAN=1140.67;GQ_STDDEV=275.76;MLEAC=3;MLEAF=1;MQ=56.84;MQ0=0;NCC=0;QD=30.86;SOR=0.767;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000018610|CXorf56|ENST00000371594|1/7|||-/222|protein_coding,5_prime_UTR_variant|||ENSG00000018610|CXorf56|ENST00000536133|1/6|||-/208|protein_coding,5_prime_UTR_variant|||ENSG00000018610|CXorf56|ENST00000320339|1/7|||-/173|protein_coding GT:AD:DP:GQ:PL 1:0,42:42:99:1459,0 1:0,37:37:99:975,0 1:0,31:31:99:988,0 chrX 118752312 . T C 745.64 PASS AC=1;AF=1;AN=1;DP=29;FS=0;GQ_MEAN=773;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.71;SOR=0.76;set=variant2;CSQ=downstream_gene_variant|||ENSG00000125354|SEPT6|ENST00000467310|||||processed_transcript,intron_variant&NMD_transcript_variant|||ENSG00000125354|SEPT6|ENST00000460411||||-/267|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000394610|11/11|||-/427|protein_coding,intron_variant|||ENSG00000125354|SEPT6|ENST00000354228||||-/429|protein_coding,3_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000354416|10/10|||-/431|protein_coding,3_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000343984|10/10|||-/434|protein_coding,intron_variant|||ENSG00000125354|SEPT6|ENST00000489216||||-/427|protein_coding,intron_variant|||ENSG00000125354|SEPT6|ENST00000360156||||-/427|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,29:29:99:773,0 .:0,0:.:.:. chrX 118827317 . A C 267.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=295;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=29.74;SOR=2.093;set=variant2;CSQ=5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000125354|SEPT6|ENST00000460411|1/10|||-/267|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000125354|SEPT6|ENST00000394617||||-/457|protein_coding,upstream_gene_variant|||ENSG00000125354|SEPT6|ENST00000394616||||-/369|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000354228|1/10|||-/429|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000394610|1/11|||-/427|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000343984|1/10|||-/434|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000489216|1/11|||-/427|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000354416|1/10|||-/431|protein_coding,5_prime_UTR_variant|||ENSG00000125354|SEPT6|ENST00000360156|1/11|||-/427|protein_coding GT:AD:DP:GQ:PL 1:0,9:9:99:295,0 .:0,0:.:.:. .:0,0:.:.:. chrX 119005705 . C G 1686.64 PASS AC=2;AF=1;AN=2;DP=50;FS=0;GQ_MEAN=857;GQ_STDDEV=66.47;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.73;SOR=1.519;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000125352|RNF113A|ENST00000371442|1/1|||-/343|protein_coding,5_prime_UTR_variant|||ENSG00000125356|NDUFA1|ENST00000371437|1/3|||-/70|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:810,0 .:0,0:.:.:. 1:0,26:26:99:904,0 chrX 119370777 . G C 35.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.72;ClippingRankSum=0.72;DP=6;FS=11.761;GQ_MEAN=63;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.72;NCC=2;QD=5.94;ReadPosRankSum=1.38;SOR=3.223;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000233382|NKAPP1|ENST00000555168|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000233382|NKAPP1|ENST00000452254|3/3||||processed_transcript,downstream_gene_variant|||ENSG00000233382|NKAPP1|ENST00000592037|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000233382|NKAPP1|ENST00000554109|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000233382|NKAPP1|ENST00000554946|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:2,4:6:63:63,0 .:0,0:.:.:. chrX 119387833 . C CTGA 3097.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.493;ClippingRankSum=-1.283;DP=85;FS=0;GQ_MEAN=1041.67;GQ_STDDEV=563.17;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.296;NCC=0;QD=30.94;ReadPosRankSum=0.493;SOR=0.814;set=variant;CSQ=inframe_insertion|tct/tcTGAt|S/SD|ENSG00000177485|ZBTB33|ENST00000557385|3/3|||188/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371352||||-/185|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000309720||||-/349|protein_coding,inframe_insertion|tct/tcTGAt|S/SD|ENSG00000177485|ZBTB33|ENST00000326624|2/2|||188/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000440464||||-/241|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371369||||-/325|protein_coding GT:AD:DP:GQ:PL 1:0,32:32:99:1513,0 1:2,11:13:99:418,0 1:0,25:25:99:1194,0 chrX 119389966 . C T 96.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=124;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=19.33;SOR=1.981;set=variant2;CSQ=downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371369||||-/325|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000440464||||-/241|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371352||||-/185|protein_coding,downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000557385||||-/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000309720||||-/349|protein_coding,3_prime_UTR_variant|||ENSG00000177485|ZBTB33|ENST00000326624|2/2|||-/672|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:124,0 .:0,0:.:.:. chrX 119390465 . A G 198.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.348;ClippingRankSum=-0.696;DP=10;FS=0;GQ_MEAN=226;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.348;NCC=2;QD=19.86;ReadPosRankSum=0;SOR=0.525;set=variant2;CSQ=downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371369||||-/325|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000440464||||-/241|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000309720||||-/349|protein_coding,3_prime_UTR_variant|||ENSG00000177485|ZBTB33|ENST00000326624|2/2|||-/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371352||||-/185|protein_coding,downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000557385||||-/672|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,9:10:99:226,0 .:0,0:.:.:. chrX 119390665 . A T 515.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-1.187;ClippingRankSum=0.822;DP=20;FS=3.245;GQ_MEAN=543;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.187;NCC=2;QD=27.14;ReadPosRankSum=-0.639;SOR=0.556;set=variant2;CSQ=downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371369||||-/325|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000440464||||-/241|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000309720||||-/349|protein_coding,3_prime_UTR_variant|||ENSG00000177485|ZBTB33|ENST00000326624|2/2|||-/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371352||||-/185|protein_coding,downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000557385||||-/672|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,18:19:99:543,0 .:0,0:.:.:. chrX 119391880 . G A 952.64 PASS AC=1;AF=1;AN=1;DP=42;FS=0;GQ_MEAN=980;MLEAC=1;MLEAF=1;MQ=57.28;MQ0=0;NCC=2;QD=22.68;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371369||||-/325|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000440464||||-/241|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000371352||||-/185|protein_coding,downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000557385||||-/672|protein_coding,3_prime_UTR_variant|||ENSG00000177485|ZBTB33|ENST00000326624|2/2|||-/672|protein_coding,downstream_gene_variant|||ENSG00000125355|TMEM255A|ENST00000309720||||-/349|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,42:42:99:980,0 .:0,0:.:.:. chrX 119392796 . G A 918.64 PASS AC=1;AF=1;AN=1;DP=36;FS=0;GQ_MEAN=946;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.25;SOR=0.749;set=variant2;CSQ=downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000326624||||-/672|protein_coding,3_prime_UTR_variant|||ENSG00000125355|TMEM255A|ENST00000309720|10/10|||-/349|protein_coding,downstream_gene_variant|||ENSG00000177485|ZBTB33|ENST00000557385||||-/672|protein_coding,3_prime_UTR_variant|||ENSG00000125355|TMEM255A|ENST00000371352|5/5|||-/185|protein_coding,3_prime_UTR_variant|||ENSG00000125355|TMEM255A|ENST00000440464|7/7|||-/241|protein_coding,3_prime_UTR_variant|||ENSG00000125355|TMEM255A|ENST00000371369|9/9|||-/325|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,35:35:99:946,0 .:0,0:.:.:. chrX 122318386 . A AG 3127.64 PASS AC=3;AF=1;AN=3;DP=79;FS=0;GQ_MEAN=1051.67;GQ_STDDEV=621.22;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=24.67;SOR=0.914;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000371251|1/15|||-/894|protein_coding,5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000542149|1/17|||-/824|protein_coding,upstream_gene_variant|||ENSG00000125675|GRIA3|ENST00000541091||||-/662|protein_coding,upstream_gene_variant|||ENSG00000125675|GRIA3|ENST00000479118|||||processed_transcript,5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000371266|2/5|||-/164|protein_coding,5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000371264|1/4|||-/164|protein_coding,5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000264357|1/16|||-/894|protein_coding,5_prime_UTR_variant|||ENSG00000125675|GRIA3|ENST00000371256|1/16|||-/894|protein_coding GT:AD:DP:GQ:PL 1:0,41:41:99:1630,0 1:0,9:9:99:395,0 1:0,28:28:99:1130,0 chrX 123047453 . T A 807.64 PASS AC=1;AF=1;AN=1;DP=35;FS=0;GQ_MEAN=835;MLEAC=1;MLEAF=1;MQ=57.89;MQ0=0;NCC=2;QD=23.75;SOR=0.693;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101966|XIAP|ENST00000496602|2/2||||processed_transcript,3_prime_UTR_variant|||ENSG00000101966|XIAP|ENST00000371199|7/7|||-/497|protein_coding,3_prime_UTR_variant|||ENSG00000101966|XIAP|ENST00000355640|7/7|||-/497|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,34:34:99:835,0 .:0,0:.:.:. chrX 123506104 . T A 505.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=533;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.98;SOR=0.963;set=variant2;CSQ=downstream_gene_variant|||ENSG00000009694|TENM1|ENST00000371130||||-/2725|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000101972|STAG2|ENST00000469481|||||processed_transcript,downstream_gene_variant|||ENSG00000183918|SH2D1A|ENST00000494073|||||processed_transcript,downstream_gene_variant|||ENSG00000183918|SH2D1A|ENST00000477673||||-/76|protein_coding,downstream_gene_variant|||ENSG00000183918|SH2D1A|ENST00000360027||||-/125|protein_coding,downstream_gene_variant|||ENSG00000183918|SH2D1A|ENST00000491950|||||processed_transcript,downstream_gene_variant|||ENSG00000009694|TENM1|ENST00000422452||||-/2732|protein_coding,3_prime_UTR_variant|||ENSG00000183918|SH2D1A|ENST00000371139|4/4|||-/128|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:533,0 .:0,0:.:.:. chrX 123513104 . T G 246.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=274;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.66;SOR=1.085;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000101972|STAG2|ENST00000469481|||||processed_transcript,3_prime_UTR_variant|||ENSG00000009694|TENM1|ENST00000371130|31/31|||-/2725|protein_coding,3_prime_UTR_variant|||ENSG00000009694|TENM1|ENST00000422452|32/32|||-/2732|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:274,0 .:0,0:.:.:. chrX 123514006 . G A 151.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=179;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.27;SOR=2.303;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000009694|TENM1|ENST00000371130|31/31|||-/2725|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000101972|STAG2|ENST00000469481|||||processed_transcript,3_prime_UTR_variant|||ENSG00000009694|TENM1|ENST00000422452|32/32|||-/2732|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:179,0 .:0,0:.:.:. chrX 123540315 . G T 964.64 PASS AC=3;AF=1;AN=3;DP=29;FS=0;GQ_MEAN=330.67;GQ_STDDEV=154.59;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.26;SOR=3.334;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000101972|STAG2|ENST00000469481|||||processed_transcript,synonymous_variant|acC/acA|T|ENSG00000009694|TENM1|ENST00000371130|25/31|||1662/2725|protein_coding,synonymous_variant|acC/acA|T|ENSG00000009694|TENM1|ENST00000422452|26/32|||1669/2732|protein_coding GT:AD:DP:GQ:PL 1:0,14:14:99:506,0 1:0,8:8:99:214,0 1:0,7:7:99:272,0 chrX 125955428 . G A 5081.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.499;ClippingRankSum=-0.029;DP=156;FS=0;GQ_MEAN=1703;GQ_STDDEV=1387.51;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.2;NCC=0;QD=32.78;ReadPosRankSum=1.09;SOR=0.223;set=variant2;CSQ=synonymous_variant|ccG/ccA|P|ENSG00000183631|CXorf64|ENST00000371125|2/2|||269/298|protein_coding GT:AD:DP:GQ:PL 1:0,88:88:99:2958,0 1:0,8:8:99:213,0 1:1,58:59:99:1938,0 chrX 125955644 . A T 1127.64 PASS AC=2;AF=1;AN=2;DP=34;FS=0;GQ_MEAN=577.5;GQ_STDDEV=127.99;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.99;SOR=1.911;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000183631|CXorf64|ENST00000371125|2/2|||-/298|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:668,0 .:0,0:.:.:. 1:0,14:14:99:487,0 chrX 128880614 . T C 1801.64 PASS AC=3;AF=1;AN=3;DP=66;FS=0;GQ_MEAN=609.67;GQ_STDDEV=430.29;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.72;SOR=1.162;set=variant2;CSQ=synonymous_variant|ccT/ccC|P|ENSG00000122121|XPNPEP2|ENST00000371105|6/6|||149/183|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000122121|XPNPEP2|ENST00000371106|6/21|||149/674|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:428,0 1:0,45:45:99:1101,0 1:0,8:8:99:300,0 chrX 129147079 . T C 1965.64 PASS AC=3;AF=1;AN=3;DP=58;FS=0;GQ_MEAN=664.33;GQ_STDDEV=409.14;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.89;SOR=0.836;set=variant2;CSQ=missense_variant|Ttc/Ctc|F/L|ENSG00000085185|BCORL1|ENST00000218147|4/13|unknown(0)||111/1711|protein_coding,upstream_gene_variant|||ENSG00000085185|BCORL1|ENST00000441294||||-/741|protein_coding,upstream_gene_variant|||ENSG00000085185|BCORL1|ENST00000456822||||-/1385|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000085185|BCORL1|ENST00000540052|3/12|unknown(0)||111/1711|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000085185|BCORL1|ENST00000359304|4/12|benign(0.002)||111/1581|protein_coding,missense_variant|Ttc/Ctc|F/L|ENSG00000085185|BCORL1|ENST00000303743|4/14|unknown(0)||111/1785|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000085185|BCORL1|ENST00000488135|6/6|||-/45|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,17:17:99:638,0 1:0,9:9:99:269,0 1:0,32:32:99:1086,0 chrX 129484693 . C T 2443.64 PASS AC=3;AF=1;AN=3;DP=70;FS=0;GQ_MEAN=823.67;GQ_STDDEV=514.1;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.91;SOR=1.418;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000478474|3/8||||processed_transcript,downstream_gene_variant|||ENSG00000102078|SLC25A14|ENST00000467346|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000467496|6/9||||processed_transcript,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000218197|5/10|||162/325|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000464342|5/8||||processed_transcript,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000543953|5/8|||127/205|protein_coding,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000339231|5/11|||159/353|protein_coding,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000545805|6/8|||162/240|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000464184|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000471795|2/4||||processed_transcript,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000361980|5/10|||159/322|protein_coding,synonymous_variant|acC/acT|T|ENSG00000102078|SLC25A14|ENST00000424447|6/7|||162/198|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000102078|SLC25A14|ENST00000495156|||||processed_transcript GT:AD:DP:GQ:PL 1:0,28:28:99:1027,0 1:0,9:9:99:239,0 1:0,33:33:99:1205,0 chrX 130223137 . G A 522.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=550;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.76;SOR=0.874;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000147256|ARHGAP36|ENST00000370922|12/12|||-/535|protein_coding,3_prime_UTR_variant|||ENSG00000147256|ARHGAP36|ENST00000276211|12/12|||-/547|protein_coding,3_prime_UTR_variant|||ENSG00000147256|ARHGAP36|ENST00000370921|9/9|||-/411|protein_coding,downstream_gene_variant|||ENSG00000147256|ARHGAP36|ENST00000423277||||-/218|protein_coding,3_prime_UTR_variant|||ENSG00000147256|ARHGAP36|ENST00000412432|12/12|||-/516|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,22:22:99:550,0 .:0,0:.:.:. chrX 130416480 . A C 1816.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.011;ClippingRankSum=-0.867;DP=58;FS=0;GQ_MEAN=614.67;GQ_STDDEV=265.61;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.45;NCC=0;QD=31.32;ReadPosRankSum=0.433;SOR=0.38;set=variant2;CSQ=downstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000370900||||-/242|protein_coding,missense_variant|cTt/cGt|L/R|ENSG00000147255|IGSF1|ENST00000361420|7/20|benign(0.021)|tolerated(0.34)|395/1336|protein_coding,missense_variant|cTt/cGt|L/R|ENSG00000147255|IGSF1|ENST00000370903|7/20|benign(0.012)|tolerated(0.33)|395/1341|protein_coding,missense_variant|cTt/cGt|L/R|ENSG00000147255|IGSF1|ENST00000370910|6/19|benign(0.012)|tolerated(0.33)|386/1327|protein_coding,downstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000370901||||-/242|protein_coding,missense_variant|cTt/cGt|L/R|ENSG00000147255|IGSF1|ENST00000370904|13/26|benign(0.012)|tolerated(0.33)|386/1327|protein_coding,upstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000467244|||||processed_transcript,upstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000469836|||||processed_transcript GT:AD:DP:GQ:PL 1:1,23:24:99:764,0 1:0,10:10:99:308,0 1:0,24:24:99:772,0 chrX 130416958 . C T 2091.64 PASS AC=2;AF=1;AN=2;DP=71;FS=0;GQ_MEAN=1059.5;GQ_STDDEV=167.58;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=29.88;SOR=0.811;set=variant2;CSQ=synonymous_variant|gtG/gtA|V|ENSG00000147255|IGSF1|ENST00000370910|5/19|||307/1327|protein_coding,downstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000370901||||-/242|protein_coding,upstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000469836|||||processed_transcript,downstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000370900||||-/242|protein_coding,synonymous_variant|gtG/gtA|V|ENSG00000147255|IGSF1|ENST00000370904|12/26|||307/1327|protein_coding,synonymous_variant|gtG/gtA|V|ENSG00000147255|IGSF1|ENST00000361420|6/20|||316/1336|protein_coding,synonymous_variant|gtG/gtA|V|ENSG00000147255|IGSF1|ENST00000370903|6/20|||316/1341|protein_coding GT:AD:DP:GQ:PL 1:0,38:38:99:1178,0 .:0,0:.:.:. 1:0,32:32:99:941,0 chrX 130420006 . T C 731.64 PASS AC=2;AF=1;AN=2;DP=21;FS=0;GQ_MEAN=379.5;GQ_STDDEV=19.09;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.84;SOR=6.184;set=variant2;CSQ=synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000370903|4/20|||38/1341|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000361420|4/20|||38/1336|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000370900|4/5|||38/242|protein_coding,upstream_gene_variant|||ENSG00000147255|IGSF1|ENST00000469836|||||processed_transcript,synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000370904|10/26|||29/1327|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000370901|4/5|||38/242|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000147255|IGSF1|ENST00000370910|3/19|||29/1327|protein_coding GT:AD:DP:GQ:PL 1:0,11:11:99:393,0 .:0,0:.:.:. 1:0,10:10:99:366,0 chrX 130420415 . T C 1761.64 PASS AC=3;AF=1;AN=3;DP=52;FS=0;GQ_MEAN=596.33;GQ_STDDEV=303.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.54;SOR=2.004;set=variant2;CSQ=synonymous_variant|tcA/tcG|S|ENSG00000147255|IGSF1|ENST00000361420|3/20|||31/1336|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000147255|IGSF1|ENST00000370903|3/20|||31/1341|protein_coding,intron_variant|||ENSG00000147255|IGSF1|ENST00000370910||||-/1327|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000147255|IGSF1|ENST00000370901|3/5|||31/242|protein_coding,synonymous_variant|tcA/tcG|S|ENSG00000147255|IGSF1|ENST00000370900|3/5|||31/242|protein_coding,intron_variant|||ENSG00000147255|IGSF1|ENST00000370904||||-/1327|protein_coding GT:AD:DP:GQ:PL 1:0,22:22:99:796,0 1:0,10:10:99:247,0 1:0,19:19:99:746,0 chrX 130678467 . A G 5380.64 PASS AC=3;AF=1;AN=3;DP=158;FS=0;GQ_MEAN=1802.67;GQ_STDDEV=1279.87;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.05;SOR=0.914;set=variant2;CSQ=synonymous_variant|gtA/gtG|V|ENSG00000171054|OR13H1|ENST00000338616|1/1|||140/308|protein_coding GT:AD:DP:GQ:PL 1:0,78:78:99:2747,0 1:0,14:14:99:346,0 1:0,66:66:99:2315,0 chrX 130678596 . C G 6793.64 PASS AC=3;AF=1;AN=3;DP=197;FS=0;GQ_MEAN=2273.67;GQ_STDDEV=1447.99;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.49;SOR=0.724;set=variant2;CSQ=synonymous_variant|ctC/ctG|L|ENSG00000171054|OR13H1|ENST00000338616|1/1|||183/308|protein_coding GT:AD:DP:GQ:PL 1:0,85:85:99:3081,0 1:0,22:22:99:602,0 1:0,90:90:99:3138,0 chrX 130678844 . A C 4581.64 PASS AC=3;AF=1;AN=3;DP=141;FS=0;GQ_MEAN=1536.33;GQ_STDDEV=710.18;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.49;SOR=0.707;set=variant2;CSQ=missense_variant|tAc/tCc|Y/S|ENSG00000171054|OR13H1|ENST00000338616|1/1|benign(0.002)|tolerated(1)|266/308|protein_coding GT:AD:DP:GQ:PL 1:0,56:56:99:2012,0 1:0,28:28:99:720,0 1:0,57:57:99:1877,0 chrX 130918008 . T C 285.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=313;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.8;SOR=1.022;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000213468|RP11-453F18__B.1|ENST00000427391|6/13||||lincRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:313,0 .:0,0:.:.:. chrX 131211235 . T A 594.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.6;ClippingRankSum=-1.733;DP=25;FS=0;GQ_MEAN=622;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.624;NCC=2;QD=23.79;ReadPosRankSum=0.624;SOR=0.223;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000165694|FRMD7|ENST00000298542|12/12|||-/714|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394334||||-/416|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000496850||||-/354|protein_coding,3_prime_UTR_variant|||ENSG00000165694|FRMD7|ENST00000370879|8/8|||-/594|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000481105||||-/438|protein_coding,downstream_gene_variant|||ENSG00000165694|FRMD7|ENST00000464296||||-/699|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000354719||||-/392|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394335||||-/339|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,24:25:99:622,0 .:0,0:.:.:. chrX 131212512 . A G 2836.64 PASS AC=3;AF=1;AN=3;DP=76;FS=0;GQ_MEAN=954.67;GQ_STDDEV=659.24;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.42;SOR=0.801;set=variant2;CSQ=downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394335||||-/339|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000354719||||-/392|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000481105||||-/438|protein_coding,synonymous_variant|atT/atC|I|ENSG00000165694|FRMD7|ENST00000464296|12/12|||496/699|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394334||||-/416|protein_coding,synonymous_variant|atT/atC|I|ENSG00000165694|FRMD7|ENST00000370879|8/8|||391/594|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000496850||||-/354|protein_coding,synonymous_variant|atT/atC|I|ENSG00000165694|FRMD7|ENST00000298542|12/12|||511/714|protein_coding GT:AD:DP:GQ:PL 1:0,37:37:99:1412,0 1:0,6:6:99:199,0 1:0,33:33:99:1253,0 chrX 131212642 . C T 4457.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.532;ClippingRankSum=-1.532;DP=144;FS=3.259;GQ_MEAN=1495;GQ_STDDEV=386.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.333;NCC=0;QD=30.96;ReadPosRankSum=-0.933;SOR=0.427;set=variant2;CSQ=downstream_gene_variant|||ENSG00000134602|MST4|ENST00000354719||||-/392|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394335||||-/339|protein_coding,missense_variant|cGt/cAt|R/H|ENSG00000165694|FRMD7|ENST00000464296|12/12|benign(0.282)|tolerated(0.09)|453/699|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000481105||||-/438|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000496850||||-/354|protein_coding,missense_variant|cGt/cAt|R/H|ENSG00000165694|FRMD7|ENST00000370879|8/8|benign(0.146)|tolerated(0.21)|348/594|protein_coding,downstream_gene_variant|||ENSG00000134602|MST4|ENST00000394334||||-/416|protein_coding,missense_variant|cGt/cAt|R/H|ENSG00000165694|FRMD7|ENST00000298542|12/12|benign(0.146)|tolerated(0.09)|468/714|protein_coding GT:AD:DP:GQ:PL 1:1,51:52:99:1695,0 1:0,42:42:99:1049,0 1:0,50:50:99:1741,0 chrX 131216391 . C T 1989.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.523;ClippingRankSum=0.742;DP=64;FS=0;GQ_MEAN=672.33;GQ_STDDEV=465.61;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.742;NCC=0;QD=31.09;ReadPosRankSum=0.362;SOR=0.43;set=variant2;CSQ=missense_variant&splice_region_variant|aGt/aAt|S/N|ENSG00000165694|FRMD7|ENST00000370879|5/8|probably_damaging(0.996)|deleterious(0)|182/594|protein_coding,missense_variant&splice_region_variant|aGt/aAt|S/N|ENSG00000165694|FRMD7|ENST00000298542|9/12|probably_damaging(0.996)|deleterious(0)|302/714|protein_coding,missense_variant&splice_region_variant|aGt/aAt|S/N|ENSG00000165694|FRMD7|ENST00000464296|9/12|probably_damaging(0.997)|deleterious(0)|287/699|protein_coding GT:AD:DP:GQ:PL 1:2,29:31:99:908,0 1:1,6:7:99:136,0 1:0,26:26:99:973,0 chrX 131352061 . A G 152.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=29.65;SOR=0.693;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000490400|||||processed_transcript,5_prime_UTR_variant|||ENSG00000123728|RAP2C|ENST00000342983|1/4|||-/183|protein_coding,upstream_gene_variant|||ENSG00000232160|RAP2C-AS1|ENST00000441399|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000460462|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000232160|RAP2C-AS1|ENST00000421483|||||antisense,intron_variant|||ENSG00000123728|RAP2C|ENST00000370874||||-/183|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:180,0 .:0,0:.:.:. chrX 131352071 . T G 152.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.91;SOR=0.693;set=variant2;CSQ=intron_variant|||ENSG00000123728|RAP2C|ENST00000370874||||-/183|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232160|RAP2C-AS1|ENST00000421483|||||antisense,upstream_gene_variant|||ENSG00000232160|RAP2C-AS1|ENST00000441399|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000460462|||||processed_transcript,5_prime_UTR_variant|||ENSG00000123728|RAP2C|ENST00000342983|1/4|||-/183|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000490400|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:180,0 .:0,0:.:.:. chrX 131352074 . C CG 152.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=30.71;SOR=0.693;set=variant;CSQ=intron_variant|||ENSG00000123728|RAP2C|ENST00000370874||||-/183|protein_coding,upstream_gene_variant|||ENSG00000232160|RAP2C-AS1|ENST00000441399|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000460462|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000232160|RAP2C-AS1|ENST00000421483|||||antisense,5_prime_UTR_variant|||ENSG00000123728|RAP2C|ENST00000342983|1/4|||-/183|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000123728|RAP2C|ENST00000490400|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:180,0 .:0,0:.:.:. chrX 131760779 . C T 79.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=107;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=15.93;SOR=1.981;set=variant2;CSQ=downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000521489||||-/645|protein_coding,downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000406696||||-/331|protein_coding,downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000370833||||-/462|protein_coding,3_prime_UTR_variant|||ENSG00000171004|HS6ST2|ENST00000370836|4/4|||-/605|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:107,0 .:0,0:.:.:. chrX 131760865 . G A 563.64 PASS AC=1;AF=1;AN=1;DP=24;FS=0;GQ_MEAN=591;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.49;SOR=0.859;set=variant2;CSQ=downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000521489||||-/645|protein_coding,downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000370833||||-/462|protein_coding,3_prime_UTR_variant|||ENSG00000171004|HS6ST2|ENST00000370836|4/4|||-/605|protein_coding,downstream_gene_variant|||ENSG00000171004|HS6ST2|ENST00000406696||||-/331|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,24:24:99:591,0 .:0,0:.:.:. chrX 132351002 . TAAA T 44.87 PASS AC=1;AF=0.333;AN=3;DP=9;FS=0;GQ_MEAN=96.33;GQ_STDDEV=18.15;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=14.96;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000183434|TFDP3|ENST00000310125|1/1|||-/405|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,113 1:0,2,1:3:77:77,0 0:3,0:3:99:0,99 chrX 132437337 . G A 2004.64 PASS AC=3;AF=1;AN=3;DP=62;FS=0;GQ_MEAN=677.33;GQ_STDDEV=333.57;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.33;SOR=1.43;set=variant2;CSQ=missense_variant|gCc/gTc|A/V|ENSG00000076716|GPC4|ENST00000370828|8/9|probably_damaging(0.994)|tolerated(0.07)|442/556|protein_coding,missense_variant|gCc/gTc|A/V|ENSG00000076716|GPC4|ENST00000535467|8/9|probably_damaging(0.994)||372/486|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:915,0 1:0,12:12:99:296,0 1:0,25:25:99:821,0 chrX 132438872 . C A 2066.64 PASS AC=3;AF=1;AN=3;DP=63;FS=0;GQ_MEAN=698;GQ_STDDEV=343.29;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.8;SOR=2.494;set=variant2;CSQ=missense_variant|gaG/gaT|E/D|ENSG00000076716|GPC4|ENST00000535467|7/9|probably_damaging(0.973)||321/486|protein_coding,missense_variant|gaG/gaT|E/D|ENSG00000076716|GPC4|ENST00000370828|7/9|probably_damaging(0.973)|tolerated(0.33)|391/556|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:843,0 1:0,12:12:99:306,0 1:0,28:28:99:945,0 chrX 132549013 . G A 2632.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=2.08;ClippingRankSum=-1.713;DP=93;FS=0;GQ_MEAN=886.67;GQ_STDDEV=125.34;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.602;NCC=0;QD=28.31;ReadPosRankSum=-0.694;SOR=1.389;set=variant2;CSQ=upstream_gene_variant|||ENSG00000076716|GPC4|ENST00000535467||||-/486|protein_coding,5_prime_UTR_variant|||ENSG00000076716|GPC4|ENST00000370828|1/9|||-/556|protein_coding GT:AD:DP:GQ:PL 1:0,24:24:99:789,0 1:0,42:42:99:1028,0 1:2,25:27:99:843,0 chrX 133379551 . C T 2816.64 PASS AC=3;AF=1;AN=3;DP=83;FS=0;GQ_MEAN=948;GQ_STDDEV=654.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.94;SOR=0.872;set=variant2;CSQ=synonymous_variant|Cta/Tta|L|ENSG00000203952|CCDC160|ENST00000370809|2/2|||241/325|protein_coding,synonymous_variant|Cta/Tta|L|ENSG00000203952|CCDC160|ENST00000517294|3/3|||241/325|protein_coding GT:AD:DP:GQ:PL 1:0,41:41:99:1407,0 1:0,7:7:99:198,0 1:0,35:35:99:1239,0 chrX 133561092 . A AT 883.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.203;ClippingRankSum=-0.654;DP=41;FS=0;GQ_MEAN=911;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.609;NCC=2;QD=22.09;ReadPosRankSum=0.023;SOR=0.804;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000394292|11/11|||-/366|protein_coding,3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000332070|10/10|||-/365|protein_coding,3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000370803|11/11|||-/365|protein_coding,downstream_gene_variant|||ENSG00000156531|PHF6|ENST00000416404||||-/331|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:4,36:40:99:911,0 .:0,0:.:.:. chrX 133561242 . G A 86.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=114;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.66;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000332070|10/10|||-/365|protein_coding,3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000394292|11/11|||-/366|protein_coding,3_prime_UTR_variant|||ENSG00000156531|PHF6|ENST00000370803|11/11|||-/365|protein_coding,downstream_gene_variant|||ENSG00000156531|PHF6|ENST00000416404||||-/331|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:114,0 .:0,0:.:.:. chrX 134022913 . A C 51.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=79;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.82;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000480721|||||processed_transcript,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000370777||||-/214|protein_coding,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000491609|||||processed_transcript,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000370779||||-/159|protein_coding,3_prime_UTR_variant|||ENSG00000101928|MOSPD1|ENST00000370783|6/6|||-/213|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:79:79,0 .:0,0:.:.:. chrX 134022943 . A G 37.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=65;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=18.82;SOR=2.303;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101928|MOSPD1|ENST00000370783|6/6|||-/213|protein_coding,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000370777||||-/214|protein_coding,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000491609|||||processed_transcript,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000370779||||-/159|protein_coding,downstream_gene_variant|||ENSG00000101928|MOSPD1|ENST00000480721|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:65:65,0 .:0,0:.:.:. chrX 134125475 . C G 418.64 PASS AC=2;AF=1;AN=2;DP=12;FS=0;GQ_MEAN=223;GQ_STDDEV=87.68;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=31.7;SOR=4.977;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000184785|SMIM10|ENST00000330288|1/1|||-/83|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:285,0 .:0,0:.:.:. 1:0,4:4:99:161,0 chrX 134125747 . T TA 50.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=78;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=16.88;SOR=2.833;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000184785|SMIM10|ENST00000330288|1/1|||-/83|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:78:78,0 .:0,0:.:.:. chrX 134156121 . G C 510.64 PASS AC=3;AF=1;AN=3;DP=16;FS=0;GQ_MEAN=179.33;GQ_STDDEV=96.03;MLEAC=3;MLEAF=1;MQ=47.01;MQ0=0;NCC=0;QD=31.92;SOR=0.941;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000212747|FAM127C|ENST00000391440|1/1|||-/113|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:202,0 1:0,8:8:99:262,0 1:0,2:2:74:74,0 chrX 134185997 . T A 2963.64 PASS AC=3;AF=1;AN=3;DP=99;FS=0;GQ_MEAN=997;GQ_STDDEV=113.58;MLEAC=3;MLEAF=1;MQ=48.36;MQ0=0;NCC=0;QD=29.94;SOR=1.808;set=variant2;CSQ=missense_variant|Agc/Tgc|S/C|ENSG00000203950|FAM127B|ENST00000370775|1/1|possibly_damaging(0.51)|deleterious(0.01)|48/113|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000203950|FAM127B|ENST00000520964|1/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000203950|FAM127B|ENST00000518153|1/2||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000203950|FAM127B|ENST00000522309|1/2||||processed_transcript GT:AD:DP:GQ:PL 1:0,26:26:99:937,0 1:0,41:41:99:926,0 1:0,32:32:99:1128,0 chrX 134420007 . G C 660.64 PASS AC=1;AF=1;AN=1;DP=23;FS=0;GQ_MEAN=688;MLEAC=1;MLEAF=1;MQ=57.67;MQ0=0;NCC=2;QD=28.72;SOR=0.963;set=variant2;CSQ=downstream_gene_variant|||ENSG00000186376|ZNF75D|ENST00000469456|||||processed_transcript,3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370766|7/7|||-/510|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000186376|ZNF75D|ENST00000494295|||||processed_transcript,3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370764|4/4|||-/415|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,23:23:99:688,0 .:0,0:.:.:. chrX 134420028 . T G 545.64 PASS AC=1;AF=1;AN=1;DP=21;FS=0;GQ_MEAN=573;MLEAC=1;MLEAF=1;MQ=57.44;MQ0=0;NCC=2;QD=25.98;SOR=0.99;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370764|4/4|||-/415|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000186376|ZNF75D|ENST00000494295|||||processed_transcript,3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370766|7/7|||-/510|protein_coding,downstream_gene_variant|||ENSG00000186376|ZNF75D|ENST00000469456|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,21:21:99:573,0 .:0,0:.:.:. chrX 134420602 . C T 372.64 PASS AC=1;AF=1;AN=1;DP=16;FS=0;GQ_MEAN=400;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.29;SOR=1.244;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370766|7/7|||-/510|protein_coding,downstream_gene_variant|||ENSG00000186376|ZNF75D|ENST00000469456|||||processed_transcript,3_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370764|4/4|||-/415|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000186376|ZNF75D|ENST00000494295|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,16:16:99:400,0 .:0,0:.:.:. chrX 134477613 . A C 452.64 PASS AC=2;AF=1;AN=2;DP=18;FS=0;GQ_MEAN=240;GQ_STDDEV=236.17;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25.15;SOR=0.914;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000186376|ZNF75D|ENST00000370766|1/7|||-/510|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000186376|ZNF75D|ENST00000494295|1/4||||processed_transcript,upstream_gene_variant|||ENSG00000173275|ZNF449|ENST00000370761||||-/164|protein_coding,upstream_gene_variant|||ENSG00000173275|ZNF449|ENST00000370760||||-/127|protein_coding,upstream_gene_variant|||ENSG00000173275|ZNF449|ENST00000339249||||-/518|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:73:73,0 1:0,16:16:99:407,0 .:0,0:.:.:. chrX 134558119 . C T 239.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=267;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.79;SOR=0.859;set=variant2;CSQ=downstream_gene_variant|||ENSG00000201440|RNA5SP515|ENST00000364570|||||rRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000178947|LINC00086|ENST00000417443|2/2||||lincRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:267,0 .:0,0:.:.:. chrX 134654818 . T C 1050.64 PASS AC=2;AF=1;AN=2;DP=32;FS=0;GQ_MEAN=539;GQ_STDDEV=25.46;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.89;SOR=2.376;set=variant2;CSQ=upstream_gene_variant|||ENSG00000165359|DDX26B|ENST00000493637|||||retained_intron,upstream_gene_variant|||ENSG00000225235|DDX26B-AS1|ENST00000430820|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165359|DDX26B|ENST00000481908|1/16||||processed_transcript,5_prime_UTR_variant|||ENSG00000165359|DDX26B|ENST00000370752|1/17|||-/861|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:521,0 .:0,0:.:.:. 1:0,15:15:99:557,0 chrX 134978425 . G A 1732.64 PASS AC=3;AF=1;AN=3;DP=65;FS=0;GQ_MEAN=586.67;GQ_STDDEV=583.4;MLEAC=3;MLEAF=1;MQ=56.74;MQ0=0;NCC=0;QD=26.66;SOR=1.646;set=variant2;CSQ=synonymous_variant|acG/acA|T|ENSG00000181433|SAGE1|ENST00000535938|2/20|||8/904|protein_coding,synonymous_variant|acG/acA|T|ENSG00000181433|SAGE1|ENST00000370709|1/19|||8/904|protein_coding,synonymous_variant|acG/acA|T|ENSG00000181433|SAGE1|ENST00000324447|2/20|||8/904|protein_coding,synonymous_variant|acG/acA|T|ENSG00000181433|SAGE1|ENST00000537770|2/12|||8/528|protein_coding GT:AD:DP:GQ:PL 1:0,8:8:99:287,0 1:0,51:51:99:1259,0 1:0,6:6:99:214,0 chrX 134986700 . T C 2358.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.397;ClippingRankSum=-2.124;DP=85;FS=0;GQ_MEAN=795.33;GQ_STDDEV=437.5;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.257;NCC=0;QD=27.75;ReadPosRankSum=0.537;SOR=0.766;set=variant2;CSQ=synonymous_variant|aaT/aaC|N|ENSG00000181433|SAGE1|ENST00000535938|4/20|||95/904|protein_coding,synonymous_variant|aaT/aaC|N|ENSG00000181433|SAGE1|ENST00000370709|3/19|||95/904|protein_coding,synonymous_variant|aaT/aaC|N|ENSG00000181433|SAGE1|ENST00000537770|4/12|||95/528|protein_coding,synonymous_variant|aaT/aaC|N|ENSG00000181433|SAGE1|ENST00000324447|4/20|||95/904|protein_coding GT:AD:DP:GQ:PL 1:0,19:19:99:650,0 1:2,51:53:99:1287,0 1:0,13:13:99:449,0 chrX 134991078 . A G 2960.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.578;ClippingRankSum=-1.735;DP=100;FS=0;GQ_MEAN=996;GQ_STDDEV=361.14;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.771;NCC=0;QD=29.91;ReadPosRankSum=-1.349;SOR=0.417;set=variant2;CSQ=synonymous_variant|caA/caG|Q|ENSG00000181433|SAGE1|ENST00000370709|12/19|||499/904|protein_coding,synonymous_variant|caA/caG|Q|ENSG00000181433|SAGE1|ENST00000535938|13/20|||499/904|protein_coding,synonymous_variant|caA/caG|Q|ENSG00000181433|SAGE1|ENST00000324447|13/20|||499/904|protein_coding,intron_variant|||ENSG00000181433|SAGE1|ENST00000537770||||-/528|protein_coding GT:AD:DP:GQ:PL 1:0,34:34:99:1203,0 1:0,47:47:99:1206,0 1:1,17:18:99:579,0 chrX 134994005 . T C 1335.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.53;ClippingRankSum=1.06;DP=45;FS=0;GQ_MEAN=454.33;GQ_STDDEV=207.88;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.354;NCC=0;QD=30.36;ReadPosRankSum=-0.354;SOR=1.402;set=variant2;CSQ=missense_variant|tTg/tCg|L/S|ENSG00000181433|SAGE1|ENST00000324447|18/20|benign(0)|tolerated(1)|805/904|protein_coding,missense_variant|tTg/tCg|L/S|ENSG00000181433|SAGE1|ENST00000537770|10/12|benign(0.001)|tolerated(1)|429/528|protein_coding,missense_variant|tTg/tCg|L/S|ENSG00000181433|SAGE1|ENST00000370709|17/19|benign(0)|tolerated(1)|805/904|protein_coding,missense_variant|tTg/tCg|L/S|ENSG00000181433|SAGE1|ENST00000535938|18/20|benign(0)|tolerated(1)|805/904|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:628,0 1:2,9:11:99:224,0 1:0,15:15:99:511,0 chrX 134994054 . G A 1552.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.202;ClippingRankSum=1.07;DP=60;FS=0;GQ_MEAN=526.67;GQ_STDDEV=375.73;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.721;NCC=0;QD=25.88;ReadPosRankSum=0.375;SOR=0.914;set=variant2;CSQ=synonymous_variant|aaG/aaA|K|ENSG00000181433|SAGE1|ENST00000324447|18/20|||821/904|protein_coding,synonymous_variant|aaG/aaA|K|ENSG00000181433|SAGE1|ENST00000537770|10/12|||445/528|protein_coding,synonymous_variant|aaG/aaA|K|ENSG00000181433|SAGE1|ENST00000535938|18/20|||821/904|protein_coding,synonymous_variant|aaG/aaA|K|ENSG00000181433|SAGE1|ENST00000370709|17/19|||821/904|protein_coding GT:AD:DP:GQ:PL 1:0,8:8:99:279,0 1:2,41:43:99:959,0 1:0,9:9:99:342,0 chrX 135095545 . A C 1619.64 PASS AC=3;AF=1;AN=3;DP=51;FS=0;GQ_MEAN=549;GQ_STDDEV=321.86;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.76;SOR=0.813;set=variant2;CSQ=synonymous_variant|gcA/gcC|A|ENSG00000198689|SLC9A6|ENST00000370695|9/16|||395/701|protein_coding,synonymous_variant|gcA/gcC|A|ENSG00000198689|SLC9A6|ENST00000370701|10/17|||343/649|protein_coding,synonymous_variant|gcA/gcC|A|ENSG00000198689|SLC9A6|ENST00000370698|9/16|||363/669|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:796,0 1:0,7:7:99:185,0 1:0,19:19:99:666,0 chrX 135426693 . A G 2982.64 PASS AC=3;AF=1;AN=3;DP=90;FS=0;GQ_MEAN=1003.33;GQ_STDDEV=742.77;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.28;SOR=0.863;set=variant2;CSQ=missense_variant|atA/atG|I/M|ENSG00000156920|GPR112|ENST00000287534|4/17|benign(0.192)||213/2804|protein_coding,missense_variant|atA/atG|I/M|ENSG00000156920|GPR112|ENST00000394143|6/26|benign(0.01)|tolerated(0.05)|276/3080|protein_coding,missense_variant|atA/atG|I/M|ENSG00000156920|GPR112|ENST00000370652|4/24|benign(0.01)|tolerated(0.05)|276/3080|protein_coding,missense_variant|atA/atG|I/M|ENSG00000156920|GPR112|ENST00000412101|3/23|benign(0.015)|tolerated(0.05)|71/2875|protein_coding,missense_variant|atA/atG|I/M|ENSG00000156920|GPR112|ENST00000394141|3/23|benign(0.015)|tolerated(0.05)|71/2875|protein_coding GT:AD:DP:GQ:PL 1:0,40:40:99:1473,0 1:0,6:6:99:147,0 1:0,41:41:99:1390,0 chrX 135426968 . C A 3192.69 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.733;ClippingRankSum=0.056;DP=105;FS=3.268;GQ_MEAN=1073.33;GQ_STDDEV=267.07;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.95;NCC=0;QD=30.7;ReadPosRankSum=0.28;SOR=0.442;set=variant2;CSQ=missense_variant|cCt/cAt|P/H|ENSG00000156920|GPR112|ENST00000394141|3/23|benign(0.443)|deleterious(0)|163/2875|protein_coding,missense_variant|cCt/cAt|P/H|ENSG00000156920|GPR112|ENST00000412101|3/23|benign(0.443)|deleterious(0)|163/2875|protein_coding,missense_variant|cCt/cAt|P/H|ENSG00000156920|GPR112|ENST00000394143|6/26|benign(0.087)|deleterious(0)|368/3080|protein_coding,missense_variant|cCt/cAt|P/H|ENSG00000156920|GPR112|ENST00000370652|4/24|benign(0.087)|deleterious(0)|368/3080|protein_coding,missense_variant|cCt/cAt|P/H|ENSG00000156920|GPR112|ENST00000287534|4/17|possibly_damaging(0.481)||305/2804|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1249,0 1:1,30:31:99:766,0 1:0,37:37:99:1205,0 chrX 135429503 . C A 3377.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.58;ClippingRankSum=-1.583;DP=105;FS=3.181;GQ_MEAN=1135;GQ_STDDEV=476.92;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-1.281;NCC=0;QD=32.48;ReadPosRankSum=1.58;SOR=0.378;set=variant2;CSQ=missense_variant|aCc/aAc|T/N|ENSG00000156920|GPR112|ENST00000287534|4/17|benign(0.003)||1150/2804|protein_coding,missense_variant|aCc/aAc|T/N|ENSG00000156920|GPR112|ENST00000394143|6/26|benign(0.003)|tolerated(0.07)|1213/3080|protein_coding,missense_variant|aCc/aAc|T/N|ENSG00000156920|GPR112|ENST00000370652|4/24|benign(0.003)|tolerated(0.07)|1213/3080|protein_coding,missense_variant|aCc/aAc|T/N|ENSG00000156920|GPR112|ENST00000412101|3/23|benign(0.006)|tolerated(0.07)|1008/2875|protein_coding,missense_variant|aCc/aAc|T/N|ENSG00000156920|GPR112|ENST00000394141|3/23|benign(0.006)|tolerated(0.07)|1008/2875|protein_coding GT:AD:DP:GQ:PL 1:0,43:43:99:1434,0 1:1,22:23:99:585,0 1:0,38:38:99:1386,0 chrX 135430044 . T C 2678.64 PASS AC=3;AF=1;AN=3;DP=82;FS=0;GQ_MEAN=902;GQ_STDDEV=694.43;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.67;SOR=0.846;set=variant2;CSQ=synonymous_variant|acT/acC|T|ENSG00000156920|GPR112|ENST00000370652|4/24|||1393/3080|protein_coding,synonymous_variant|acT/acC|T|ENSG00000156920|GPR112|ENST00000394143|6/26|||1393/3080|protein_coding,synonymous_variant|acT/acC|T|ENSG00000156920|GPR112|ENST00000287534|4/17|||1330/2804|protein_coding,synonymous_variant|acT/acC|T|ENSG00000156920|GPR112|ENST00000394141|3/23|||1188/2875|protein_coding,synonymous_variant|acT/acC|T|ENSG00000156920|GPR112|ENST00000412101|3/23|||1188/2875|protein_coding GT:AD:DP:GQ:PL 1:0,38:38:99:1202,0 1:0,3:3:99:108,0 1:0,41:41:99:1396,0 chrX 135430483 . T C 3829.64 PASS AC=3;AF=1;AN=3;DP=115;FS=0;GQ_MEAN=1285.67;GQ_STDDEV=897.13;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.59;SOR=0.922;set=variant2;CSQ=missense_variant|Tct/Cct|S/P|ENSG00000156920|GPR112|ENST00000287534|4/17|probably_damaging(0.994)||1477/2804|protein_coding,missense_variant|Tct/Cct|S/P|ENSG00000156920|GPR112|ENST00000394143|6/26|probably_damaging(0.916)|deleterious(0.04)|1540/3080|protein_coding,missense_variant|Tct/Cct|S/P|ENSG00000156920|GPR112|ENST00000370652|4/24|probably_damaging(0.916)|deleterious(0.04)|1540/3080|protein_coding,missense_variant|Tct/Cct|S/P|ENSG00000156920|GPR112|ENST00000412101|3/23|probably_damaging(0.948)|deleterious(0.04)|1335/2875|protein_coding,missense_variant|Tct/Cct|S/P|ENSG00000156920|GPR112|ENST00000394141|3/23|probably_damaging(0.948)|deleterious(0.04)|1335/2875|protein_coding GT:AD:DP:GQ:PL 1:0,49:49:99:1731,0 1:0,10:10:99:253,0 1:0,55:55:99:1873,0 chrX 135431236 . T C 3428.64 PASS AC=3;AF=1;AN=3;DP=94;FS=0;GQ_MEAN=1152;GQ_STDDEV=922.62;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=35.35;SOR=0.924;set=variant2;CSQ=missense_variant|Ttt/Ctt|F/L|ENSG00000156920|GPR112|ENST00000394141|3/23|benign(0)|tolerated(1)|1586/2875|protein_coding,missense_variant|Ttt/Ctt|F/L|ENSG00000156920|GPR112|ENST00000412101|3/23|benign(0)|tolerated(1)|1586/2875|protein_coding,missense_variant|Ttt/Ctt|F/L|ENSG00000156920|GPR112|ENST00000370652|4/24|benign(0)|tolerated(1)|1791/3080|protein_coding,missense_variant|Ttt/Ctt|F/L|ENSG00000156920|GPR112|ENST00000394143|6/26|benign(0)|tolerated(1)|1791/3080|protein_coding,missense_variant|Ttt/Ctt|F/L|ENSG00000156920|GPR112|ENST00000287534|4/17|benign(0.001)||1728/2804|protein_coding GT:AD:DP:GQ:PL 1:0,52:52:99:1996,0 1:0,6:6:99:167,0 1:0,36:36:99:1293,0 chrX 135431358 . C T 4060.64 PASS AC=3;AF=1;AN=3;DP=116;FS=0;GQ_MEAN=1362.67;GQ_STDDEV=993.87;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.71;SOR=0.763;set=variant2;CSQ=synonymous_variant|ccC/ccT|P|ENSG00000156920|GPR112|ENST00000412101|3/23|||1626/2875|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000156920|GPR112|ENST00000394141|3/23|||1626/2875|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000156920|GPR112|ENST00000287534|4/17|||1768/2804|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000156920|GPR112|ENST00000394143|6/26|||1831/3080|protein_coding,synonymous_variant|ccC/ccT|P|ENSG00000156920|GPR112|ENST00000370652|4/24|||1831/3080|protein_coding GT:AD:DP:GQ:PL 1:0,59:59:99:2119,0 1:0,8:8:99:237,0 1:0,49:49:99:1732,0 chrX 135474420 . C A 1092.64 PASS AC=2;AF=1;AN=2;DP=36;FS=0;GQ_MEAN=560;GQ_STDDEV=74.95;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=32.14;SOR=1.244;set=variant2;CSQ=synonymous_variant|acC/acA|T|ENSG00000156920|GPR112|ENST00000394141|14/23|||2442/2875|protein_coding,synonymous_variant|acC/acA|T|ENSG00000156920|GPR112|ENST00000412101|14/23|||2442/2875|protein_coding,synonymous_variant|acC/acA|T|ENSG00000156920|GPR112|ENST00000394143|17/26|||2647/3080|protein_coding,synonymous_variant|acC/acA|T|ENSG00000156920|GPR112|ENST00000370652|15/24|||2647/3080|protein_coding,synonymous_variant|acC/acA|T|ENSG00000156920|GPR112|ENST00000287534|9/17|||2400/2804|protein_coding GT:AD:DP:GQ:PL 1:0,19:19:99:613,0 .:0,0:.:.:. 1:0,15:15:99:507,0 chrX 135474444 . AGAT A 1836.64 PASS AC=3;AF=1;AN=3;DP=42;FS=0;GQ_MEAN=621.33;GQ_STDDEV=343.37;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.79;SOR=0.788;set=variant;CSQ=inframe_deletion|GAT/-|D/-|ENSG00000156920|GPR112|ENST00000412101|14/23|||2451/2875|protein_coding,inframe_deletion|GAT/-|D/-|ENSG00000156920|GPR112|ENST00000394141|14/23|||2451/2875|protein_coding,inframe_deletion|GAT/-|D/-|ENSG00000156920|GPR112|ENST00000287534|9/17|||2409/2804|protein_coding,inframe_deletion|GAT/-|D/-|ENSG00000156920|GPR112|ENST00000370652|15/24|||2656/3080|protein_coding,inframe_deletion|GAT/-|D/-|ENSG00000156920|GPR112|ENST00000394143|17/26|||2656/3080|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:810,0 1:0,5:5:99:225,0 1:0,19:19:99:829,0 chrX 135480126 . T C 963.64 PASS AC=3;AF=1;AN=3;DP=35;FS=0;GQ_MEAN=330.33;GQ_STDDEV=114.55;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=27.53;SOR=1.148;set=variant2;CSQ=synonymous_variant|ttT/ttC|F|ENSG00000156920|GPR112|ENST00000412101|17/23|||2552/2875|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000156920|GPR112|ENST00000394141|17/23|||2552/2875|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000156920|GPR112|ENST00000287534|12/17|||2510/2804|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000156920|GPR112|ENST00000394143|20/26|||2757/3080|protein_coding,synonymous_variant|ttT/ttC|F|ENSG00000156920|GPR112|ENST00000370652|18/24|||2757/3080|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:234,0 1:0,19:19:99:457,0 1:0,10:10:99:300,0 chrX 135496398 . G A 1883.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=0.822;ClippingRankSum=-0.456;DP=68;FS=0;GQ_MEAN=637;GQ_STDDEV=335.8;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.456;NCC=0;QD=27.7;ReadPosRankSum=-1.369;SOR=0.235;set=variant2;CSQ=synonymous_variant|acG/acA|T|ENSG00000156920|GPR112|ENST00000287534|16/17|||2758/2804|protein_coding,synonymous_variant|acG/acA|T|ENSG00000156920|GPR112|ENST00000370652|23/24|||3039/3080|protein_coding,synonymous_variant|acG/acA|T|ENSG00000156920|GPR112|ENST00000394143|25/26|||3039/3080|protein_coding,synonymous_variant|acG/acA|T|ENSG00000156920|GPR112|ENST00000412101|22/23|||2834/2875|protein_coding,synonymous_variant|acG/acA|T|ENSG00000156920|GPR112|ENST00000394141|22/23|||2834/2875|protein_coding GT:AD:DP:GQ:PL 1:0,31:31:99:995,0 1:1,18:19:99:329,0 1:0,18:18:99:587,0 chrX 135593629 . C T 3805.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-1.733;ClippingRankSum=-0.473;DP=118;FS=0;GQ_MEAN=1277.67;GQ_STDDEV=580.64;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.42;NCC=0;QD=32.25;ReadPosRankSum=-1.313;SOR=0.275;set=variant2;CSQ=synonymous_variant|gaC/gaT|D|ENSG00000102241|HTATSF1|ENST00000535601|10/10|||575/755|protein_coding,synonymous_variant|gaC/gaT|D|ENSG00000102241|HTATSF1|ENST00000218364|9/9|||575/755|protein_coding GT:AD:DP:GQ:PL 1:0,53:53:99:1890,0 1:1,32:33:99:735,0 1:0,32:32:99:1208,0 chrX 135960146 . G GAA 221.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.45;ClippingRankSum=-0.629;DP=41;FS=0;GQ_MEAN=146;GQ_STDDEV=149.91;MLEAC=1;MLEAF=0.5;MQ=46.29;MQ0=0;MQRankSum=-0.274;NCC=1;QD=5.54;ReadPosRankSum=-0.246;SOR=0.668;set=variant;CSQ=intron_variant&NMD_transcript_variant|||ENSG00000147274|RBMX|ENST00000464781||||-/78|nonsense_mediated_decay,intron_variant|||ENSG00000147274|RBMX|ENST00000431446||||-/196|protein_coding,upstream_gene_variant|||ENSG00000147274|RBMX|ENST00000496459|||||processed_transcript,frameshift_variant|-/TT|-/X|ENSG00000147274|RBMX|ENST00000419968|3/8|||107-108/292|protein_coding,frameshift_variant|-/TT|-/X|ENSG00000147274|RBMX|ENST00000320676|4/9|||105-106/391|protein_coding,5_prime_UTR_variant|||ENSG00000147274|RBMX|ENST00000565438|2/7|||-/263|protein_coding,downstream_gene_variant|||ENSG00000206979|SNORD61|ENST00000384252|||||snoRNA,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000147274|RBMX|ENST00000563370|4/4|||-/37|nonsense_mediated_decay,intron_variant&NMD_transcript_variant|||ENSG00000147274|RBMX|ENST00000568578||||-/78|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000147274|RBMX|ENST00000561733|||||processed_transcript,intron_variant|||ENSG00000147274|RBMX|ENST00000570135||||-/256|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000147274|RBMX|ENST00000567262|||||processed_transcript,frameshift_variant|-/TT|-/X|ENSG00000147274|RBMX|ENST00000562646|4/8|||105-106/296|protein_coding,downstream_gene_variant|||ENSG00000147274|RBMX|ENST00000565907|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:17,23:40:99:252,0 0:1,0:1:40:0,40 chrX 137793423 . GC G 133.64 PASS AC=1;AF=1;AN=1;DP=4;FS=0;GQ_MEAN=161;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=33.41;SOR=1.609;set=variant;CSQ=intron_variant|||ENSG00000129682|FGF13|ENST00000441825||||-/226|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000455663||||-/206|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000305414||||-/192|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000370603||||-/255|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000436198||||-/221|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000541469||||-/199|protein_coding,upstream_gene_variant|||ENSG00000226031|FGF13-AS1|ENST00000446383|||||antisense,intron_variant|||ENSG00000129682|FGF13|ENST00000448673||||-/98|protein_coding,5_prime_UTR_variant|||ENSG00000129682|FGF13|ENST00000315930|1/5|||-/245|protein_coding,upstream_gene_variant|||ENSG00000226031|FGF13-AS1|ENST00000438238|||||antisense GT:AD:DP:GQ:PL 1:0,4:4:99:161,0 .:0,0:.:.:. .:0,0:.:.:. chrX 137793449 . C G 46.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=74;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.32;SOR=2.303;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000129682|FGF13|ENST00000315930|1/5|||-/245|protein_coding,upstream_gene_variant|||ENSG00000226031|FGF13-AS1|ENST00000438238|||||antisense,intron_variant|||ENSG00000129682|FGF13|ENST00000448673||||-/98|protein_coding,upstream_gene_variant|||ENSG00000226031|FGF13-AS1|ENST00000446383|||||antisense,intron_variant|||ENSG00000129682|FGF13|ENST00000541469||||-/199|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000436198||||-/221|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000370603||||-/255|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000441825||||-/226|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000455663||||-/206|protein_coding,intron_variant|||ENSG00000129682|FGF13|ENST00000305414||||-/192|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:74:74,0 .:0,0:.:.:. .:0,0:.:.:. chrX 138724725 . G A 1159.64 PASS AC=3;AF=1;AN=3;DP=44;FS=0;GQ_MEAN=395.67;GQ_STDDEV=423.46;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=26.36;SOR=0.99;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000101977|MCF2|ENST00000536274|1/22|||-/821|protein_coding,intron_variant|||ENSG00000101977|MCF2|ENST00000519895||||-/1001|protein_coding,intron_variant|||ENSG00000101977|MCF2|ENST00000414978||||-/985|protein_coding,intron_variant|||ENSG00000101977|MCF2|ENST00000520602||||-/985|protein_coding,intron_variant|||ENSG00000101977|MCF2|ENST00000370578||||-/1070|protein_coding,upstream_gene_variant|||ENSG00000101977|MCF2|ENST00000338585||||-/941|protein_coding,upstream_gene_variant|||ENSG00000101977|MCF2|ENST00000370573||||-/860|protein_coding,5_prime_UTR_variant|||ENSG00000101977|MCF2|ENST00000370576|1/25|||-/925|protein_coding GT:AD:DP:GQ:PL 1:0,4:4:99:130,0 1:0,35:35:99:884,0 1:0,5:5:99:173,0 chrX 138809002 . T C 142.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=170;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.53;SOR=3.611;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000370557|29/29|||-/1113|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000361648|29/29|||-/1119|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000450801|7/7|||-/172|protein_coding,downstream_gene_variant|||ENSG00000101974|ATP11C|ENST00000460773|||||processed_transcript,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000433868|6/6|||-/165|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000327569|30/30|||-/1132|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:170,0 .:0,0:.:.:. chrX 138811003 . G A 972.64 PASS AC=2;AF=1;AN=2;DP=28;FS=0;GQ_MEAN=500;GQ_STDDEV=234.76;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.74;SOR=2.468;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000450801|7/7|||-/172|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101974|ATP11C|ENST00000460773|21/21||||processed_transcript,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000433868|6/6|||-/165|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000327569|30/30|||-/1132|protein_coding,downstream_gene_variant|||ENSG00000101974|ATP11C|ENST00000370543||||-/1128|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000370557|29/29|||-/1113|protein_coding,3_prime_UTR_variant|||ENSG00000101974|ATP11C|ENST00000361648|29/29|||-/1119|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:666,0 .:0,0:.:.:. 1:0,10:10:99:334,0 chrX 138897130 . A C 592.64 PASS AC=2;AF=1;AN=2;DP=18;FS=0;GQ_MEAN=310;GQ_STDDEV=205.06;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.86;SOR=0.804;set=variant2;CSQ=missense_variant|tgT/tgG|C/W|ENSG00000101974|ATP11C|ENST00000327569|5/30|benign(0)|tolerated(1)|114/1132|protein_coding,missense_variant|tgT/tgG|C/W|ENSG00000101974|ATP11C|ENST00000370543|5/29|benign(0)||114/1128|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000101974|ATP11C|ENST00000485626|5/7||||processed_transcript,missense_variant|tgT/tgG|C/W|ENSG00000101974|ATP11C|ENST00000359686|5/29|benign(0)||114/1108|protein_coding,missense_variant|tgT/tgG|C/W|ENSG00000101974|ATP11C|ENST00000361648|5/29|benign(0)|tolerated(1)|114/1119|protein_coding,missense_variant|tgT/tgG|C/W|ENSG00000101974|ATP11C|ENST00000370557|5/29|benign(0)|tolerated(1)|111/1113|protein_coding GT:AD:DP:GQ:PL 1:0,12:12:99:455,0 .:0,0:.:.:. 1:0,5:5:99:165,0 chrX 139866477 . T C 7765.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=-0.577;ClippingRankSum=-0.933;DP=260;FS=6.956;GQ_MEAN=2597.67;GQ_STDDEV=2056.16;MLEAC=3;MLEAF=1;MQ=59.86;MQ0=0;MQRankSum=0.252;NCC=0;QD=29.87;ReadPosRankSum=-0.133;SOR=0.502;set=variant2;CSQ=missense_variant|Ata/Gta|I/V|ENSG00000184258|CDR1|ENST00000370532|1/1|benign(0)|tolerated(1)|19/262|protein_coding GT:AD:DP:GQ:PL 1:1,132:133:99:3859,0 1:0,10:10:99:225,0 1:1,116:117:99:3709,0 chrX 140270418 . T C 224.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=252;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.96;SOR=2.093;set=variant2;CSQ=upstream_gene_variant|||ENSG00000261212|RP3-507I15.2|ENST00000566241|||||sense_overlapping,3_prime_UTR_variant|||ENSG00000182195|LDOC1|ENST00000370526|1/1|||-/146|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182195|LDOC1|ENST00000460721|2/2||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,9:9:99:252,0 .:0,0:.:.:. chrX 140271268 . G C 826.63 PASS AC=1;AF=0.5;AN=2;DP=29;FS=0;GQ_MEAN=478;GQ_STDDEV=535.99;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=31.79;SOR=2.67;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000182195|LDOC1|ENST00000370526|1/1|||-/146|protein_coding,upstream_gene_variant|||ENSG00000182195|LDOC1|ENST00000460721|||||processed_transcript,upstream_gene_variant|||ENSG00000261212|RP3-507I15.2|ENST00000566241|||||sense_overlapping GT:AD:DP:GQ:PL 1:0,26:26:99:857,0 .:0,0:.:.:. 0:3,0:3:99:0,99 chrX 140335742 . G C 1123.64 PASS AC=1;AF=1;AN=1;DP=42;FS=0;GQ_MEAN=1151;MLEAC=1;MLEAF=1;MQ=41.32;MQ0=0;NCC=2;QD=26.75;SOR=0.892;set=variant2;CSQ=missense_variant|Ctg/Gtg|L/V|ENSG00000198573|SPANXC|ENST00000358993|2/2|benign(0.001)||68/97|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,42:42:99:1151,0 .:0,0:.:.:. chrX 140336615 . T A 309.63 PASS AC=1;AF=0.5;AN=2;DP=16;FS=0;GQ_MEAN=189.5;GQ_STDDEV=212.84;MLEAC=1;MLEAF=0.5;MQ=53.29;MQ0=0;NCC=1;QD=20.64;SOR=0.818;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000198573|SPANXC|ENST00000358993|1/2|||-/97|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,15:15:99:340,0 0:1,0:1:39:0,39 chrX 140983064 . G A 1481.64 PASS AC=3;AF=1;AN=3;DP=47;FS=0;GQ_MEAN=503;GQ_STDDEV=165.5;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=32.21;SOR=2.985;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000165509|MAGEC3|ENST00000544766|2/5|||-/346|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000536088||||-/346|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000443323||||-/266|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000165509|MAGEC3|ENST00000298296|5/8|benign(0)|tolerated(0.12)|307/643|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165509|MAGEC3|ENST00000483584|2/5||||processed_transcript,upstream_gene_variant|||ENSG00000165509|MAGEC3|ENST00000409007||||-/346|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000165509|MAGEC3|ENST00000448920|4/4|benign(0.011)||59/126|protein_coding GT:AD:DP:GQ:PL 1:0,16:16:99:622,0 1:0,14:14:99:314,0 1:0,16:16:99:573,0 chrX 140983103 . C T 1719.87 PASS AC=2;AF=0.667;AN=3;DP=81;FS=0;GQ_MEAN=773;GQ_STDDEV=184.24;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.87;SOR=1.214;set=variant2;CSQ=synonymous_variant|Ctg/Ttg|L|ENSG00000165509|MAGEC3|ENST00000448920|4/4|||72/126|protein_coding,upstream_gene_variant|||ENSG00000165509|MAGEC3|ENST00000409007||||-/346|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165509|MAGEC3|ENST00000483584|2/5||||processed_transcript,intron_variant|||ENSG00000165509|MAGEC3|ENST00000443323||||-/266|protein_coding,synonymous_variant|Ctg/Ttg|L|ENSG00000165509|MAGEC3|ENST00000298296|5/8|||320/643|protein_coding,5_prime_UTR_variant|||ENSG00000165509|MAGEC3|ENST00000544766|2/5|||-/346|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000536088||||-/346|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:830,0 1:0,41:41:99:922,0 0:16,0:16:99:0,567 chrX 140983127 . G A 2929.64 PASS AC=3;AF=1;AN=3;DP=100;FS=0;GQ_MEAN=985.67;GQ_STDDEV=188.8;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.3;SOR=1.225;set=variant2;CSQ=intron_variant|||ENSG00000165509|MAGEC3|ENST00000536088||||-/346|protein_coding,5_prime_UTR_variant|||ENSG00000165509|MAGEC3|ENST00000544766|2/5|||-/346|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000443323||||-/266|protein_coding,missense_variant|Gca/Aca|A/T|ENSG00000165509|MAGEC3|ENST00000298296|5/8|possibly_damaging(0.483)|deleterious(0.04)|328/643|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165509|MAGEC3|ENST00000483584|2/5||||processed_transcript,upstream_gene_variant|||ENSG00000165509|MAGEC3|ENST00000409007||||-/346|protein_coding,missense_variant|Gca/Aca|A/T|ENSG00000165509|MAGEC3|ENST00000448920|4/4|possibly_damaging(0.682)||80/126|protein_coding GT:AD:DP:GQ:PL 1:0,29:29:99:1055,0 1:0,48:48:99:1130,0 1:0,23:23:99:772,0 chrX 140984250 . C T 406.87 PASS AC=1;AF=0.333;AN=3;DP=19;FS=0;GQ_MEAN=214;GQ_STDDEV=194.87;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.91;SOR=5.136;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000165509|MAGEC3|ENST00000544766|4/5|||-/346|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000536088||||-/346|protein_coding,5_prime_UTR_variant|||ENSG00000165509|MAGEC3|ENST00000443323|2/3|||-/266|protein_coding,intron_variant|||ENSG00000165509|MAGEC3|ENST00000298296||||-/643|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000165509|MAGEC3|ENST00000483584|4/5||||processed_transcript,intron_variant|||ENSG00000165509|MAGEC3|ENST00000409007||||-/346|protein_coding,downstream_gene_variant|||ENSG00000165509|MAGEC3|ENST00000448920||||-/126|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,99 0:4,0:4:99:0,104 1:0,12:12:99:439,0 chrX 140991741 . TTA T 102.87 PASS AC=1;AF=0.333;AN=3;DP=10;FS=0;GQ_MEAN=110;GQ_STDDEV=22.91;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.29;SOR=2.833;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000155495|MAGEC1|ENST00000285879|1/4|||-/1142|protein_coding,upstream_gene_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:90:0,90 0:4,0:4:99:0,105 1:0,3:3:99:135,0 chrX 140993264 . G A 2978.87 PASS AC=2;AF=0.667;AN=3;DP=110;FS=0;GQ_MEAN=1138.67;GQ_STDDEV=1166.69;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.36;SOR=0.999;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000155495|MAGEC1|ENST00000406005|3/4|||-/209|protein_coding,missense_variant|tGt/tAt|C/Y|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.384)|tolerated_low_confidence(0.08)|25/1142|protein_coding GT:AD:DP:GQ:PL 1:0,74:74:99:2484,0 1:0,21:21:99:527,0 0:14,0:14:99:0,405 chrX 140993642 . C T 993.63 PASS AC=1;AF=0.5;AN=2;DP=54;FS=0;GQ_MEAN=714.5;GQ_STDDEV=437.7;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=34.26;SOR=0.76;set=variant2;CSQ=missense_variant|aCt/aTt|T/I|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.001)|deleterious_low_confidence(0)|151/1142|protein_coding,intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding GT:AD:DP:GQ:PL 1:0,29:29:99:1024,0 .:0,0:.:.:. 0:14,0:14:99:0,405 chrX 140993852 . C G 551.87 PASS AC=1;AF=0.333;AN=3;DP=39;FS=0;GQ_MEAN=287.67;GQ_STDDEV=261.75;MLEAC=1;MLEAF=0.333;MQ=53.96;MQ0=0;NCC=0;QD=27.62;SOR=1.329;set=variant2;CSQ=missense_variant|aCt/aGt|T/S|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0)|tolerated_low_confidence(0.6)|221/1142|protein_coding,intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding GT:AD:DP:GQ:PL 0:15,0:15:88:0,88 0:10,0:10:99:0,191 1:0,14:14:99:584,0 chrX 140993859 . T A 476.87 PASS AC=1;AF=0.333;AN=3;DP=35;FS=0;GQ_MEAN=247.33;GQ_STDDEV=238.54;MLEAC=1;MLEAF=0.333;MQ=54.16;MQ0=0;NCC=0;QD=35.51;SOR=1.27;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,missense_variant|agT/agA|S/R|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.008)|deleterious_low_confidence(0)|223/1142|protein_coding GT:AD:DP:GQ:PL 0:14,0:14:42:0,42 0:10,0:10:99:0,191 1:0,11:11:99:509,0 chrX 140993864 . T C 363.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=0.791;ClippingRankSum=-0.474;DP=34;FS=4.393;GQ_MEAN=222.67;GQ_STDDEV=159.87;MLEAC=1;MLEAF=0.333;MQ=55.81;MQ0=0;MQRankSum=-1.739;NCC=0;QD=33.08;ReadPosRankSum=1.11;SOR=1.447;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,missense_variant|tTt/tCt|F/S|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.008)|deleterious_low_confidence(0.03)|225/1142|protein_coding GT:AD:DP:GQ:PL 0:13,0:13:81:0,81 0:10,0:10:99:0,191 1:1,10:11:99:396,0 chrX 140993877 . C A 211.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=0.742;ClippingRankSum=0.742;DP=26;FS=0;GQ_MEAN=216.5;GQ_STDDEV=36.06;MLEAC=1;MLEAF=0.5;MQ=53.27;MQ0=0;MQRankSum=0.742;NCC=1;QD=30.23;ReadPosRankSum=-0.742;SOR=0.223;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,synonymous_variant|gcC/gcA|A|ENSG00000155495|MAGEC1|ENST00000285879|4/4|||229/1142|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 0:10,0:10:99:0,191 1:1,6:7:99:242,0 chrX 140994037 . C A 247.87 PASS AC=1;AF=0.333;AN=3;DP=21;FS=0;GQ_MEAN=188.67;GQ_STDDEV=81.12;MLEAC=1;MLEAF=0.333;MQ=56.02;MQ0=0;NCC=0;QD=27.54;SOR=1.402;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,missense_variant|Ctt/Att|L/I|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.001)|tolerated_low_confidence(0.16)|283/1142|protein_coding GT:AD:DP:GQ:PL 0:4,0:4:99:0,125 0:8,0:8:99:0,161 1:0,9:9:99:280,0 chrX 140994171 . C G 1629.64 PASS AC=3;AF=1;AN=3;DP=59;FS=0;GQ_MEAN=552.33;GQ_STDDEV=489.79;MLEAC=3;MLEAF=1;MQ=49.1;MQ0=0;NCC=0;QD=27.62;SOR=0.871;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,missense_variant|caC/caG|H/Q|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0)|tolerated_low_confidence(1)|327/1142|protein_coding GT:AD:DP:GQ:PL 1:0,10:10:99:343,0 1:0,43:43:99:1112,0 1:0,6:6:99:202,0 chrX 140994280 . A G 75.87 PASS AC=1;AF=0.333;AN=3;DP=28;FS=0;GQ_MEAN=264.67;GQ_STDDEV=194.96;MLEAC=1;MLEAF=0.333;MQ=57.16;MQ0=0;NCC=0;QD=25.29;SOR=1.179;set=variant2;CSQ=intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding,missense_variant|Act/Gct|T/A|ENSG00000155495|MAGEC1|ENST00000285879|4/4|unknown(0)|tolerated_low_confidence(0.66)|364/1142|protein_coding GT:AD:DP:GQ:PL 0:6,0:6:99:0,203 0:19,0:19:99:0,483 1:0,3:3:99:108,0 chrX 140994591 . C G 2071.87 PASS AC=2;AF=0.667;AN=3;DP=74;FS=0;GQ_MEAN=737.33;GQ_STDDEV=648.26;MLEAC=2;MLEAF=0.667;MQ=50.4;MQ0=0;NCC=0;QD=29.18;SOR=1.042;set=variant2;CSQ=missense_variant|caC/caG|H/Q|ENSG00000155495|MAGEC1|ENST00000285879|4/4|benign(0.227)|tolerated_low_confidence(1)|467/1142|protein_coding,intron_variant|||ENSG00000155495|MAGEC1|ENST00000406005||||-/209|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:701,0 1:0,53:53:99:1403,0 0:3,0:3:99:0,108 chrX 141290865 . C T 2525.64 PASS AC=2;AF=1;AN=2;DP=77;FS=0;GQ_MEAN=1276.5;GQ_STDDEV=70;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=34.13;SOR=1.134;set=variant2;CSQ=synonymous_variant|ccG/ccA|P|ENSG00000046774|MAGEC2|ENST00000247452|3/3|||303/373|protein_coding GT:AD:DP:GQ:PL 1:0,36:36:99:1227,0 .:0,0:.:.:. 1:0,38:38:99:1326,0 chrX 141293039 . T C 471.64 PASS AC=3;AF=1;AN=3;DP=16;FS=0;GQ_MEAN=166.33;GQ_STDDEV=82.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.48;SOR=1.609;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000046774|MAGEC2|ENST00000247452|1/3|||-/373|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:82:82,0 1:0,9:9:99:247,0 1:0,5:5:99:170,0 chrX 142122058 . T G 1041.64 PASS AC=2;AF=1;AN=2;DP=32;FS=0;GQ_MEAN=534.5;GQ_STDDEV=33.23;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=33.6;SOR=1.839;set=variant2;CSQ=intron_variant|||ENSG00000189326|SPANXN4|ENST00000370504||||-/156|protein_coding,3_prime_UTR_variant|||ENSG00000189326|SPANXN4|ENST00000446864|2/2|||-/99|protein_coding GT:AD:DP:GQ:PL 1:0,14:14:99:511,0 .:0,0:.:.:. 1:0,17:17:99:558,0 chrX 142716114 . G A 527.64 PASS AC=1;AF=1;AN=1;DP=22;FS=0;GQ_MEAN=555;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.98;SOR=1.085;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000179542|SLITRK4|ENST00000356928|2/2|||-/837|protein_coding,3_prime_UTR_variant|||ENSG00000179542|SLITRK4|ENST00000381779|2/2|||-/837|protein_coding,3_prime_UTR_variant|||ENSG00000179542|SLITRK4|ENST00000338017|2/2|||-/837|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,22:22:99:555,0 .:0,0:.:.:. chrX 142795225 . G A 548.64 PASS AC=1;AF=1;AN=1;DP=33;FS=0;GQ_MEAN=576;MLEAC=1;MLEAF=1;MQ=55.55;MQ0=0;NCC=2;QD=32.27;SOR=2.179;set=variant2;CSQ=synonymous_variant|gaC/gaT|D|ENSG00000203924|SPANXN2|ENST00000370498|2/2|||151/180|protein_coding GT:AD:DP:GQ:PL 1:0,17:17:99:576,0 .:0,0:.:.:. .:0,0:.:.:. chrX 142804304 . A AT 369.64 PASS AC=1;AF=1;AN=1;DP=12;FS=0;GQ_MEAN=397;MLEAC=1;MLEAF=1;MQ=57.94;MQ0=0;NCC=2;QD=30.8;SOR=1.981;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000203924|SPANXN2|ENST00000370498|1/2|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:397,0 .:0,0:.:.:. chrX 142804326 . C T 387.64 PASS AC=1;AF=1;AN=1;DP=16;FS=0;GQ_MEAN=415;MLEAC=1;MLEAF=1;MQ=57.35;MQ0=0;NCC=2;QD=24.23;SOR=1.244;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000203924|SPANXN2|ENST00000370498|1/2|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,16:16:99:415,0 .:0,0:.:.:. chrX 142804493 . T C 725.64 PASS AC=1;AF=1;AN=1;DP=26;FS=0;GQ_MEAN=753;MLEAC=1;MLEAF=1;MQ=59.6;MQ0=0;NCC=2;QD=27.91;SOR=1.445;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000203924|SPANXN2|ENST00000370498|1/2|||-/180|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:753,0 .:0,0:.:.:. chrX 144337667 . C A 90.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=118;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=30.21;SOR=2.833;set=variant2;CSQ=downstream_gene_variant|||ENSG00000203923|SPANXN1|ENST00000370493||||-/72|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:118,0 .:0,0:.:.:. .:0,0:.:.:. chrX 144902889 . T C 51.63 PASS AC=1;AF=0.5;AN=2;DP=6;FS=0;GQ_MEAN=96.5;GQ_STDDEV=20.51;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=25.82;SOR=2.303;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000447897|2/2|||-/845|protein_coding,5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000428560|1/2|||-/845|protein_coding,5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000370490|1/1|||-/845|protein_coding,5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000434188|1/3|||-/845|protein_coding,5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000335565|3/5|||-/724|protein_coding,5_prime_UTR_variant|||ENSG00000185985|SLITRK2|ENST00000413937|1/3|||-/845|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 0:4,0:4:99:0,111 1:0,2:2:82:82,0 chrX 144904252 . G A 1633.87 PASS AC=1;AF=0.333;AN=3;DP=52;FS=0;GQ_MEAN=626.67;GQ_STDDEV=900.11;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=32.44;SOR=0.874;set=variant2;CSQ=upstream_gene_variant|||ENSG00000221870|TMEM257|ENST00000408967||||-/111|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000413937|3/3|||103/845|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000335565|5/5|||103/724|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000434188|3/3|||103/845|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000447897|2/2|||103/845|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000428560|2/2|||103/845|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185985|SLITRK2|ENST00000370490|1/1|||103/845|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,113 0:3,0:3:99:0,101 1:0,46:46:99:1666,0 chrX 144904882 . T C 5148.64 PASS AC=3;AF=1;AN=3;DP=151;FS=0;GQ_MEAN=1725.33;GQ_STDDEV=1401.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=34.1;SOR=0.818;set=variant2;CSQ=synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000428560|2/2|||313/845|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000370490|1/1|||313/845|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000447897|2/2|||313/845|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000335565|5/5|||313/724|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000434188|3/3|||313/845|protein_coding,upstream_gene_variant|||ENSG00000221870|TMEM257|ENST00000408967||||-/111|protein_coding,synonymous_variant|ccT/ccC|P|ENSG00000185985|SLITRK2|ENST00000413937|3/3|||313/845|protein_coding GT:AD:DP:GQ:PL 1:0,79:79:99:2726,0 1:0,4:4:99:123,0 1:0,68:68:99:2327,0 chrX 146991129 . G T 32.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.731;ClippingRankSum=-0.731;DP=5;FS=0;GQ_MEAN=60;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.731;NCC=2;QD=6.53;ReadPosRankSum=-0.731;SOR=0.223;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000439526||||-/592|protein_coding,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000334557||||-/297|protein_coding,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000370475||||-/632|protein_coding,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000218200||||-/611|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000268066|FMR1-AS1|ENST00000594922|2/2||||antisense,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000370470||||-/590|protein_coding,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000495717|||||processed_transcript,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000370477||||-/582|protein_coding,upstream_gene_variant|||ENSG00000102081|FMR1|ENST00000370471||||-/537|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000268066|FMR1-AS1|ENST00000596112|3/3||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000268066|FMR1-AS1|ENST00000601841|1/1||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000268066|FMR1-AS1|ENST00000598667|2/2||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,4:5:60:60,0 .:0,0:.:.:. chrX 147031538 . C T 511.64 PASS AC=1;AF=1;AN=1;DP=24;FS=0;GQ_MEAN=539;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=24.36;SOR=1.828;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102081|FMR1|ENST00000218200|16/16|||-/611|protein_coding,3_prime_UTR_variant|||ENSG00000102081|FMR1|ENST00000370475|17/17|||-/632|protein_coding,downstream_gene_variant|||ENSG00000236337|FMR1-IT1|ENST00000441414|||||sense_intronic,downstream_gene_variant|||ENSG00000102081|FMR1|ENST00000478848|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102081|FMR1|ENST00000439526|16/16|||-/592|protein_coding,downstream_gene_variant|||ENSG00000102081|FMR1|ENST00000463120|||||processed_transcript,downstream_gene_variant|||ENSG00000102081|FMR1|ENST00000370470||||-/590|protein_coding,3_prime_UTR_variant|||ENSG00000102081|FMR1|ENST00000370477|16/16|||-/582|protein_coding,3_prime_UTR_variant|||ENSG00000102081|FMR1|ENST00000370471|16/16|||-/537|protein_coding,downstream_gene_variant|||ENSG00000102081|FMR1|ENST00000440235||||-/262|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,21:21:99:539,0 .:0,0:.:.:. chrX 147088249 . C T 1271.87 PASS AC=2;AF=0.667;AN=3;DP=48;FS=0;GQ_MEAN=469;GQ_STDDEV=444.76;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=28.91;SOR=1.364;set=variant2;CSQ=downstream_gene_variant|||ENSG00000201285|5S_rRNA|ENST00000364415|||||rRNA,missense_variant|gCa/gTa|A/V|ENSG00000176988|FMR1NB|ENST00000370467|3/6|benign(0)|tolerated(1)|142/255|protein_coding,upstream_gene_variant|||ENSG00000176988|FMR1NB|ENST00000489034||||-/72|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,29:29:99:964,0 1:0,15:15:99:340,0 0:3,0:3:99:0,103 chrX 147582157 . T C 159.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=187;MLEAC=1;MLEAF=1;MQ=50.6;MQ0=0;NCC=2;QD=26.61;SOR=2.303;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370457|1/20|||-/1276|protein_coding,upstream_gene_variant|||ENSG00000155966|AFF2|ENST00000342251||||-/1278|protein_coding,5_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370460|1/21|||-/1311|protein_coding,upstream_gene_variant|||ENSG00000237741|AC002368.4|ENST00000456981|||||antisense,upstream_gene_variant|||ENSG00000155966|AFF2|ENST00000370458||||-/427|protein_coding GT:AD:DP:GQ:PL 1:0,6:6:99:187,0 .:0,0:.:.:. .:0,0:.:.:. chrX 148079639 . A C 1096.64 PASS AC=1;AF=1;AN=1;DP=43;FS=0;GQ_MEAN=1124;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.5;SOR=0.836;set=variant2;CSQ=downstream_gene_variant|||ENSG00000155966|AFF2|ENST00000342251||||-/1278|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370457|20/20|||-/1276|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000286437|18/18|||-/952|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370460|21/21|||-/1311|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,43:43:99:1124,0 .:0,0:.:.:. chrX 148079740 . A C 256.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=284;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=32.08;SOR=1.179;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370457|20/20|||-/1276|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000286437|18/18|||-/952|protein_coding,downstream_gene_variant|||ENSG00000155966|AFF2|ENST00000342251||||-/1278|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370460|21/21|||-/1311|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:284,0 .:0,0:.:.:. chrX 148079877 . T C 1131.64 PASS AC=1;AF=1;AN=1;DP=44;FS=0;GQ_MEAN=1159;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.72;SOR=0.99;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370457|20/20|||-/1276|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000286437|18/18|||-/952|protein_coding,downstream_gene_variant|||ENSG00000155966|AFF2|ENST00000342251||||-/1278|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370460|21/21|||-/1311|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,44:44:99:1159,0 .:0,0:.:.:. chrX 148081451 . A G 113.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=141;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.41;SOR=3.258;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370457|20/20|||-/1276|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000286437|18/18|||-/952|protein_coding,3_prime_UTR_variant|||ENSG00000155966|AFF2|ENST00000370460|21/21|||-/1311|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,4:4:99:141,0 .:0,0:.:.:. chrX 148560611 . G A 50.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=78;MLEAC=1;MLEAF=1;MQ=50.99;MQ0=0;NCC=2;QD=25.32;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000010404|IDS|ENST00000537071||||-/153|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000422081||||-/339|protein_coding,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000541269||||-/339|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000441880|||||processed_transcript,3_prime_UTR_variant|||ENSG00000010404|IDS|ENST00000340855|9/9|||-/550|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:78:78,0 .:0,0:.:.:. .:0,0:.:.:. chrX 148561274 . T C 42.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=70;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.32;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000010404|IDS|ENST00000541269||||-/339|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000441880|||||processed_transcript,3_prime_UTR_variant|||ENSG00000010404|IDS|ENST00000340855|9/9|||-/550|protein_coding,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000537071||||-/153|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000422081||||-/339|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:70:70,0 .:0,0:.:.:. chrX 148561332 . C T 42.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=70;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=14.21;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000010404|IDS|ENST00000537071||||-/153|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000422081||||-/339|protein_coding,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000541269||||-/339|protein_coding,3_prime_UTR_variant|||ENSG00000010404|IDS|ENST00000340855|9/9|||-/550|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000441880|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:70:70,0 .:0,0:.:.:. chrX 148562599 . G A 89.64 PASS AC=1;AF=1;AN=1;DP=6;FS=0;GQ_MEAN=117;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=14.94;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000010404|IDS|ENST00000537071||||-/153|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000422081||||-/339|protein_coding,3_prime_UTR_variant|||ENSG00000010404|IDS|ENST00000340855|9/9|||-/550|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000441880|||||processed_transcript,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000541269||||-/339|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:117,0 .:0,0:.:.:. chrX 148563150 . C T 271.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.992;ClippingRankSum=-1.736;DP=14;FS=0;GQ_MEAN=299;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0;NCC=2;QD=19.4;ReadPosRankSum=1.49;SOR=0.283;set=variant2;CSQ=downstream_gene_variant|||ENSG00000241489|IDS|ENST00000422081||||-/339|protein_coding,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000537071||||-/153|protein_coding,downstream_gene_variant|||ENSG00000010404|IDS|ENST00000541269||||-/339|protein_coding,3_prime_UTR_variant|||ENSG00000010404|IDS|ENST00000340855|9/9|||-/550|protein_coding,downstream_gene_variant|||ENSG00000241489|IDS|ENST00000441880|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,13:14:99:299,0 .:0,0:.:.:. chrX 148622730 . G A 1729.64 PASS AC=3;AF=1;AN=3;DP=60;FS=0;GQ_MEAN=585.67;GQ_STDDEV=178.34;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.83;SOR=1.071;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000423421|1/5|||-/158|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608342|||||antisense,intron_variant|||ENSG00000197620|CXorf40A|ENST00000514208||||-/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609369|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000431214|||||antisense,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000434353|1/6|||-/146|protein_coding,intron_variant|||ENSG00000197620|CXorf40A|ENST00000431132||||-/30|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608355|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000447209|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609314|||||antisense,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000422892||||-/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609161|||||antisense,intron_variant|||ENSG00000197620|CXorf40A|ENST00000450602||||-/158|protein_coding,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000441248|1/4|||-/158|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608616|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609651|||||antisense,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000359293||||-/158|protein_coding,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000423540|1/5|||-/158|protein_coding,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000448332|||||processed_transcript,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000393985|1/5|||-/158|protein_coding,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000428236||||-/96|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000436708|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000541582|||||antisense GT:AD:DP:GQ:PL 1:0,16:16:99:538,0 1:0,32:32:99:783,0 1:0,12:12:99:436,0 chrX 148622745 . T A 1841.64 PASS AC=3;AF=1;AN=3;DP=64;FS=0;GQ_MEAN=623;GQ_STDDEV=127.31;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=28.78;SOR=1.044;set=variant2;CSQ=upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608342|||||antisense,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000423421|1/5|||-/158|protein_coding,intron_variant|||ENSG00000197620|CXorf40A|ENST00000514208||||-/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609369|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000431214|||||antisense,intron_variant|||ENSG00000197620|CXorf40A|ENST00000431132||||-/30|protein_coding,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000434353|1/6|||-/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608355|||||antisense,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000422892||||-/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609314|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000447209|||||antisense,intron_variant|||ENSG00000197620|CXorf40A|ENST00000450602||||-/158|protein_coding,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000441248|1/4|||-/158|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609161|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608616|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609651|||||antisense,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000423540|1/5|||-/158|protein_coding,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000359293||||-/158|protein_coding,5_prime_UTR_variant|||ENSG00000197620|CXorf40A|ENST00000393985|1/5|||-/158|protein_coding,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000448332|||||processed_transcript,upstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000428236||||-/96|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000541582|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000436708|||||antisense GT:AD:DP:GQ:PL 1:0,21:21:99:696,0 1:0,30:30:99:697,0 1:0,13:13:99:476,0 chrX 148627384 . A G 36.64 my_snp_filter AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=64;MLEAC=1;MLEAF=1;MQ=27;MQ0=0;NCC=2;QD=18.32;SOR=2.303;set=FilteredInAll;CSQ=downstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000431132||||-/30|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000434353|4/6|benign(0)||70/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000608355|||||antisense,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000422892|3/5|benign(0)||70/146|protein_coding,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609314|||||antisense,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000441248|3/4|benign(0)||70/158|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000450602|4/5|benign(0)||70/158|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000423421|4/5|benign(0)||70/158|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000514208|4/6|benign(0)||70/146|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000393985|4/5|benign(0)||70/158|protein_coding,downstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000448332|||||processed_transcript,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000428236|3/4|benign(0)||8/96|protein_coding,downstream_gene_variant|||ENSG00000225261|RP5-937E21.8|ENST00000431993|||||antisense,upstream_gene_variant|||ENSG00000241769|LINC00893|ENST00000609651|||||antisense,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000423540|4/5|benign(0)||70/158|protein_coding,missense_variant|Acc/Gcc|T/A|ENSG00000197620|CXorf40A|ENST00000359293|1/2|benign(0)||70/158|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,2:2:64:64,0 .:0,0:.:.:. chrX 148628490 . A T 1138.64 PASS AC=3;AF=1;AN=3;DP=33;FS=0;GQ_MEAN=388.67;GQ_STDDEV=177.18;MLEAC=3;MLEAF=1;MQ=41.01;MQ0=0;NCC=0;QD=34.5;SOR=5.61;set=variant2;CSQ=synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000393985|5/5|||153/158|protein_coding,downstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000431132||||-/30|protein_coding,downstream_gene_variant|||ENSG00000197620|CXorf40A|ENST00000448332|||||processed_transcript,intron_variant|||ENSG00000197620|CXorf40A|ENST00000434353||||-/146|protein_coding,intron_variant|||ENSG00000197620|CXorf40A|ENST00000422892||||-/146|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000428236|4/4|||91/96|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000441248|4/4|||153/158|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000450602|5/5|||153/158|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000423421|5/5|||153/158|protein_coding,downstream_gene_variant|||ENSG00000225261|RP5-937E21.8|ENST00000431993|||||antisense,intron_variant|||ENSG00000197620|CXorf40A|ENST00000514208||||-/146|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000423540|5/5|||153/158|protein_coding,synonymous_variant|ccA/ccT|P|ENSG00000197620|CXorf40A|ENST00000359293|2/2|||153/158|protein_coding GT:AD:DP:GQ:PL 1:0,15:15:99:587,0 1:0,9:9:99:246,0 1:0,9:9:99:333,0 chrX 148678807 . A G 443.64 my_snp_filter AC=1;AF=1;AN=1;DP=19;FS=0;GQ_MEAN=471;MLEAC=1;MLEAF=1;MQ=39.12;MQ0=0;NCC=2;QD=24.65;SOR=0.914;set=FilteredInAll;CSQ=downstream_gene_variant|||ENSG00000155984|TMEM185A|ENST00000502858||||-/223|protein_coding,downstream_gene_variant|||ENSG00000155984|TMEM185A|ENST00000502618||||-/60|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000171129|HSFX2|ENST00000522155||||-/220|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000155984|TMEM185A|ENST00000316916|7/7|||-/350|protein_coding,3_prime_UTR_variant|||ENSG00000155984|TMEM185A|ENST00000536359|6/6|||-/291|protein_coding,downstream_gene_variant|||ENSG00000155984|TMEM185A|ENST00000519015|||||retained_intron,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000155984|TMEM185A|ENST00000513505|4/4|||-/45|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000171129|HSFX2|ENST00000524178||||-/423|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,18:18:99:471,0 .:0,0:.:.:. chrX 148798223 . T C 496.63 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;GQ_MEAN=315.5;GQ_STDDEV=299.11;MLEAC=1;MLEAF=0.5;MQ=55.19;MQ0=0;NCC=1;QD=29.68;SOR=1.765;set=variant2;CSQ=synonymous_variant|ctT/ctC|L|ENSG00000185247|MAGEA11|ENST00000333104|4/4|||330/400|protein_coding,synonymous_variant|ctT/ctC|L|ENSG00000185247|MAGEA11|ENST00000355220|5/5|||359/429|protein_coding,downstream_gene_variant|||ENSG00000185247|MAGEA11|ENST00000412632||||-/295|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000185247|MAGEA11|ENST00000518694|7/7||||retained_intron GT:AD:DP:GQ:PL 0:3,0:3:99:0,104 .:0,0:.:.:. 1:0,14:14:99:527,0 chrX 149013727 . A G 1404.87 PASS AC=1;AF=0.333;AN=3;DP=50;FS=0;GQ_MEAN=545;GQ_STDDEV=772.53;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=32.67;SOR=0.739;set=variant2;CSQ=upstream_gene_variant|||ENSG00000230899|MAGEA8-AS1|ENST00000427671|||||antisense,synonymous_variant|gcA/gcG|A|ENSG00000156009|MAGEA8|ENST00000286482|3/3|||227/318|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000156009|MAGEA8|ENST00000542674|3/3|||227/318|protein_coding,downstream_gene_variant|||ENSG00000156009|MAGEA8|ENST00000493910|||||processed_transcript,downstream_gene_variant|||ENSG00000156009|MAGEA8|ENST00000345830|||||processed_transcript,synonymous_variant|gcA/gcG|A|ENSG00000156009|MAGEA8|ENST00000535454|4/4|||227/318|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,106 0:4,0:4:92:0,92 1:0,43:43:99:1437,0 chrX 149638920 . C T 900.63 PASS AC=1;AF=0.5;AN=2;DP=31;FS=0;GQ_MEAN=517.5;GQ_STDDEV=584.78;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=32.17;SOR=0.836;set=variant2;CSQ=missense_variant|Cca/Tca|P/S|ENSG00000013619|MAMLD1|ENST00000426613|2/6|benign(0.22)|deleterious(0.02)|334/749|protein_coding,missense_variant|Cca/Tca|P/S|ENSG00000013619|MAMLD1|ENST00000370401|4/8|benign(0.184)|deleterious(0.02)|359/774|protein_coding,upstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000455522||||-/214|protein_coding,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000358892||||-/136|protein_coding,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000468306|||||processed_transcript,missense_variant|Cca/Tca|P/S|ENSG00000013619|MAMLD1|ENST00000262858|3/7|benign(0.184)|deleterious(0.02)|359/774|protein_coding,missense_variant|Cca/Tca|P/S|ENSG00000013619|MAMLD1|ENST00000432680|3/5|benign(0.403)|deleterious(0.02)|334/998|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,104 .:0,0:.:.:. 1:0,28:28:99:931,0 chrX 149642019 . A G 1020.87 PASS AC=1;AF=0.333;AN=3;DP=37;FS=0;GQ_MEAN=423.67;GQ_STDDEV=545.02;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.03;SOR=0.826;set=variant2;CSQ=intron_variant|||ENSG00000013619|MAMLD1|ENST00000432680||||-/998|protein_coding,missense_variant|aAc/aGc|N/S|ENSG00000013619|MAMLD1|ENST00000262858|4/7|benign(0.007)|tolerated_low_confidence(0.19)|662/774|protein_coding,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000468306|||||processed_transcript,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000358892||||-/136|protein_coding,intron_variant|||ENSG00000013619|MAMLD1|ENST00000455522||||-/214|protein_coding,missense_variant|aAc/aGc|N/S|ENSG00000013619|MAMLD1|ENST00000370401|5/8|benign(0.007)|tolerated_low_confidence(0.19)|662/774|protein_coding,missense_variant|aAc/aGc|N/S|ENSG00000013619|MAMLD1|ENST00000426613|3/6|benign(0.005)|tolerated_low_confidence(0.17)|637/749|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,109 0:4,0:4:99:0,109 1:0,30:30:99:1053,0 chrX 149680554 . C T 3524.64 PASS AC=3;AF=1;AN=3;DP=106;FS=0;GQ_MEAN=1184;GQ_STDDEV=996.56;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.25;SOR=0.731;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000262858|7/7|||-/774|protein_coding,synonymous_variant|agC/agT|S|ENSG00000013619|MAMLD1|ENST00000432680|5/5|||736/998|protein_coding,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000455522||||-/214|protein_coding,3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000426613|6/6|||-/749|protein_coding,3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000370401|8/8|||-/774|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000013619|MAMLD1|ENST00000464149|2/2||||retained_intron GT:AD:DP:GQ:PL 1:0,59:59:99:1985,0 1:0,2:2:68:68,0 1:0,45:45:99:1499,0 chrX 149681925 . T C 654.64 PASS AC=1;AF=1;AN=1;DP=26;FS=0;GQ_MEAN=682;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.18;SOR=1.22;set=variant2;CSQ=downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000432680||||-/998|protein_coding,3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000262858|7/7|||-/774|protein_coding,downstream_gene_variant|||ENSG00000013619|MAMLD1|ENST00000455522||||-/214|protein_coding,3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000370401|8/8|||-/774|protein_coding,3_prime_UTR_variant|||ENSG00000013619|MAMLD1|ENST00000426613|6/6|||-/749|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000013619|MAMLD1|ENST00000464149|2/2||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:682,0 .:0,0:.:.:. chrX 149931106 . C T 2539.64 PASS AC=3;AF=1;AN=3;DP=86;FS=0;GQ_MEAN=855.67;GQ_STDDEV=558.4;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.88;SOR=1.039;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000485376|16/17|||-/568|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000346693|||||processed_transcript,synonymous_variant|ggC/ggT|G|ENSG00000063601|MTMR1|ENST00000370390|15/16|||634/665|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000370377||||-/262|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000063601|MTMR1|ENST00000544228|15/15|||634/665|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000355149||||-/190|protein_coding,intron_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000488357||||-/405|nonsense_mediated_decay,intron_variant|||ENSG00000063601|MTMR1|ENST00000538506||||-/393|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000063601|MTMR1|ENST00000445323|16/16|||642/673|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000437787||||-/189|protein_coding,synonymous_variant|ggC/ggT|G|ENSG00000063601|MTMR1|ENST00000541925|16/16|||540/571|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1022,0 1:0,10:10:99:233,0 1:0,40:40:99:1312,0 chrX 149933120 . TG T 156.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=184;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.11;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000485376|17/17|||-/568|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000346693|||||processed_transcript,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000466436||||-/213|protein_coding,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000544228|15/15|||-/665|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000370377||||-/262|protein_coding,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000370390|16/16|||-/665|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000541925||||-/571|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000437787||||-/189|protein_coding,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000538506|13/13|||-/393|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000355149||||-/190|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000488357|13/13|||-/405|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000445323|16/16|||-/673|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:184,0 .:0,0:.:.:. chrX 149933341 . T C 1001.64 PASS AC=1;AF=1;AN=1;DP=32;FS=0;GQ_MEAN=1029;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.3;SOR=2.165;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000538506|13/13|||-/393|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000355149||||-/190|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000488357|13/13|||-/405|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000445323|16/16|||-/673|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000541925||||-/571|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000437787||||-/189|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000370377||||-/262|protein_coding,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000370390|16/16|||-/665|protein_coding,3_prime_UTR_variant|||ENSG00000063601|MTMR1|ENST00000544228|15/15|||-/665|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000466436||||-/213|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000346693|||||processed_transcript,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000063601|MTMR1|ENST00000485376|17/17|||-/568|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,32:32:99:1029,0 .:0,0:.:.:. chrX 149936748 . C G 277.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=305;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.36;SOR=0.836;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000355149|8/8|||-/190|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000488357||||-/405|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000538506||||-/393|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000445323||||-/673|protein_coding,3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000437787|8/8|||-/189|protein_coding,downstream_gene_variant|||ENSG00000102181|CD99L2|ENST00000466436||||-/213|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102181|CD99L2|ENST00000346693|12/12||||processed_transcript,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000485376||||-/568|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000370390||||-/665|protein_coding,3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000370377|11/11|||-/262|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000544228||||-/665|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:305,0 .:0,0:.:.:. chrX 149937404 . T C 999.87 PASS AC=2;AF=0.667;AN=3;DP=39;FS=0;GQ_MEAN=380.67;GQ_STDDEV=241.96;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=27.77;SOR=0.804;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000466436|9/9|||-/213|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000485376||||-/568|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102181|CD99L2|ENST00000346693|12/12||||processed_transcript,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000370390||||-/665|protein_coding,3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000370377|11/11|||-/262|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000544228||||-/665|protein_coding,3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000355149|8/8|||-/190|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000538506||||-/393|protein_coding,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000488357||||-/405|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000063601|MTMR1|ENST00000445323||||-/673|protein_coding,3_prime_UTR_variant|||ENSG00000102181|CD99L2|ENST00000437787|8/8|||-/189|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:576,0 1:0,18:18:99:456,0 0:3,0:3:99:0,110 chrX 150157025 . AAT A 189.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=217;MLEAC=1;MLEAF=1;MQ=56.6;MQ0=0;NCC=2;QD=34.23;SOR=3.611;set=variant;CSQ=downstream_gene_variant|||ENSG00000029993|HMGB3|ENST00000448905||||-/200|protein_coding,upstream_gene_variant|||ENSG00000230508|RPL19P21|ENST00000424919|||||processed_pseudogene,downstream_gene_variant|||ENSG00000029993|HMGB3|ENST00000419110||||-/188|protein_coding,downstream_gene_variant|||ENSG00000029993|HMGB3|ENST00000455596||||-/193|protein_coding,3_prime_UTR_variant|||ENSG00000029993|HMGB3|ENST00000325307|5/5|||-/200|protein_coding,downstream_gene_variant|||ENSG00000029993|HMGB3|ENST00000430118||||-/153|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:217,0 .:0,0:.:.:. chrX 150349533 . G A 3265.87 PASS AC=2;AF=0.667;AN=3;DP=102;FS=0;GQ_MEAN=1135;GQ_STDDEV=1541.97;MLEAC=2;MLEAF=0.667;MQ=60.92;MQ0=0;NCC=0;QD=33.33;SOR=0.734;set=variant2;CSQ=upstream_gene_variant|||ENSG00000234696|GPR50-AS1|ENST00000454196|||||antisense,missense_variant|aGt/aAt|S/N|ENSG00000102195|GPR50|ENST00000218316|2/2|benign(0.395)|deleterious_low_confidence(0)|493/617|protein_coding,upstream_gene_variant|||ENSG00000269993|AF003625.3|ENST00000602313|||||lincRNA GT:AD:DP:GQ:PL 1:0,82:82:99:2908,0 1:0,16:16:99:390,0 0:3,0:3:99:0,107 chrX 150349557 . CCACCACTGGCCA C 4227.87 PASS AC=2;AF=0.667;AN=3;DP=104;FS=0;GQ_MEAN=1455.67;GQ_STDDEV=1511.24;MLEAC=2;MLEAF=0.667;MQ=61.02;MQ0=0;NCC=0;QD=10.9;SOR=1.099;set=variant;CSQ=upstream_gene_variant|||ENSG00000269993|AF003625.3|ENST00000602313|||||lincRNA,inframe_deletion|ccCACCACTGGCCAc/ccc|PTTGH/P|ENSG00000102195|GPR50|ENST00000218316|2/2|||501-505/617|protein_coding,upstream_gene_variant|||ENSG00000234696|GPR50-AS1|ENST00000454196|||||antisense GT:AD:DP:GQ:PL 1:0,71:71:99:3089,0 1:0,26:26:99:1171,0 0:3,0:3:99:0,107 chrX 150349649 . A G 3603.87 PASS AC=2;AF=0.667;AN=3;DP=120;FS=0;GQ_MEAN=1247.67;GQ_STDDEV=1605.01;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.8;SOR=1.066;set=variant2;CSQ=missense_variant|Act/Gct|T/A|ENSG00000102195|GPR50|ENST00000218316|2/2|benign(0)|tolerated_low_confidence(0.56)|532/617|protein_coding,upstream_gene_variant|||ENSG00000269993|AF003625.3|ENST00000602313|||||lincRNA,upstream_gene_variant|||ENSG00000234696|GPR50-AS1|ENST00000454196|||||antisense GT:AD:DP:GQ:PL 1:0,95:95:99:3083,0 1:0,22:22:99:553,0 0:3,0:3:99:0,107 chrX 150573743 . G GTTAAA 467.64 PASS AC=2;AF=1;AN=2;DP=11;FS=0;GQ_MEAN=247.5;GQ_STDDEV=222.74;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25.51;SOR=1.802;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000160131|VMA21|ENST00000330374|3/3|||-/101|protein_coding,downstream_gene_variant|||ENSG00000160131|VMA21|ENST00000370361||||-/156|protein_coding,downstream_gene_variant|||ENSG00000160131|VMA21|ENST00000477649|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,9:9:99:405,0 1:0,2:2:90:90,0 chrX 150732081 . T C 204.64 PASS AC=2;AF=1;AN=2;DP=7;FS=0;GQ_MEAN=116;GQ_STDDEV=16.97;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=29.23;SOR=1.609;set=variant2;CSQ=upstream_gene_variant|||ENSG00000166049|PASD1|ENST00000464219|||||retained_intron,upstream_gene_variant|||ENSG00000166049|PASD1|ENST00000370357||||-/773|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:104,0 1:0,4:4:99:128,0 .:0,0:.:.:. chrX 150840185 . T C 792.87 PASS AC=2;AF=0.667;AN=3;DP=29;FS=0;GQ_MEAN=309;GQ_STDDEV=374.23;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.49;SOR=1.697;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166049|PASD1|ENST00000464219|13/15||||retained_intron,synonymous_variant|ggT/ggC|G|ENSG00000166049|PASD1|ENST00000370357|13/16|||457/773|protein_coding,downstream_gene_variant|||ENSG00000239429|RP11-45D17.1|ENST00000413236|||||unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,22:22:99:741,0 1:0,4:4:84:84,0 0:3,0:3:99:0,102 chrX 150840916 . C T 527.87 PASS AC=1;AF=0.333;AN=3;DP=24;FS=0;GQ_MEAN=251;GQ_STDDEV=269.22;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=29.33;SOR=1.493;set=variant2;CSQ=downstream_gene_variant|||ENSG00000239429|RP11-45D17.1|ENST00000413236|||||unprocessed_pseudogene,synonymous_variant|Ctg/Ttg|L|ENSG00000166049|PASD1|ENST00000370357|14/16|||567/773|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166049|PASD1|ENST00000464219|14/15||||retained_intron GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:2,0:2:67:0,67 1:0,18:18:99:560,0 chrX 150844702 . G A 576.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-1.734;ClippingRankSum=0.347;DP=24;FS=0;GQ_MEAN=363;GQ_STDDEV=345.07;MLEAC=1;MLEAF=0.5;MQ=60.54;MQ0=0;MQRankSum=1.04;NCC=1;QD=28.83;ReadPosRankSum=1.21;SOR=0.941;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166049|PASD1|ENST00000464219|15/15||||retained_intron,3_prime_UTR_variant|||ENSG00000166049|PASD1|ENST00000370357|16/16|||-/773|protein_coding GT:AD:DP:GQ:PL 1:1,19:20:99:607,0 .:0,0:.:.:. 0:3,0:3:99:0,119 chrX 150844738 . CTTAT C 699.87 PASS AC=2;AF=0.667;AN=3;DP=20;FS=0;GQ_MEAN=283.67;GQ_STDDEV=250.54;MLEAC=2;MLEAF=0.667;MQ=62.65;MQ0=0;NCC=0;QD=30.88;SOR=2.179;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000166049|PASD1|ENST00000370357|16/16|||-/773|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000166049|PASD1|ENST00000464219|15/15||||retained_intron GT:AD:DP:GQ:PL 1:0,13:13:99:572,0 1:0,4:4:99:160,0 0:3,0:3:99:0,119 chrX 150869267 . A G 985.87 PASS AC=2;AF=0.667;AN=3;DP=30;FS=0;GQ_MEAN=374;GQ_STDDEV=488.59;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.61;SOR=1.101;set=variant2;CSQ=downstream_gene_variant|||ENSG00000130032|PRRG3|ENST00000448726||||-/52|protein_coding,intron_variant|||ENSG00000130032|PRRG3|ENST00000448324||||-/91|protein_coding,missense_variant|aAc/aGc|N/S|ENSG00000130032|PRRG3|ENST00000538575|4/4|benign(0)|tolerated(1)|153/231|protein_coding,missense_variant|aAc/aGc|N/S|ENSG00000130032|PRRG3|ENST00000370353|4/4|benign(0)|tolerated(1)|153/231|protein_coding,downstream_gene_variant|||ENSG00000130032|PRRG3|ENST00000370354||||-/102|protein_coding GT:AD:DP:GQ:PL 1:0,25:25:99:938,0 1:0,2:2:80:80,0 0:3,0:3:99:0,104 chrX 150869697 . G A 569.64 PASS AC=2;AF=1;AN=2;DP=25;FS=0;GQ_MEAN=298.5;GQ_STDDEV=317.49;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=22.79;SOR=1.609;set=variant2;CSQ=downstream_gene_variant|||ENSG00000130032|PRRG3|ENST00000448726||||-/52|protein_coding,intron_variant|||ENSG00000130032|PRRG3|ENST00000448324||||-/91|protein_coding,3_prime_UTR_variant|||ENSG00000130032|PRRG3|ENST00000538575|4/4|||-/231|protein_coding,3_prime_UTR_variant|||ENSG00000130032|PRRG3|ENST00000370353|4/4|||-/231|protein_coding,downstream_gene_variant|||ENSG00000130032|PRRG3|ENST00000370354||||-/102|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:74:74,0 1:0,23:23:99:523,0 .:0,0:.:.:. chrX 150884620 . C T 2457.87 PASS AC=2;AF=0.667;AN=3;DP=97;FS=0;GQ_MEAN=865.33;GQ_STDDEV=693.43;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.15;SOR=0.78;set=variant2;CSQ=missense_variant|gCg/gTg|A/V|ENSG00000147378|FATE1|ENST00000417321|1/4|benign(0.001)|deleterious(0)|2/80|protein_coding,missense_variant|gCg/gTg|A/V|ENSG00000147378|FATE1|ENST00000370350|1/5|benign(0.001)|deleterious(0)|10/183|protein_coding GT:AD:DP:GQ:PL 1:0,30:30:99:1025,0 1:0,64:64:99:1465,0 0:3,0:3:99:0,106 chrX 150891336 . C T 598.87 PASS AC=2;AF=0.667;AN=3;DP=23;FS=0;GQ_MEAN=246;GQ_STDDEV=205.46;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.94;SOR=1.721;set=variant2;CSQ=downstream_gene_variant|||ENSG00000147378|FATE1|ENST00000417321||||-/80|protein_coding,3_prime_UTR_variant|||ENSG00000147378|FATE1|ENST00000370350|5/5|||-/183|protein_coding GT:AD:DP:GQ:PL 1:0,13:13:99:482,0 1:0,7:7:99:149,0 0:3,0:3:99:0,107 chrX 150911796 . G A 1914.87 PASS AC=1;AF=0.333;AN=3;DP=67;FS=0;GQ_MEAN=729.33;GQ_STDDEV=1054.63;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.01;SOR=0.836;set=variant2;CSQ=missense_variant|cGc/cAc|R/H|ENSG00000183862|CNGA2|ENST00000329903|6/6|benign(0.209)|deleterious(0.01)|274/664|protein_coding GT:AD:DP:GQ:PL 0:5,0:5:99:0,135 0:4,0:4:99:0,106 1:0,58:58:99:1947,0 chrX 150912962 . G A 993.87 PASS AC=1;AF=0.333;AN=3;DP=36;FS=0;GQ_MEAN=421.33;GQ_STDDEV=523.9;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=25.23;SOR=0.765;set=variant2;CSQ=missense_variant|Gag/Aag|E/K|ENSG00000183862|CNGA2|ENST00000329903|6/6|benign(0)|tolerated_low_confidence(0.5)|663/664|protein_coding GT:AD:DP:GQ:PL 0:5,0:5:99:0,135 0:4,0:4:99:0,103 1:0,27:27:99:1026,0 chrX 151092126 . C G 1178.87 PASS AC=1;AF=0.333;AN=3;DP=40;FS=0;GQ_MEAN=478.67;GQ_STDDEV=634.22;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=32.31;SOR=0.752;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000431971|3/3|||-/241|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000416020|2/2|||-/230|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000360243|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000393920|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000441865|3/3|||-/241|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000448295|3/3|||-/217|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000370337|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000430273|3/3|||-/241|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000393921|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000370335|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000276344|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000370340|3/3|||-/317|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000425182|3/3|||-/217|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000457310|3/3|||-/241|protein_coding,5_prime_UTR_variant|||ENSG00000147381|MAGEA4|ENST00000431963|4/4|||-/171|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,110 0:4,0:4:99:0,115 1:0,33:33:99:1211,0 chrX 151092220 . A G 851.87 PASS AC=1;AF=0.333;AN=3;DP=31;FS=0;GQ_MEAN=369.67;GQ_STDDEV=445.43;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=28.4;SOR=1.051;set=variant2;CSQ=synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000431963|4/4|||28/171|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000457310|3/3|||28/241|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000425182|3/3|||28/217|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000370335|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000370340|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000276344|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000430273|3/3|||28/241|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000393921|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000448295|3/3|||28/217|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000370337|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000441865|3/3|||28/241|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000431971|3/3|||28/241|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000416020|2/2|||28/230|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000360243|3/3|||28/317|protein_coding,synonymous_variant|gcA/gcG|A|ENSG00000147381|MAGEA4|ENST00000393920|3/3|||28/317|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,110 0:4,0:4:99:0,115 1:0,24:24:99:884,0 chrX 151092653 . G A 2007.87 PASS AC=1;AF=0.333;AN=3;DP=71;FS=0;GQ_MEAN=755;GQ_STDDEV=1112.85;MLEAC=1;MLEAF=0.333;MQ=59.64;MQ0=0;NCC=0;QD=31.87;SOR=0.859;set=variant2;CSQ=missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000370335|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000370340|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000276344|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000425182|3/3|benign(0.002)|tolerated(1)|173/217|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000457310|3/3|benign(0.002)|tolerated(1)|173/241|protein_coding,downstream_gene_variant|||ENSG00000147381|MAGEA4|ENST00000431963||||-/171|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000431971|3/3|benign(0.002)|tolerated(1)|173/241|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000360243|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000416020|2/2|benign(0.002)|tolerated(1)|173/230|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000393920|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000441865|3/3|benign(0.002)|tolerated(1)|173/241|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000370337|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000448295|3/3|benign(0.002)|tolerated(1)|173/217|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000430273|3/3|benign(0.002)|tolerated(1)|173/241|protein_coding,missense_variant|Gcc/Acc|A/T|ENSG00000147381|MAGEA4|ENST00000393921|3/3|benign(0.002)|tolerated(1)|173/317|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,110 0:4,0:4:99:0,115 1:0,63:63:99:2040,0 chrX 151122248 . T C 278.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=306;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.43;SOR=0.836;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370328|9/9|||-/506|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000462018|||||processed_transcript,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000393914||||-/139|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000476016|||||retained_intron,3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370325|9/9|||-/365|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000441219||||-/43|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000489333|||||retained_intron,downstream_gene_variant|||ENSG00000264120|AF274855.1|ENST00000582865|||||miRNA,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000495862|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000483564|4/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000486255|3/3||||retained_intron,downstream_gene_variant|||ENSG00000207621|MIR224|ENST00000384889|||||miRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:306,0 .:0,0:.:.:. chrX 151122596 . T A 52.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=80;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.32;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000462018|||||processed_transcript,3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370328|9/9|||-/506|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000393914||||-/139|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000495862|||||retained_intron,downstream_gene_variant|||ENSG00000264120|AF274855.1|ENST00000582865|||||miRNA,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000489333|||||retained_intron,3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370325|9/9|||-/365|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000476016|||||retained_intron,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000441219||||-/43|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000207621|MIR224|ENST00000384889|||||miRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000483564|4/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000486255|3/3||||retained_intron GT:AD:DP:GQ:PL 1:0,2:2:80:80,0 .:0,0:.:.:. .:0,0:.:.:. chrX 151122772 . A G 201.64 PASS AC=1;AF=1;AN=1;DP=9;FS=0;GQ_MEAN=229;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.21;SOR=1.863;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000393914||||-/139|protein_coding,3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370328|9/9|||-/506|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000462018|||||processed_transcript,downstream_gene_variant|||ENSG00000207621|MIR224|ENST00000384889|||||miRNA,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000486255|3/3||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000483564|4/4||||processed_transcript,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000495862|||||retained_intron,3_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000370325|9/9|||-/365|protein_coding,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000476016|||||retained_intron,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000441219||||-/43|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000489333|||||retained_intron,downstream_gene_variant|||ENSG00000264120|AF274855.1|ENST00000582865|||||miRNA GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:229,0 .:0,0:.:.:. chrX 151138179 . A C 2362.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.57;ClippingRankSum=0.443;DP=85;FS=3.854;GQ_MEAN=796.67;GQ_STDDEV=196.4;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=-0.04;NCC=0;QD=27.8;ReadPosRankSum=0.04;SOR=0.864;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000491339|||||retained_intron,missense_variant|Tcc/Gcc|S/A|ENSG00000102287|GABRE|ENST00000370328|3/9|benign(0.187)|tolerated(0.15)|102/506|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000465405|2/2||||retained_intron,5_prime_UTR_variant|||ENSG00000102287|GABRE|ENST00000393914|4/8|||-/139|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102287|GABRE|ENST00000474932|1/3||||retained_intron,missense_variant|Tcc/Gcc|S/A|ENSG00000102287|GABRE|ENST00000370325|3/9|benign(0.038)||102/365|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102287|GABRE|ENST00000441219|4/8|||-/43|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102287|GABRE|ENST00000417300||||-/43|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,23:23:99:775,0 1:1,42:43:99:1003,0 1:0,19:19:99:612,0 chrX 151282610 . G A 191.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=219;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.96;SOR=1.863;set=variant2;CSQ=downstream_gene_variant|||ENSG00000242520|MAGEA5|ENST00000446757|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,8:8:99:219,0 .:0,0:.:.:. chrX 151282862 . G A 619.63 PASS AC=1;AF=0.5;AN=2;DP=27;FS=0;GQ_MEAN=344.5;GQ_STDDEV=432.04;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=24.79;SOR=0.77;set=variant2;CSQ=downstream_gene_variant|||ENSG00000242520|MAGEA5|ENST00000446757|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,25:25:99:650,0 0:1,0:1:39:0,39 chrX 151283004 . G C 475.64 PASS AC=3;AF=1;AN=3;DP=15;FS=0;GQ_MEAN=167.67;GQ_STDDEV=45.21;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.71;SOR=1.911;set=variant2;CSQ=downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,downstream_gene_variant|||ENSG00000242520|MAGEA5|ENST00000446757|||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,3:3:99:116,0 1:0,7:7:99:187,0 1:0,5:5:99:200,0 chrX 151283108 . T C 441.87 PASS AC=2;AF=0.667;AN=3;DP=18;FS=0;GQ_MEAN=194.67;GQ_STDDEV=86.56;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.46;SOR=0.818;set=variant2;CSQ=downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,8:8:99:283,0 1:0,7:7:99:191,0 0:3,0:3:99:0,110 chrX 151283336 . T C 679.87 PASS AC=1;AF=0.333;AN=3;DP=34;FS=0;GQ_MEAN=375.67;GQ_STDDEV=306.53;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.99;SOR=1.127;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 0:9,0:9:99:0,303 0:5,0:5:99:0,112 1:0,20:20:99:712,0 chrX 151283436 . ATTATC A 937.87 PASS AC=1;AF=0.333;AN=3;DP=36;FS=0;GQ_MEAN=461.67;GQ_STDDEV=450.47;MLEAC=1;MLEAF=0.333;MQ=60.49;MQ0=0;NCC=0;QD=25.58;SOR=2.737;set=variant;CSQ=downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 0:9,0:9:99:0,303 0:5,0:5:99:0,112 1:0,22:22:99:970,0 chrX 151283447 . C G 1799.87 PASS AC=2;AF=0.667;AN=3;DP=76;FS=0;GQ_MEAN=898.67;GQ_STDDEV=620.73;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.61;SOR=1.358;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene,downstream_gene_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript GT:AD:DP:GQ:PL 1:0,43:43:99:1536,0 1:0,9:9:99:296,0 0:24,0:24:99:0,864 chrX 151283567 . A T 3240.64 PASS AC=3;AF=1;AN=3;DP=96;FS=0;GQ_MEAN=1089.33;GQ_STDDEV=516.74;MLEAC=3;MLEAF=1;MQ=57.11;MQ0=0;NCC=0;QD=33.76;SOR=0.823;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|4/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|3/3||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,31:31:99:1170,0 1:0,20:20:99:537,0 1:0,45:45:99:1561,0 chrX 151283599 . T G 3400.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.6;ClippingRankSum=-1.317;DP=107;FS=0;GQ_MEAN=1142.67;GQ_STDDEV=452.34;MLEAC=3;MLEAF=1;MQ=57.11;MQ0=0;MQRankSum=-0.208;NCC=0;QD=31.78;ReadPosRankSum=-0.208;SOR=0.238;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|3/3||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|4/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,41:41:99:1426,0 1:1,24:25:99:621,0 1:0,41:41:99:1381,0 chrX 151283627 . G A 1825.87 PASS AC=2;AF=0.667;AN=3;DP=60;FS=0;GQ_MEAN=661.67;GQ_STDDEV=517.46;MLEAC=2;MLEAF=0.667;MQ=58.98;MQ0=0;NCC=0;QD=32.6;SOR=0.922;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|3/3||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000446757|1/1||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000242520|MAGEA5|ENST00000427663|3/3||||transcribed_unprocessed_pseudogene,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|4/4||||processed_transcript GT:AD:DP:GQ:PL 1:0,31:31:99:1160,0 1:0,25:25:99:698,0 0:4,0:4:99:0,127 chrX 151303393 . C T 2717.64 PASS AC=2;AF=1;AN=2;DP=77;FS=0;GQ_MEAN=1372.5;GQ_STDDEV=181.73;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=27.3;SOR=0.719;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000427322||||-/161|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000577437|||||processed_transcript,missense_variant|Gtc/Atc|V/I|ENSG00000124260|MAGEA10|ENST00000244096|5/5|benign(0.003)|tolerated(1)|234/369|protein_coding,downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000579960||||-/58|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,missense_variant|Gtc/Atc|V/I|ENSG00000124260|MAGEA10|ENST00000370323|4/4|benign(0.003)|tolerated(1)|234/369|protein_coding,downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000444834||||-/184|protein_coding,upstream_gene_variant|||ENSG00000231937|RP11-329E24.6|ENST00000453915|||||antisense,downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000583480||||-/71|protein_coding GT:AD:DP:GQ:PL 1:0,43:43:99:1501,0 .:0,0:.:.:. 1:0,34:34:99:1244,0 chrX 151303596 . C T 4017.64 PASS AC=3;AF=1;AN=3;DP=120;FS=0;GQ_MEAN=1348.33;GQ_STDDEV=622.13;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.48;SOR=0.95;set=variant2;CSQ=downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000583480||||-/71|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000124260|MAGEA10|ENST00000444834|5/5|benign(0.019)|tolerated(1)|166/184|protein_coding,upstream_gene_variant|||ENSG00000231937|RP11-329E24.6|ENST00000453915|||||antisense,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000583636|||||processed_transcript,missense_variant|aGa/aAa|R/K|ENSG00000124260|MAGEA10|ENST00000370323|4/4|benign(0.019)|tolerated(1)|166/369|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000509345|||||processed_transcript,downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000579960||||-/58|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000266560|RP11-1007I13.4|ENST00000577437|||||processed_transcript,downstream_gene_variant|||ENSG00000124260|MAGEA10|ENST00000427322||||-/161|protein_coding,missense_variant|aGa/aAa|R/K|ENSG00000124260|MAGEA10|ENST00000244096|5/5|benign(0.019)|tolerated(1)|166/369|protein_coding GT:AD:DP:GQ:PL 1:0,54:54:99:1963,0 1:0,28:28:99:719,0 1:0,38:38:99:1363,0 chrX 151619708 . T G 1285.64 PASS AC=1;AF=1;AN=1;DP=51;FS=0;GQ_MEAN=1313;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.21;SOR=0.732;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000011677|GABRA3|ENST00000370314|1/10|||-/492|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,51:51:99:1313,0 .:0,0:.:.:. chrX 151821277 . T A 2206.87 PASS AC=1;AF=0.333;AN=3;DP=72;FS=0;GQ_MEAN=807.67;GQ_STDDEV=1239.75;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=33.44;SOR=0.957;set=variant2;CSQ=missense_variant|Ttt/Att|F/I|ENSG00000147402|GABRQ|ENST00000370306|9/9|benign(0)||478/632|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,113 0:2,0:2:71:0,71 1:0,66:66:99:2239,0 chrX 151899355 . T C 705.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=733;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.14;SOR=1.22;set=variant2;CSQ=upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000583763|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000535353|||||transcribed_unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393869|3/3|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000452779||||-/78|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000361211||||-/27|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370287||||-/78|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000357916|2/2|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370291||||-/73|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393900|3/3|||-/314|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:733,0 .:0,0:.:.:. chrX 151899760 . A G 449.64 PASS AC=2;AF=1;AN=2;DP=16;FS=0;GQ_MEAN=238.5;GQ_STDDEV=224.15;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=29.98;SOR=1.473;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393869|3/3|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000452779||||-/78|protein_coding,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000583763|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000535353|||||transcribed_unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000357916|2/2|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370287||||-/78|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000361211||||-/27|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393900|3/3|||-/314|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370291||||-/73|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:397,0 1:0,2:2:80:80,0 chrX 151899789 . G A 81.87 PASS AC=2;AF=0.667;AN=3;DP=7;FS=0;GQ_MEAN=75.33;GQ_STDDEV=37;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=20.47;SOR=1.609;set=variant2;CSQ=upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000583763|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000535353|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000452779||||-/78|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393869|3/3|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000361211||||-/27|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000357916|2/2|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370287||||-/78|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393900|3/3|||-/314|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370291||||-/73|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:76:76,0 1:0,2:2:38:38,0 0:3,0:3:99:0,112 chrX 151899818 . C T 127.87 PASS AC=2;AF=0.667;AN=3;DP=9;FS=0;GQ_MEAN=98.33;GQ_STDDEV=31.9;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=25.57;SOR=1.022;set=variant2;CSQ=upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000361211||||-/27|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000357916|2/2|||-/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370287||||-/78|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393900|3/3|||-/314|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370291||||-/73|protein_coding,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000583763|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000535353|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000452779||||-/78|protein_coding,3_prime_UTR_variant|||ENSG00000213401|MAGEA12|ENST00000393869|3/3|||-/314|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:83:83,0 1:0,3:3:77:77,0 0:4,0:4:99:0,135 chrX 151899913 . T C 803.87 PASS AC=2;AF=0.667;AN=3;DP=31;FS=0;GQ_MEAN=316.33;GQ_STDDEV=176.5;MLEAC=2;MLEAF=0.667;MQ=59.42;MQ0=0;NCC=0;QD=29.77;SOR=1.781;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript,synonymous_variant|ggA/ggG|G|ENSG00000213401|MAGEA12|ENST00000393900|3/3|||296/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370291||||-/73|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000213401|MAGEA12|ENST00000357916|2/2|||296/314|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000370287||||-/78|protein_coding,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000361211||||-/27|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000198930|CSAG1|ENST00000452779||||-/78|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000213401|MAGEA12|ENST00000393869|3/3|||296/314|protein_coding,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000583763|||||transcribed_unprocessed_pseudogene,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000535353|||||transcribed_unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,10:10:99:406,0 1:0,17:17:99:430,0 0:3,0:3:99:0,113 chrX 151904488 . C A 897.63 PASS AC=1;AF=0.5;AN=2;DP=38;FS=0;GQ_MEAN=482;GQ_STDDEV=630.74;MLEAC=1;MLEAF=0.5;MQ=47.36;MQ0=0;NCC=1;QD=24.26;SOR=1.27;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000198930|CSAG1|ENST00000452779|2/4|||-/78|protein_coding,upstream_gene_variant|||ENSG00000213401|MAGEA12|ENST00000393869||||-/314|protein_coding,5_prime_UTR_variant|||ENSG00000198930|CSAG1|ENST00000370291|3/4|||-/73|protein_coding,upstream_gene_variant|||ENSG00000213401|MAGEA12|ENST00000393900||||-/314|protein_coding,upstream_gene_variant|||ENSG00000242599|CSAG4|ENST00000361201|||||processed_transcript,5_prime_UTR_variant|||ENSG00000198930|CSAG1|ENST00000370287|3/5|||-/78|protein_coding,upstream_gene_variant|||ENSG00000213401|MAGEA12|ENST00000357916||||-/314|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000198930|CSAG1|ENST00000361211|2/4|||-/27|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,37:37:99:928,0 0:1,0:1:36:0,36 chrX 152018832 . T G 1481.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.24;ClippingRankSum=-0.744;DP=49;FS=4.025;GQ_MEAN=503;GQ_STDDEV=186.95;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.49;NCC=0;QD=30.87;ReadPosRankSum=1.49;SOR=1.009;set=variant2;CSQ=synonymous_variant|ggT/ggG|G|ENSG00000147383|NSDHL|ENST00000370274|3/8|||44/373|protein_coding,synonymous_variant|ggT/ggG|G|ENSG00000147383|NSDHL|ENST00000432467|4/8|||44/254|protein_coding,synonymous_variant|ggT/ggG|G|ENSG00000147383|NSDHL|ENST00000440023|4/9|||44/373|protein_coding GT:AD:DP:GQ:PL 1:0,14:14:99:518,0 1:1,13:14:99:309,0 1:0,20:20:99:682,0 chrX 152225379 . C A 1547.63 PASS AC=1;AF=0.5;AN=2;DP=56;FS=0;GQ_MEAN=848.5;GQ_STDDEV=1031.67;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=29.76;SOR=1.747;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000370265|2/3|||-/455|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000183837|PNMA3|ENST00000424805|2/3|||-/463|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000447306|2/2|||-/463|protein_coding,upstream_gene_variant|||ENSG00000183837|PNMA3|ENST00000370264||||-/463|protein_coding,upstream_gene_variant|||ENSG00000229979|U82670.9|ENST00000421099|||||processed_pseudogene GT:AD:DP:GQ:PL 0:3,0:3:99:0,119 .:0,0:.:.:. 1:0,52:52:99:1578,0 chrX 152226542 . T C 1593.64 PASS AC=3;AF=1;AN=3;DP=44;FS=0;GQ_MEAN=540.33;GQ_STDDEV=298.9;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=29.75;SOR=1.23;set=variant2;CSQ=missense_variant&NMD_transcript_variant|gTg/gCg|V/A|ENSG00000183837|PNMA3|ENST00000424805|2/3|benign(0)||377/463|nonsense_mediated_decay,missense_variant|gTg/gCg|V/A|ENSG00000183837|PNMA3|ENST00000370265|2/3|benign(0)||377/455|protein_coding,missense_variant|gTg/gCg|V/A|ENSG00000183837|PNMA3|ENST00000370264|1/1|benign(0)||377/463|protein_coding,missense_variant|gTg/gCg|V/A|ENSG00000183837|PNMA3|ENST00000447306|2/2|benign(0)||377/463|protein_coding GT:AD:DP:GQ:PL 1:0,21:21:99:815,0 1:0,7:7:99:222,0 1:0,16:16:99:584,0 chrX 152227581 . AAGG A 197.64 PASS AC=1;AF=1;AN=1;DP=5;FS=0;GQ_MEAN=225;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=30.04;SOR=1.022;set=variant;CSQ=intron_variant&NMD_transcript_variant|||ENSG00000183837|PNMA3|ENST00000424805||||-/463|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000370265|3/3|||-/455|protein_coding,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000447306|2/2|||-/463|protein_coding,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000370264|1/1|||-/463|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:225,0 .:0,0:.:.:. chrX 152227929 . C T 978.64 PASS AC=1;AF=1;AN=1;DP=41;FS=0;GQ_MEAN=1006;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.87;SOR=0.954;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000183837|PNMA3|ENST00000424805|3/3|||-/463|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000370265|3/3|||-/455|protein_coding,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000447306|2/2|||-/463|protein_coding,downstream_gene_variant|||ENSG00000183837|PNMA3|ENST00000370264||||-/463|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,41:41:99:1006,0 .:0,0:.:.:. chrX 152228447 . G A 332.63 PASS AC=1;AF=0.5;AN=2;DP=17;FS=0;GQ_MEAN=201.5;GQ_STDDEV=228.4;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=22.18;SOR=0.818;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000447306|2/2|||-/463|protein_coding,downstream_gene_variant|||ENSG00000183837|PNMA3|ENST00000370264||||-/463|protein_coding,3_prime_UTR_variant|||ENSG00000183837|PNMA3|ENST00000370265|3/3|||-/455|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000183837|PNMA3|ENST00000424805|3/3|||-/463|nonsense_mediated_decay GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,15:15:99:363,0 0:1,0:1:40:0,40 chrX 152481928 . T C 812.63 PASS AC=1;AF=0.5;AN=2;DP=32;FS=0;GQ_MEAN=441.5;GQ_STDDEV=567.81;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=27.09;SOR=1.329;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000198681|MAGEA1|ENST00000356661|3/3|||-/309|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,30:30:99:843,0 0:1,0:1:40:0,40 chrX 152482017 . G C 468.87 PASS AC=2;AF=0.667;AN=3;DP=18;FS=0;GQ_MEAN=201.67;GQ_STDDEV=92.93;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.26;SOR=1.911;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000198681|MAGEA1|ENST00000356661|3/3|||-/309|protein_coding GT:AD:DP:GQ:PL 1:0,8:8:99:289,0 1:0,7:7:99:212,0 0:3,0:3:99:0,104 chrX 152482796 . C T 2398.87 PASS AC=2;AF=0.667;AN=3;DP=76;FS=0;GQ_MEAN=845;GQ_STDDEV=1225.88;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.86;SOR=0.72;set=variant2;CSQ=missense_variant|cGa/cAa|R/Q|ENSG00000198681|MAGEA1|ENST00000356661|3/3|benign(0.041)|tolerated(0.25)|72/309|protein_coding GT:AD:DP:GQ:PL 1:0,66:66:99:2260,0 1:0,7:7:99:171,0 0:3,0:3:99:0,104 chrX 152482917 . T C 2482.87 PASS AC=2;AF=0.667;AN=3;DP=87;FS=0;GQ_MEAN=873;GQ_STDDEV=954.3;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.56;SOR=0.954;set=variant2;CSQ=missense_variant|Acc/Gcc|T/A|ENSG00000198681|MAGEA1|ENST00000356661|3/3|benign(0.001)|tolerated(1)|32/309|protein_coding GT:AD:DP:GQ:PL 1:0,61:61:99:1941,0 1:0,23:23:99:574,0 0:3,0:3:99:0,104 chrX 152483030 . G A 1841.87 PASS AC=2;AF=0.667;AN=3;DP=79;FS=0;GQ_MEAN=659.33;GQ_STDDEV=500.62;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=25.58;SOR=1.002;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000198681|MAGEA1|ENST00000356661|3/3|||-/309|protein_coding GT:AD:DP:GQ:PL 1:0,23:23:99:798,0 1:0,49:49:99:1076,0 0:3,0:3:99:0,104 chrX 152613112 . C T 2958.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=-1.209;ClippingRankSum=0.49;DP=88;FS=0;GQ_MEAN=1493;GQ_STDDEV=379.01;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.425;NCC=1;QD=34.81;ReadPosRankSum=-1.079;SOR=0.286;set=variant2;CSQ=upstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000438239|||||processed_transcript,upstream_gene_variant|||ENSG00000239037|snoU13|ENST00000459572|||||snoRNA,synonymous_variant|tgC/tgT|C|ENSG00000063587|ZNF275|ENST00000440091|4/4|||353/459|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000063587|ZNF275|ENST00000370249|2/2|||270/376|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000063587|ZNF275|ENST00000421401|4/4|||323/429|protein_coding,splice_region_variant&synonymous_variant|tgC/tgT|C|ENSG00000063587|ZNF275|ENST00000370251|4/5|||323/329|protein_coding GT:AD:DP:GQ:PL 1:1,52:53:99:1761,0 .:0,0:.:.:. 1:0,32:32:99:1225,0 chrX 152616741 . A T 493.64 PASS AC=1;AF=1;AN=1;DP=22;FS=0;GQ_MEAN=521;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.51;SOR=1.508;set=variant2;CSQ=upstream_gene_variant|||ENSG00000239037|snoU13|ENST00000459572|||||snoRNA,upstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000438239|||||processed_transcript,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000370249|2/2|||-/376|protein_coding,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000440091|4/4|||-/459|protein_coding,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000421401|4/4|||-/429|protein_coding,upstream_gene_variant|||ENSG00000232249|LL0XNC01-37G1.2|ENST00000428521|||||unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000370251|5/5|||-/329|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,21:21:99:521,0 .:0,0:.:.:. chrX 152616952 . A G 486.64 PASS AC=2;AF=1;AN=2;DP=18;FS=0;GQ_MEAN=257;GQ_STDDEV=294.16;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=27.04;SOR=1.179;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000440091|4/4|||-/459|protein_coding,downstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000370249||||-/376|protein_coding,upstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000438239|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000239037|snoU13|ENST00000459572|1/1||||snoRNA,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000370251|5/5|||-/329|protein_coding,upstream_gene_variant|||ENSG00000232249|LL0XNC01-37G1.2|ENST00000428521|||||unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000421401|4/4|||-/429|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:49:49,0 1:0,16:16:99:465,0 .:0,0:.:.:. chrX 152616983 . G C 280.64 PASS AC=2;AF=1;AN=2;DP=10;FS=0;GQ_MEAN=154;GQ_STDDEV=148.49;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=28.06;SOR=1.085;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000239037|snoU13|ENST00000459572|1/1||||snoRNA,upstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000438239|||||processed_transcript,downstream_gene_variant|||ENSG00000063587|ZNF275|ENST00000370249||||-/376|protein_coding,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000440091|4/4|||-/459|protein_coding,upstream_gene_variant|||ENSG00000232249|LL0XNC01-37G1.2|ENST00000428521|||||unprocessed_pseudogene,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000421401|4/4|||-/429|protein_coding,3_prime_UTR_variant|||ENSG00000063587|ZNF275|ENST00000370251|5/5|||-/329|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:49:49,0 1:0,8:8:99:259,0 .:0,0:.:.:. chrX 152771509 . C T 257.64 PASS AC=2;AF=1;AN=2;DP=7;FS=0;GQ_MEAN=142.5;GQ_STDDEV=23.33;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=30.5;SOR=4.174;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182492|BGN|ENST00000492658|1/3||||processed_transcript,synonymous_variant|agC/agT|S|ENSG00000182492|BGN|ENST00000331595|4/8|||180/368|protein_coding,synonymous_variant|agC/agT|S|ENSG00000182492|BGN|ENST00000431891|4/5|||197/238|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182492|BGN|ENST00000472615|4/8||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182492|BGN|ENST00000480756|4/8||||processed_transcript GT:AD:DP:GQ:PL 1:0,3:3:99:126,0 .:0,0:.:.:. 1:0,4:4:99:159,0 chrX 152774745 . A G 286.64 PASS AC=2;AF=1;AN=2;DP=13;FS=0;GQ_MEAN=157;GQ_STDDEV=114.55;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.06;SOR=0.859;set=variant2;CSQ=downstream_gene_variant|||ENSG00000182492|BGN|ENST00000492658|||||processed_transcript,3_prime_UTR_variant|||ENSG00000182492|BGN|ENST00000331595|8/8|||-/368|protein_coding,downstream_gene_variant|||ENSG00000182492|BGN|ENST00000431891||||-/238|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182492|BGN|ENST00000480756|8/8||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000182492|BGN|ENST00000472615|8/8||||processed_transcript GT:AD:DP:GQ:PL 1:0,2:2:76:76,0 1:0,9:9:99:238,0 .:0,0:.:.:. chrX 152815089 . A G 2816.64 PASS AC=3;AF=1;AN=3;DP=86;FS=0;GQ_MEAN=948;GQ_STDDEV=590.38;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.14;SOR=0.765;set=variant2;CSQ=synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000393842|9/20|||477/1154|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000370181|8/20|||477/1159|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000263519|9/20|||491/1220|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000349466|10/21|||491/1220|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000359149|9/21|||491/1173|protein_coding,synonymous_variant|ggA/ggG|G|ENSG00000067842|ATP2B3|ENST00000370186|9/21|||477/1159|protein_coding GT:AD:DP:GQ:PL 1:0,39:39:99:1407,0 1:0,12:12:99:282,0 1:0,34:34:99:1155,0 chrX 152847291 . T C 1120.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=1148;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.14;SOR=0.846;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000263519|20/20|||-/1220|protein_coding,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370181|20/20|||-/1159|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000349466||||-/1220|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000359149||||-/1173|protein_coding,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370186|21/21|||-/1159|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000496610|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:1148,0 .:0,0:.:.:. chrX 152847301 . G C 1120.64 PASS AC=1;AF=1;AN=1;DP=27;FS=0;GQ_MEAN=1148;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.3;SOR=0.846;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370181|20/20|||-/1159|protein_coding,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000263519|20/20|||-/1220|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000496610|||||processed_transcript,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370186|21/21|||-/1159|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000349466||||-/1220|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000359149||||-/1173|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:1148,0 .:0,0:.:.:. chrX 152847488 . T G 314.64 PASS AC=1;AF=1;AN=1;DP=12;FS=0;GQ_MEAN=342;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.22;SOR=1.445;set=variant2;CSQ=downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000349466||||-/1220|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000359149||||-/1173|protein_coding,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370186|21/21|||-/1159|protein_coding,downstream_gene_variant|||ENSG00000067842|ATP2B3|ENST00000496610|||||processed_transcript,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000263519|20/20|||-/1220|protein_coding,3_prime_UTR_variant|||ENSG00000067842|ATP2B3|ENST00000370181|20/20|||-/1159|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:342,0 .:0,0:.:.:. chrX 152864477 . G GC 3632.64 PASS AC=3;AF=1;AN=3;DP=121;FS=0;GQ_MEAN=1220;GQ_STDDEV=1027.77;MLEAC=3;MLEAF=1;MQ=53.09;MQ0=0;NCC=0;QD=33.33;SOR=1.885;set=variant;CSQ=frameshift_variant&splice_region_variant|ggc/ggGc|G/GX|ENSG00000147382|FAM58A|ENST00000406277|2/7|||17/246|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000428722|1/3||||processed_transcript,intron_variant|||ENSG00000147382|FAM58A|ENST00000482182||||-/141|protein_coding,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000562749|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000465867|1/5||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000276345|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000569906|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370175|1/5||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370171|1/5||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000470284|1/4||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370173|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000429336||||-/94|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000440428||||-/121|protein_coding GT:AD:DP:GQ:PL 1:0,65:65:99:2217,0 1:0,5:5:99:164,0 1:0,39:39:99:1279,0 chrX 152864513 . G GC 2261.64 PASS AC=2;AF=1;AN=2;DP=71;FS=0;GQ_MEAN=1144.5;GQ_STDDEV=183.14;MLEAC=2;MLEAF=1;MQ=50.89;MQ0=0;NCC=1;QD=34.79;SOR=3.511;set=variant;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370175|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000569906|||||antisense,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000276345|1/5||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000465867|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000562749|||||antisense,intron_variant|||ENSG00000147382|FAM58A|ENST00000482182||||-/141|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000428722|||||processed_transcript,coding_sequence_variant|||ENSG00000147382|FAM58A|ENST00000406277||||-/246|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000440428||||-/121|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370173|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000429336||||-/94|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000470284|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370171|1/5||||processed_transcript GT:AD:DP:GQ:PL 1:0,36:36:99:1274,0 .:0,0:.:.:. 1:0,29:29:99:1015,0 chrX 152864609 . G GC 214.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=242;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=28.48;SOR=3.912;set=variant;CSQ=upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000370171|||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000470284|||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000429336||||-/94|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000370173|||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000440428||||-/121|protein_coding,5_prime_UTR_variant|||ENSG00000147382|FAM58A|ENST00000406277|1/7|||-/246|protein_coding,intron_variant|||ENSG00000147382|FAM58A|ENST00000482182||||-/141|protein_coding,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000428722|||||processed_transcript,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000562749|||||antisense,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000276345|||||processed_transcript,upstream_gene_variant|||ENSG00000147382|FAM58A|ENST00000465867|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147382|FAM58A|ENST00000370175|1/5||||processed_transcript,upstream_gene_variant|||ENSG00000260081|RP11-66N11.8|ENST00000569906|||||antisense GT:AD:DP:GQ:PL 1:0,6:6:99:242,0 .:0,0:.:.:. .:0,0:.:.:. chrX 152916023 . T G 1200.64 PASS AC=1;AF=1;AN=1;DP=25;FS=0;GQ_MEAN=1228;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=29.58;SOR=1.609;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000370167|4/4|||-/384|protein_coding,downstream_gene_variant|||ENSG00000130829|DUSP9|ENST00000477033|||||processed_transcript,3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000342782|4/4|||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,25:25:99:1228,0 .:0,0:.:.:. chrX 152916030 . G A 1225.64 PASS AC=1;AF=1;AN=1;DP=35;FS=0;GQ_MEAN=1253;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=27.13;SOR=1.002;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000370167|4/4|||-/384|protein_coding,downstream_gene_variant|||ENSG00000130829|DUSP9|ENST00000477033|||||processed_transcript,3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000342782|4/4|||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,35:35:99:1253,0 .:0,0:.:.:. chrX 152916112 . C CCACAGGG 1036.64 PASS AC=1;AF=1;AN=1;DP=29;FS=0;GQ_MEAN=1064;MLEAC=1;MLEAF=1;MQ=59.71;MQ0=0;NCC=2;QD=15.87;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000342782|4/4|||-/384|protein_coding,downstream_gene_variant|||ENSG00000130829|DUSP9|ENST00000477033|||||processed_transcript,3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000370167|4/4|||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,28:28:99:1064,0 .:0,0:.:.:. chrX 152916122 . C CAGTCCCGCCCCTGTCCCCA 734.64 PASS AC=1;AF=1;AN=1;DP=15;FS=0;GQ_MEAN=762;MLEAC=1;MLEAF=1;MQ=59.44;MQ0=0;NCC=2;QD=7.73;SOR=1.911;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000370167|4/4|||-/384|protein_coding,downstream_gene_variant|||ENSG00000130829|DUSP9|ENST00000477033|||||processed_transcript,3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000342782|4/4|||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,15:15:99:762,0 .:0,0:.:.:. chrX 152916236 . A AG 47.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=75;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.82;SOR=0.693;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000370167|4/4|||-/384|protein_coding,downstream_gene_variant|||ENSG00000130829|DUSP9|ENST00000477033|||||processed_transcript,3_prime_UTR_variant|||ENSG00000130829|DUSP9|ENST00000342782|4/4|||-/384|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. .:0,0:.:.:. 1:0,2:2:75:75,0 chrX 152939728 . C T 1593.63 PASS AC=1;AF=0.5;AN=2;DP=50;FS=0;GQ_MEAN=879.5;GQ_STDDEV=1052.88;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=34.64;SOR=1.329;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000370145||||-/360|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000411968||||-/82|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000489536|||||retained_intron,splice_donor_variant|||ENSG00000130822|PNCK|ENST00000370142||||-/366|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000340888||||-/343|protein_coding,intron_variant|||ENSG00000130822|PNCK|ENST00000418241||||-/94|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000422811||||-/224|protein_coding,intron_variant|||ENSG00000130822|PNCK|ENST00000423545||||-/42|protein_coding,intron_variant|||ENSG00000130822|PNCK|ENST00000458354||||-/42|protein_coding,splice_donor_variant&non_coding_transcript_variant|||ENSG00000130822|PNCK|ENST00000488168|||||retained_intron,intron_variant|||ENSG00000130822|PNCK|ENST00000425526||||-/42|protein_coding,intron_variant|||ENSG00000130822|PNCK|ENST00000419804||||-/42|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130822|PNCK|ENST00000462280|1/2||||processed_transcript,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000463548|||||retained_intron,5_prime_UTR_variant|||ENSG00000130822|PNCK|ENST00000393831|1/12|||-/366|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000466662|||||retained_intron,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000439087||||-/226|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000473680|||||retained_intron,downstream_gene_variant|||ENSG00000130822|PNCK|ENST00000460106|||||processed_transcript,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000434652||||-/86|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000433470||||-/99|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000475172|||||processed_transcript,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000472324|||||retained_intron,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000370150||||-/343|protein_coding,5_prime_UTR_variant|||ENSG00000130822|PNCK|ENST00000447676|1/12|||-/426|protein_coding,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000465303|||||retained_intron,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000466638|||||retained_intron,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000466074|||||retained_intron,intron_variant&non_coding_transcript_variant|||ENSG00000130822|PNCK|ENST00000488994|||||retained_intron,upstream_gene_variant|||ENSG00000130822|PNCK|ENST00000438984||||-/81|protein_coding GT:AD:DP:GQ:PL 0:4,0:4:99:0,135 .:0,0:.:.:. 1:0,46:46:99:1624,0 chrX 152969507 . C T 965.87 PASS AC=2;AF=0.667;AN=3;DP=40;FS=0;GQ_MEAN=373;GQ_STDDEV=251.5;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.1;SOR=1.27;set=variant2;CSQ=synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000345046|5/8|||128/246|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000430088|4/4|||128/138|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000416815|5/6|||128/182|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000441714|5/8|||128/246|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000429550|5/6|||128/187|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000423827|5/6|||128/178|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000442093|5/6|||128/188|protein_coding,synonymous_variant|acG/acA|T|ENSG00000185825|BCAP31|ENST00000458587|5/8|||195/313|protein_coding GT:AD:DP:GQ:PL 1:0,11:11:99:374,0 1:0,26:26:99:624,0 0:3,0:3:99:0,121 chrX 152989830 . A C 219.64 PASS AC=1;AF=1;AN=1;DP=10;FS=0;GQ_MEAN=247;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.96;SOR=1.085;set=variant2;CSQ=upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000468947|||||processed_transcript,5_prime_UTR_variant|||ENSG00000185825|BCAP31|ENST00000345046|1/8|||-/246|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000430088||||-/138|protein_coding,upstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000370129||||-/227|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000423827||||-/178|protein_coding,intron_variant|||ENSG00000185825|BCAP31|ENST00000429550||||-/187|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000458587||||-/313|protein_coding,5_prime_UTR_variant|||ENSG00000185825|BCAP31|ENST00000442093|1/6|||-/188|protein_coding,5_prime_UTR_variant|||ENSG00000185825|BCAP31|ENST00000441714|1/8|||-/246|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000416815||||-/182|protein_coding,upstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000218104||||-/745|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,10:10:99:247,0 .:0,0:.:.:. chrX 152990663 . C T 1287.87 PASS AC=1;AF=0.333;AN=3;DP=49;FS=0;GQ_MEAN=519.33;GQ_STDDEV=693.58;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=31.41;SOR=0.954;set=variant2;CSQ=upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000430088||||-/138|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000468947|||||processed_transcript,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000345046||||-/246|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000442093||||-/188|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000458587||||-/313|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000423827||||-/178|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000429550||||-/187|protein_coding,upstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000370129||||-/227|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000416815||||-/182|protein_coding,5_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|1/10|||-/745|protein_coding,upstream_gene_variant|||ENSG00000185825|BCAP31|ENST00000441714||||-/246|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,103 0:5,0:5:99:0,135 1:0,41:41:99:1320,0 chrX 153005605 . G A 487.87 PASS AC=1;AF=0.333;AN=3;DP=23;FS=0;GQ_MEAN=245.33;GQ_STDDEV=237.97;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=28.7;SOR=1.371;set=variant2;CSQ=synonymous_variant|ctG/ctA|L|ENSG00000101986|ABCD1|ENST00000443684|5/6|||184/223|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,synonymous_variant|ctG/ctA|L|ENSG00000101986|ABCD1|ENST00000218104|6/10|||516/745|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,101 0:3,0:3:99:0,115 1:0,17:17:99:520,0 chrX 153009197 . G C 269.63 PASS AC=1;AF=0.5;AN=2;DP=15;FS=0;GQ_MEAN=207.5;GQ_STDDEV=130.81;MLEAC=1;MLEAF=0.5;MQ=54.88;MQ0=0;NCC=1;QD=26.96;SOR=0.693;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding GT:AD:DP:GQ:PL 0:4,0:4:99:0,115 .:0,0:.:.:. 1:0,10:10:99:300,0 chrX 153010059 . G T 1771.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=-1.117;ClippingRankSum=-2.471;DP=162;FS=1.442;GQ_MEAN=899.5;GQ_STDDEV=1202.79;MLEAC=2;MLEAF=1;MQ=51.46;MQ0=0;MQRankSum=-5.075;NCC=1;QD=11;ReadPosRankSum=0.204;SOR=0.561;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:40,119:159:99:1750,0 1:0,2:2:49:49,0 chrX 153010090 . G A 2218.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=-2.686;ClippingRankSum=0.437;DP=146;FS=0.706;GQ_MEAN=1123;GQ_STDDEV=1460.88;MLEAC=2;MLEAF=1;MQ=51.53;MQ0=0;MQRankSum=-7.522;NCC=1;QD=15.2;ReadPosRankSum=0.138;SOR=0.79;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:38,106:144:99:2156,0 1:0,2:2:90:90,0 chrX 153010092 . G A 2218.64 PASS AC=2;AF=1;AN=2;BaseQRankSum=-0.537;ClippingRankSum=-0.37;DP=139;FS=1.55;GQ_MEAN=1123;GQ_STDDEV=1460.88;MLEAC=2;MLEAF=1;MQ=51.17;MQ0=0;MQRankSum=-7.992;NCC=1;QD=15.96;ReadPosRankSum=0.87;SOR=0.905;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:39,98:137:99:2156,0 1:0,2:2:90:90,0 chrX 153010137 . C T 75.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-2.381;ClippingRankSum=0.589;DP=30;FS=0;GQ_MEAN=103;MLEAC=1;MLEAF=1;MQ=49.33;MQ0=0;MQRankSum=-3.889;NCC=2;QD=2.61;ReadPosRankSum=-1.249;SOR=0.498;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:9,20:29:99:103,0 .:0,0:.:.:. chrX 153010149 . G A 149.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.134;ClippingRankSum=-1.803;DP=22;FS=0;GQ_MEAN=177;MLEAC=1;MLEAF=1;MQ=49.49;MQ0=0;MQRankSum=-3.806;NCC=2;QD=6.8;ReadPosRankSum=0.267;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:9,13:22:99:177,0 .:0,0:.:.:. chrX 153010154 . G A 172.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.59;ClippingRankSum=-0.059;DP=15;FS=0;GQ_MEAN=200;MLEAC=1;MLEAF=1;MQ=48.05;MQ0=0;MQRankSum=-3.241;NCC=2;QD=11.51;ReadPosRankSum=-0.059;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:6,9:15:99:200,0 .:0,0:.:.:. chrX 153010158 . A G 152.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=0.667;ClippingRankSum=-0.933;DP=14;FS=0;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=47.08;MQ0=0;MQRankSum=-3.067;NCC=2;QD=10.9;ReadPosRankSum=-0.667;SOR=1.445;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:5,9:14:99:180,0 .:0,0:.:.:. chrX 153010162 . C T 152.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.667;ClippingRankSum=-0.933;DP=14;FS=0;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=47.08;MQ0=0;MQRankSum=-3.067;NCC=2;QD=10.9;ReadPosRankSum=-0.8;SOR=1.445;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:5,9:14:99:180,0 .:0,0:.:.:. chrX 153010165 . C T 152.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-0.825;ClippingRankSum=0.143;DP=11;FS=3.424;GQ_MEAN=180;MLEAC=1;MLEAF=1;MQ=48.76;MQ0=0;MQRankSum=-2.637;NCC=2;QD=13.88;ReadPosRankSum=0.387;SOR=2.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:5,6:11:99:180,0 .:0,0:.:.:. chrX 153010166 . C G 107.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=1.19;ClippingRankSum=0.717;DP=11;FS=3.424;GQ_MEAN=135;MLEAC=1;MLEAF=1;MQ=48.76;MQ0=0;MQRankSum=-2.637;NCC=2;QD=9.79;ReadPosRankSum=0.466;SOR=2.179;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:5,6:11:99:135,0 .:0,0:.:.:. chrX 153010169 . T C 62.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=2.38;ClippingRankSum=-1.568;DP=10;FS=3.979;GQ_MEAN=90;MLEAC=1;MLEAF=1;MQ=47.49;MQ0=0;MQRankSum=-2.383;NCC=2;QD=6.26;ReadPosRankSum=-0.365;SOR=2.584;set=variant2;CSQ=downstream_gene_variant|||ENSG00000101986|ABCD1|ENST00000443684||||-/223|protein_coding,3_prime_UTR_variant|||ENSG00000101986|ABCD1|ENST00000218104|10/10|||-/745|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense GT:AD:DP:GQ:PL .:0,0:.:.:. 1:4,6:10:90:90,0 .:0,0:.:.:. chrX 153032658 . G A 917.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-0.4;ClippingRankSum=0.933;DP=33;FS=3.979;GQ_MEAN=354.67;GQ_STDDEV=443.08;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=0;NCC=0;QD=30.6;ReadPosRankSum=0.267;SOR=1.014;set=variant2;CSQ=missense_variant|Gcc/Acc|A/T|ENSG00000198753|PLXNB3|ENST00000538966|4/37|benign(0.009)|tolerated(0.16)|149/1932|protein_coding,intron_variant|||ENSG00000198753|PLXNB3|ENST00000538543||||-/224|protein_coding,intron_variant|||ENSG00000198753|PLXNB3|ENST00000538282||||-/988|protein_coding,intron_variant|||ENSG00000198753|PLXNB3|ENST00000538776||||-/1562|protein_coding,upstream_gene_variant|||ENSG00000232725|U52111.14|ENST00000434284|||||antisense,missense_variant|Gcc/Acc|A/T|ENSG00000198753|PLXNB3|ENST00000361971|3/36|benign(0.013)|tolerated(0.15)|126/1909|protein_coding,upstream_gene_variant|||ENSG00000232725|U52111.14|ENST00000416854|||||antisense GT:AD:DP:GQ:PL 1:1,25:26:99:866,0 1:0,4:4:84:84,0 0:3,0:3:99:0,114 chrX 153049535 . A G 3683.64 PASS AC=3;AF=1;AN=3;DP=119;FS=0;GQ_MEAN=1237;GQ_STDDEV=621.6;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.22;SOR=1.227;set=variant2;CSQ=downstream_gene_variant|||ENSG00000198753|PLXNB3|ENST00000361971||||-/1909|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000184343|SRPK3|ENST00000370104|10/15|||337/566|protein_coding,downstream_gene_variant|||ENSG00000198753|PLXNB3|ENST00000538776||||-/1562|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000444450||||-/285|protein_coding,downstream_gene_variant|||ENSG00000198753|PLXNB3|ENST00000472415|||||processed_transcript,upstream_gene_variant|||ENSG00000184343|SRPK3|ENST00000458681||||-/129|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000427365||||-/322|protein_coding,downstream_gene_variant|||ENSG00000184343|SRPK3|ENST00000430541||||-/205|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000444338||||-/199|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000454076||||-/211|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000495356|||||processed_transcript,intron_variant|||ENSG00000184343|SRPK3|ENST00000370100||||-/492|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000184343|SRPK3|ENST00000489426|16/21|||405/634|protein_coding,downstream_gene_variant|||ENSG00000198753|PLXNB3|ENST00000538966||||-/1932|protein_coding,intron_variant|||ENSG00000184343|SRPK3|ENST00000393786||||-/533|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000461215|||||processed_transcript,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000370092||||-/380|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000370093||||-/340|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000184343|SRPK3|ENST00000370101|10/15|||338/567|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000497043|||||processed_transcript,intron_variant|||ENSG00000184343|SRPK3|ENST00000370108||||-/534|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000217901||||-/393|protein_coding,downstream_gene_variant|||ENSG00000198753|PLXNB3|ENST00000469190|||||processed_transcript GT:AD:DP:GQ:PL 1:0,52:52:99:1665,0 1:0,21:21:99:524,0 1:0,45:45:99:1522,0 chrX 153050984 . G A 825.87 PASS AC=1;AF=0.333;AN=3;DP=32;FS=0;GQ_MEAN=358.67;GQ_STDDEV=432.53;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.41;SOR=2.124;set=variant2;CSQ=downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000427365||||-/322|protein_coding,downstream_gene_variant|||ENSG00000184343|SRPK3|ENST00000458681||||-/129|protein_coding,downstream_gene_variant|||ENSG00000184343|SRPK3|ENST00000370104||||-/566|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000444450||||-/285|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000444338||||-/199|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000495356|||||processed_transcript,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000454076||||-/211|protein_coding,downstream_gene_variant|||ENSG00000184343|SRPK3|ENST00000430541||||-/205|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000370092||||-/380|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000461215|||||processed_transcript,3_prime_UTR_variant|||ENSG00000184343|SRPK3|ENST00000393786|16/16|||-/533|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000370093||||-/340|protein_coding,3_prime_UTR_variant|||ENSG00000184343|SRPK3|ENST00000370100|16/16|||-/492|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000491235|||||processed_transcript,3_prime_UTR_variant|||ENSG00000184343|SRPK3|ENST00000489426|21/21|||-/634|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000217901||||-/393|protein_coding,3_prime_UTR_variant|||ENSG00000184343|SRPK3|ENST00000370101|15/15|||-/567|protein_coding,3_prime_UTR_variant|||ENSG00000184343|SRPK3|ENST00000370108|16/16|||-/534|protein_coding,downstream_gene_variant|||ENSG00000067829|IDH3G|ENST00000497043|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,118 0:4,0:4:99:0,100 1:0,24:24:99:858,0 chrX 153067740 . C G 219.64 PASS AC=2;AF=1;AN=2;DP=11;FS=0;GQ_MEAN=123.5;GQ_STDDEV=105.36;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=21.96;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000482902|||||processed_transcript,3_prime_UTR_variant|||ENSG00000067840|PDZD4|ENST00000164640|8/8|||-/769|protein_coding,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000447375|||||retained_intron,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000471724|||||processed_transcript,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000485612|||||processed_transcript,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000370085||||-/148|protein_coding,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000480418|||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000483693|||||processed_transcript,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000370086||||-/173|protein_coding,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000320857||||-/173|protein_coding,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000486204|||||processed_transcript,3_prime_UTR_variant|||ENSG00000067840|PDZD4|ENST00000393758|8/8|||-/694|protein_coding,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000471880|||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000544474||||-/660|protein_coding,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000460616|||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000480650||||-/122|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000484792|||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000475140|||||processed_transcript,downstream_gene_variant|||ENSG00000180879|SSR4|ENST00000370087||||-/173|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:49:49,0 1:0,8:8:99:198,0 .:0,0:.:.:. chrX 153070999 . G A 1994.87 PASS AC=2;AF=0.667;AN=3;DP=78;FS=0;GQ_MEAN=711.67;GQ_STDDEV=523.12;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=26.6;SOR=0.955;set=variant2;CSQ=downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000483693|||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000480418|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000067840|PDZD4|ENST00000475140|6/7||||processed_transcript,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000468491|||||processed_transcript,synonymous_variant|aaC/aaT|N|ENSG00000067840|PDZD4|ENST00000393758|6/8|||129/694|protein_coding,synonymous_variant|aaC/aaT|N|ENSG00000067840|PDZD4|ENST00000544474|4/6|||95/660|protein_coding,synonymous_variant|aaC/aaT|N|ENSG00000067840|PDZD4|ENST00000164640|6/8|||204/769|protein_coding,downstream_gene_variant|||ENSG00000067840|PDZD4|ENST00000480650||||-/122|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000067840|PDZD4|ENST00000484792|5/7||||processed_transcript GT:AD:DP:GQ:PL 1:0,32:32:99:1032,0 1:0,43:43:99:995,0 0:3,0:3:99:0,108 chrX 153168154 . G A 439.63 PASS AC=1;AF=0.5;AN=2;DP=18;FS=0;GQ_MEAN=255.5;GQ_STDDEV=303.35;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=25.86;SOR=1.371;set=variant2;CSQ=upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000430697||||-/372|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000370049||||-/309|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,intron_variant&non_coding_transcript_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000537206||||-/923|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126895|AVPR2|ENST00000434679|1/4|||-/48|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000358927||||-/371|protein_coding,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000337474||||-/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,17:17:99:470,0 0:1,0:1:41:0,41 chrX 153170447 . G GC 292.64 PASS AC=2;AF=1;AN=2;DP=8;FS=0;GQ_MEAN=160;GQ_STDDEV=59.4;MLEAC=2;MLEAF=1;MQ=63.51;MQ0=0;NCC=1;QD=33.68;SOR=1.863;set=variant;CSQ=downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000442172||||-/293|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000467421|||||processed_transcript,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000370049||||-/309|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000430697||||-/372|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding,upstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000337474||||-/371|protein_coding,5_prime_UTR_variant|||ENSG00000126895|AVPR2|ENST00000358927|2/4|||-/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461739|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000454164||||-/249|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126895|AVPR2|ENST00000434679|2/4|||-/48|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000537206||||-/923|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,5:5:99:202,0 1:0,3:3:99:118,0 chrX 153170995 . G A 154.87 PASS AC=2;AF=0.667;AN=3;DP=9;FS=0;GQ_MEAN=103;GQ_STDDEV=62.7;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.08;SOR=3.611;set=variant2;CSQ=intron_variant&NMD_transcript_variant|||ENSG00000126895|AVPR2|ENST00000434679||||-/48|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000454164||||-/249|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000537206||||-/923|protein_coding,missense_variant|gGg/gAg|G/E|ENSG00000126895|AVPR2|ENST00000337474|2/3|benign(0.073)|tolerated(0.24)|12/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461739|||||retained_intron,missense_variant|gGg/gAg|G/E|ENSG00000126895|AVPR2|ENST00000358927|3/4|benign(0.073)|tolerated(0.24)|12/371|protein_coding,missense_variant|gGg/gAg|G/E|ENSG00000126895|AVPR2|ENST00000370049|2/2|benign(0.058)|tolerated(0.5)|12/309|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000467421|||||processed_transcript,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|||||retained_intron,missense_variant|gGg/gAg|G/E|ENSG00000126895|AVPR2|ENST00000430697|2/3|benign(0.095)|deleterious(0.01)|12/372|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000442172||||-/293|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding GT:AD:DP:GQ:PL 1:0,4:4:99:154,0 1:0,1:1:33:33,0 0:4,0:4:99:0,122 chrX 153171993 . A G 1625.87 PASS AC=2;AF=0.667;AN=3;DP=55;FS=0;GQ_MEAN=593.33;GQ_STDDEV=863.56;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.88;SOR=0.994;set=variant2;CSQ=synonymous_variant|ctA/ctG|L|ENSG00000126895|AVPR2|ENST00000337474|3/3|||309/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461739|||||retained_intron,synonymous_variant|ctA/ctG|L|ENSG00000126895|AVPR2|ENST00000358927|4/4|||309/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000454164||||-/249|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126895|AVPR2|ENST00000434679|4/4|||-/48|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000537206||||-/923|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000442172||||-/293|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,3_prime_UTR_variant|||ENSG00000126895|AVPR2|ENST00000370049|2/2|||-/309|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000467421|||||processed_transcript,missense_variant|tAc/tGc|Y/C|ENSG00000126895|AVPR2|ENST00000430697|3/3|benign(0.255)|tolerated(0.21)|280/372|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron GT:AD:DP:GQ:PL 1:0,49:49:99:1590,0 1:0,2:2:68:68,0 0:4,0:4:99:0,122 chrX 153172059 . C T 1536.87 PASS AC=2;AF=0.667;AN=3;DP=57;FS=0;GQ_MEAN=563.67;GQ_STDDEV=452.89;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29;SOR=1.287;set=variant2;CSQ=intron_variant&non_coding_transcript_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000442172||||-/293|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|||||retained_intron,missense_variant|gCg/gTg|A/V|ENSG00000126895|AVPR2|ENST00000430697|3/3|benign(0)|tolerated_low_confidence(0.56)|302/372|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron,3_prime_UTR_variant|||ENSG00000126895|AVPR2|ENST00000370049|2/2|||-/309|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000467421|||||processed_transcript,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461739|||||retained_intron,synonymous_variant|agC/agT|S|ENSG00000126895|AVPR2|ENST00000358927|4/4|||331/371|protein_coding,synonymous_variant|agC/agT|S|ENSG00000126895|AVPR2|ENST00000337474|3/3|||331/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000537206||||-/923|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000454164||||-/249|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000126895|AVPR2|ENST00000434679|4/4|||-/48|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,29:29:99:1027,0 1:0,24:24:99:542,0 0:4,0:4:99:0,122 chrX 153176254 . A G 809.87 PASS AC=2;AF=0.667;AN=3;DP=33;FS=0;GQ_MEAN=323;GQ_STDDEV=197.52;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=27.93;SOR=1.46;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000467421|1/6||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|10/17||||retained_intron,downstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000370049||||-/309|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000466928|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000494397|4/10||||retained_intron,downstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000430697||||-/372|protein_coding,synonymous_variant&NMD_transcript_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000420383|14/19|||546/625|nonsense_mediated_decay,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000442172|3/7|||61/293|protein_coding,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000370028|16/23|||612/986|protein_coding,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000350060|15/22|||572/946|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|11/18||||retained_intron,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000393721|12/19|||394/768|protein_coding,upstream_gene_variant|||ENSG00000198910|L1CAM|ENST00000464967|||||retained_intron,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000404127|15/22|||-/217|nonsense_mediated_decay,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000454164|2/6|||72/249|protein_coding,downstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000434679||||-/48|nonsense_mediated_decay,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000537206|15/22|||549/923|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000422918||||-/214|protein_coding,synonymous_variant|caT/caC|H|ENSG00000089820|ARHGAP4|ENST00000370016|14/21|||551/925|protein_coding,downstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000337474||||-/371|protein_coding,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000463905|||||retained_intron,downstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494813|||||retained_intron,downstream_gene_variant|||ENSG00000126895|AVPR2|ENST00000358927||||-/371|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461739|||||retained_intron GT:AD:DP:GQ:PL 1:0,16:16:99:522,0 1:0,13:13:99:320,0 0:3,0:3:99:0,127 chrX 153195393 . G A 871.87 PASS AC=2;AF=0.667;AN=3;DP=28;FS=0;GQ_MEAN=338.67;GQ_STDDEV=442.88;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.87;SOR=3.014;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000477750|||||retained_intron,3_prime_UTR_variant|||ENSG00000102030|NAA10|ENST00000393712|8/8|||-/184|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370016||||-/925|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000422091||||-/174|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000089820|ARHGAP4|ENST00000494813|||||retained_intron,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000442262||||-/176|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000404127||||-/217|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000102030|NAA10|ENST00000370015|8/8|||-/169|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470979|||||processed_transcript,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000432089||||-/145|protein_coding,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000488481|||||retained_intron,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000393710|||||processed_transcript,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000461052||||-/317|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000370028||||-/986|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000350060||||-/946|protein_coding,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000478177|||||retained_intron,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000467451|||||retained_intron,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000460996|||||retained_intron,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000420383||||-/625|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000370011||||-/142|protein_coding,3_prime_UTR_variant|||ENSG00000102030|NAA10|ENST00000464845|8/8|||-/235|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000393721||||-/768|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000470209|||||retained_intron,3_prime_UTR_variant|||ENSG00000102030|NAA10|ENST00000370009|7/7|||-/220|protein_coding,upstream_gene_variant|||ENSG00000089820|ARHGAP4|ENST00000494302|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102030|NAA10|ENST00000482485|2/2||||retained_intron,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000477882|||||retained_intron,downstream_gene_variant|||ENSG00000102030|NAA10|ENST00000484950|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102030|NAA10|ENST00000466877|7/7||||retained_intron GT:AD:DP:GQ:PL 1:0,22:22:99:849,0 1:0,3:3:55:55,0 0:3,0:3:99:0,112 chrX 153210179 . T TG 526.64 PASS AC=2;AF=1;AN=2;DP=25;FS=0;GQ_MEAN=277;GQ_STDDEV=69.3;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=30.98;SOR=4.294;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000102032|RENBP|ENST00000412763|1/10|||-/254|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000369984||||-/2080|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000423624||||-/60|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000464227|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000369997||||-/413|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000310441||||-/2035|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000354233||||-/1966|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000475904|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000393700||||-/427|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000442361||||-/159|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000471056|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000451114||||-/125|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000457282||||-/116|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000462086|||||processed_transcript GT:AD:DP:GQ:PL 1:0,10:10:99:326,0 .:0,0:.:.:. 1:0,7:7:99:228,0 chrX 153210195 . G GGC 486.64 PASS AC=2;AF=1;AN=2;DP=17;FS=0;GQ_MEAN=257;GQ_STDDEV=108.89;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25;SOR=3.442;set=variant;CSQ=upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000423624||||-/60|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000369984||||-/2080|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000310441||||-/2035|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000354233||||-/1966|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000369997||||-/413|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000464227|||||retained_intron,5_prime_UTR_variant|||ENSG00000102032|RENBP|ENST00000412763|1/10|||-/254|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000451114||||-/125|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000457282||||-/116|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000462086|||||processed_transcript,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000475904|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000442361||||-/159|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000471056|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000393700||||-/427|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:334,0 .:0,0:.:.:. 1:0,4:4:99:180,0 chrX 153210199 . GA G 486.64 PASS AC=2;AF=1;AN=2;DP=20;FS=0;GQ_MEAN=257;GQ_STDDEV=108.89;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=30.93;SOR=3.442;set=variant;CSQ=upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000471056|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000442361||||-/159|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000393700||||-/427|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000475904|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000457282||||-/116|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000462086|||||processed_transcript,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000451114||||-/125|protein_coding,5_prime_UTR_variant|||ENSG00000102032|RENBP|ENST00000412763|1/10|||-/254|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000310441||||-/2035|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000354233||||-/1966|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000369997||||-/413|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000464227|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000423624||||-/60|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000369984||||-/2080|protein_coding GT:AD:DP:GQ:PL 1:0,7:7:99:334,0 .:0,0:.:.:. 1:0,4:4:99:180,0 chrX 153214462 . A AACGC 107.64 PASS AC=1;AF=1;AN=1;DP=3;FS=0;GQ_MEAN=135;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.91;SOR=1.179;set=variant;CSQ=3_prime_UTR_variant|||ENSG00000172534|HCFC1|ENST00000310441|26/26|||-/2035|protein_coding,3_prime_UTR_variant|||ENSG00000172534|HCFC1|ENST00000354233|27/27|||-/1966|protein_coding,3_prime_UTR_variant|||ENSG00000172534|HCFC1|ENST00000444191|10/10|||-/611|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000369997||||-/413|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000464227|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000423624||||-/60|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000172534|HCFC1|ENST00000369984|26/26|||-/2080|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000412763||||-/254|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000471056|||||retained_intron,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000393700||||-/427|protein_coding,upstream_gene_variant|||ENSG00000102032|RENBP|ENST00000475904|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,3:3:99:135,0 .:0,0:.:.:. chrX 153215839 . G A 865.87 PASS AC=1;AF=0.333;AN=3;DP=33;FS=0;GQ_MEAN=369.33;GQ_STDDEV=457.85;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=32.07;SOR=1.101;set=variant2;CSQ=synonymous_variant|tgC/tgT|C|ENSG00000172534|HCFC1|ENST00000369984|24/26|||1998/2080|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000172534|HCFC1|ENST00000354233|25/27|||1884/1966|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000172534|HCFC1|ENST00000310441|24/26|||1953/2035|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000172534|HCFC1|ENST00000444191|8/10|||529/611|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,102 0:3,0:3:99:0,108 1:0,27:27:99:898,0 chrX 153218365 . C A 1381.87 PASS AC=2;AF=0.667;AN=3;DP=49;FS=0;GQ_MEAN=516.33;GQ_STDDEV=529.58;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.71;SOR=0.737;set=variant2;CSQ=synonymous_variant|ctG/ctT|L|ENSG00000172534|HCFC1|ENST00000444191|3/10|||89/611|protein_coding,synonymous_variant|ctG/ctT|L|ENSG00000172534|HCFC1|ENST00000354233|20/27|||1445/1966|protein_coding,synonymous_variant|ctG/ctT|L|ENSG00000172534|HCFC1|ENST00000310441|19/26|||1514/2035|protein_coding,synonymous_variant|ctG/ctT|L|ENSG00000172534|HCFC1|ENST00000369984|19/26|||1558/2080|protein_coding GT:AD:DP:GQ:PL 1:0,35:35:99:1121,0 1:0,10:10:99:293,0 0:4,0:4:99:0,135 chrX 153219665 . C T 1302.87 PASS AC=2;AF=0.667;AN=3;DP=49;FS=0;GQ_MEAN=481.33;GQ_STDDEV=478.47;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=28.95;SOR=0.829;set=variant2;CSQ=synonymous_variant|gcG/gcA|A|ENSG00000172534|HCFC1|ENST00000354233|18/27|||1326/1966|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000172534|HCFC1|ENST00000310441|17/26|||1395/2035|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,synonymous_variant|gcG/gcA|A|ENSG00000172534|HCFC1|ENST00000369984|17/26|||1395/2080|protein_coding GT:AD:DP:GQ:PL 1:0,32:32:99:1021,0 1:0,13:13:99:314,0 0:3,0:3:99:0,109 chrX 153220360 . A G 1171.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-1.044;ClippingRankSum=-0.696;DP=42;FS=0;GQ_MEAN=437.67;GQ_STDDEV=474.78;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=-1.741;NCC=0;QD=30.05;ReadPosRankSum=1.39;SOR=0.732;set=variant2;CSQ=missense_variant|Tcc/Ccc|S/P|ENSG00000172534|HCFC1|ENST00000369984|17/26|benign(0)|tolerated_low_confidence(1)|1164/2080|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,missense_variant|Tcc/Ccc|S/P|ENSG00000172534|HCFC1|ENST00000310441|17/26|benign(0)|tolerated_low_confidence(1)|1164/2035|protein_coding,missense_variant|Tcc/Ccc|S/P|ENSG00000172534|HCFC1|ENST00000354233|18/27|benign(0)||1095/1966|protein_coding GT:AD:DP:GQ:PL 1:0,29:29:99:982,0 1:1,9:10:99:222,0 0:3,0:3:99:0,109 chrX 153221657 . T C 212.87 PASS AC=2;AF=0.667;AN=3;DP=10;FS=0;GQ_MEAN=109.67;GQ_STDDEV=23.16;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.41;SOR=2.584;set=variant2;CSQ=downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000461098|||||processed_transcript,synonymous_variant|ccA/ccG|P|ENSG00000172534|HCFC1|ENST00000310441|16/26|||947/2035|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000172534|HCFC1|ENST00000354233|17/27|||878/1966|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,synonymous_variant|ccA/ccG|P|ENSG00000172534|HCFC1|ENST00000369984|16/26|||947/2080|protein_coding GT:AD:DP:GQ:PL 1:0,3:3:99:116,0 1:0,4:4:99:129,0 0:3,0:3:84:0,84 chrX 153222835 . G C 1018.87 PASS AC=2;AF=0.667;AN=3;DP=36;FS=0;GQ_MEAN=384;GQ_STDDEV=429.33;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.87;SOR=1.022;set=variant2;CSQ=synonymous_variant|acC/acG|T|ENSG00000172534|HCFC1|ENST00000310441|13/26|||761/2035|protein_coding,downstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000461098|||||processed_transcript,synonymous_variant|acC/acG|T|ENSG00000172534|HCFC1|ENST00000354233|14/27|||692/1966|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000444191||||-/611|protein_coding,synonymous_variant|acC/acG|T|ENSG00000172534|HCFC1|ENST00000369984|13/26|||761/2080|protein_coding GT:AD:DP:GQ:PL 1:0,26:26:99:878,0 1:0,7:7:99:173,0 0:3,0:3:99:0,101 chrX 153238220 . A G 883.64 PASS AC=1;AF=1;AN=1;DP=35;FS=0;GQ_MEAN=911;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=25.25;SOR=1.002;set=variant2;CSQ=upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000310441||||-/2035|protein_coding,downstream_gene_variant|||ENSG00000235802|HCFC1-AS1|ENST00000438219|||||antisense,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000354233||||-/1966|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000369984||||-/2080|protein_coding,5_prime_UTR_variant|||ENSG00000177854|TMEM187|ENST00000369982|1/2|||-/261|protein_coding,upstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,35:35:99:911,0 .:0,0:.:.:. chrX 153238288 . A C 427.64 PASS AC=2;AF=1;AN=2;DP=16;FS=0;GQ_MEAN=227.5;GQ_STDDEV=217.08;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=26.73;SOR=0.941;set=variant2;CSQ=5_prime_UTR_variant|||ENSG00000177854|TMEM187|ENST00000369982|1/2|||-/261|protein_coding,upstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000354233||||-/1966|protein_coding,downstream_gene_variant|||ENSG00000235802|HCFC1-AS1|ENST00000438219|||||antisense,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000310441||||-/2035|protein_coding,upstream_gene_variant|||ENSG00000172534|HCFC1|ENST00000369984||||-/2080|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:74:74,0 1:0,14:14:99:381,0 .:0,0:.:.:. chrX 153247722 . C T 1574.87 PASS AC=2;AF=0.667;AN=3;DP=50;FS=0;GQ_MEAN=570.67;GQ_STDDEV=699.46;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.51;SOR=1.251;set=variant2;CSQ=downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding,downstream_gene_variant|||ENSG00000265176|MIR3202-1|ENST00000580198|||||miRNA,missense_variant|tCg/tTg|S/L|ENSG00000177854|TMEM187|ENST00000369982|2/2|benign(0)|tolerated(0.06)|70/261|protein_coding,downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000431598||||-/33|protein_coding GT:AD:DP:GQ:PL 1:0,40:40:99:1375,0 1:0,7:7:99:232,0 0:3,0:3:99:0,105 chrX 153247745 . A G 1270.63 PASS AC=1;AF=0.5;AN=2;DP=43;FS=0;GQ_MEAN=703;GQ_STDDEV=845.7;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;NCC=1;QD=33.44;SOR=0.798;set=variant2;CSQ=downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000431598||||-/33|protein_coding,downstream_gene_variant|||ENSG00000265176|MIR3202-1|ENST00000580198|||||miRNA,missense_variant|Atg/Gtg|M/V|ENSG00000177854|TMEM187|ENST00000369982|2/2|benign(0)|tolerated(0.29)|78/261|protein_coding,downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding GT:AD:DP:GQ:PL 1:0,38:38:99:1301,0 .:0,0:.:.:. 0:3,0:3:99:0,105 chrX 153247954 . C T 1839.87 PASS AC=2;AF=0.667;AN=3;DP=67;FS=0;GQ_MEAN=659;GQ_STDDEV=532.93;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=28.75;SOR=0.892;set=variant2;CSQ=downstream_gene_variant|||ENSG00000265176|MIR3202-1|ENST00000580198|||||miRNA,synonymous_variant|tgC/tgT|C|ENSG00000177854|TMEM187|ENST00000369982|2/2|||147/261|protein_coding,downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding,downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000431598||||-/33|protein_coding GT:AD:DP:GQ:PL 1:0,34:34:99:1168,0 1:0,30:30:99:704,0 0:3,0:3:99:0,105 chrX 153248248 . G A 2643.87 PASS AC=2;AF=0.667;AN=3;DP=81;FS=0;GQ_MEAN=927;GQ_STDDEV=1349.95;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=33.9;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000431598||||-/33|protein_coding,downstream_gene_variant|||ENSG00000177854|TMEM187|ENST00000425274||||-/66|protein_coding,downstream_gene_variant|||ENSG00000265176|MIR3202-1|ENST00000580198|||||miRNA,synonymous_variant|acG/acA|T|ENSG00000177854|TMEM187|ENST00000369982|2/2|||245/261|protein_coding GT:AD:DP:GQ:PL 1:0,71:71:99:2485,0 1:0,7:7:99:191,0 0:3,0:3:99:0,105 chrX 153278829 . G A 1162.87 PASS AC=1;AF=0.333;AN=3;DP=41;FS=0;GQ_MEAN=469;GQ_STDDEV=628.74;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=27.75;SOR=1.751;set=variant2;CSQ=missense_variant|tCg/tTg|S/L|ENSG00000184216|IRAK1|ENST00000444254|2/3|benign(0)|tolerated(0.79)|88/218|protein_coding,intron_variant|||ENSG00000184216|IRAK1|ENST00000393682||||-/693|protein_coding,intron_variant|||ENSG00000184216|IRAK1|ENST00000429936||||-/708|protein_coding,missense_variant|tCg/tTg|S/L|ENSG00000184216|IRAK1|ENST00000369980|12/14|benign(0.001)|tolerated(0.33)|532/712|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000184216|IRAK1|ENST00000467236|2/2||||processed_transcript,intron_variant|||ENSG00000184216|IRAK1|ENST00000437278||||-/276|protein_coding,missense_variant|tCg/tTg|S/L|ENSG00000184216|IRAK1|ENST00000369974|11/13|benign(0)|tolerated(0.36)|453/633|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000184216|IRAK1|ENST00000369973|10/12|||-/339|nonsense_mediated_decay,intron_variant|||ENSG00000184216|IRAK1|ENST00000455690||||-/212|protein_coding,downstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000463031|||||retained_intron,intron_variant|||ENSG00000184216|IRAK1|ENST00000393687||||-/682|protein_coding,missense_variant|tCg/tTg|S/L|ENSG00000184216|IRAK1|ENST00000443220|7/7|benign(0.001)|tolerated(0.43)|281/392|protein_coding,intron_variant|||ENSG00000184216|IRAK1|ENST00000444230||||-/234|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000184216|IRAK1|ENST00000477274|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,107 0:4,0:4:99:0,105 1:0,33:33:99:1195,0 chrX 153284192 . A G 728.87 PASS AC=1;AF=0.333;AN=3;BaseQRankSum=1.4;ClippingRankSum=-1.734;DP=30;FS=0;GQ_MEAN=332;GQ_STDDEV=371.67;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;MQRankSum=-0.083;NCC=0;QD=34.71;ReadPosRankSum=1.57;SOR=3.258;set=variant2;CSQ=upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000477274|||||processed_transcript,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000455690||||-/212|protein_coding,missense_variant&NMD_transcript_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000369973|4/12|benign(0.002)|tolerated(0.55)|222/339|nonsense_mediated_decay,missense_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000393687|5/14|benign(0)|tolerated(1)|196/682|protein_coding,intron_variant|||ENSG00000184216|IRAK1|ENST00000444230||||-/234|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000437278||||-/276|protein_coding,missense_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000393682|4/14|benign(0)||222/693|protein_coding,missense_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000429936|4/13|benign(0)|tolerated(0.75)|222/708|protein_coding,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000303391||||-/486|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000184216|IRAK1|ENST00000463031|1/2||||retained_intron,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000443220||||-/392|protein_coding,missense_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000369974|5/13|benign(0)|tolerated(1)|196/633|protein_coding,downstream_gene_variant|||ENSG00000211524|MIR718|ENST00000390190|||||miRNA,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000444254||||-/218|protein_coding,missense_variant|tTt/tCt|F/S|ENSG00000184216|IRAK1|ENST00000369980|5/14|benign(0)|tolerated(1)|196/712|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000467236|||||processed_transcript GT:AD:DP:GQ:PL 0:4,0:4:99:0,128 0:5,0:5:99:0,107 1:1,20:21:99:761,0 chrX 153284483 . G A 859.87 PASS AC=1;AF=0.333;AN=3;DP=32;FS=0;GQ_MEAN=377;GQ_STDDEV=446.27;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=34.39;SOR=1.609;set=variant2;CSQ=synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000429936|3/13|||187/708|protein_coding,synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000393682|3/14|||187/693|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000437278||||-/276|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000455690||||-/212|protein_coding,synonymous_variant&NMD_transcript_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000369973|3/12|||187/339|nonsense_mediated_decay,synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000393687|4/14|||161/682|protein_coding,synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000444230|4/5|||157/234|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000477274|||||processed_transcript,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000444254||||-/218|protein_coding,synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000369980|4/14|||161/712|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000467236|||||processed_transcript,synonymous_variant|gtC/gtT|V|ENSG00000184216|IRAK1|ENST00000369974|4/13|||161/633|protein_coding,downstream_gene_variant|||ENSG00000211524|MIR718|ENST00000390190|||||miRNA,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000303391||||-/486|protein_coding,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000463031|||||retained_intron,upstream_gene_variant|||ENSG00000184216|IRAK1|ENST00000443220||||-/392|protein_coding GT:AD:DP:GQ:PL 0:4,0:4:99:0,135 0:3,0:3:99:0,104 1:0,25:25:99:892,0 chrX 153294542 . T C 220.64 PASS AC=1;AF=1;AN=1;DP=8;FS=0;GQ_MEAN=248;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=31.52;SOR=4.174;set=variant2;CSQ=downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000453960||||-/498|protein_coding,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000415944||||-/50|protein_coding,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000460227|||||processed_transcript,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000369957||||-/34|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000481807|||||processed_transcript,3_prime_UTR_variant|||ENSG00000169057|MECP2|ENST00000303391|4/4|||-/486|protein_coding,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000407218||||-/172|protein_coding,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000463644|||||processed_transcript,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000496908|||||processed_transcript,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000488293|||||processed_transcript,downstream_gene_variant|||ENSG00000169057|MECP2|ENST00000486506|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:248,0 .:0,0:.:.:. chrX 153418524 . C T 112.64 my_snp_filter AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=140;MLEAC=1;MLEAF=1;MQ=36.67;MQ0=0;NCC=2;QD=18.77;SOR=2.303;set=FilteredInAll;CSQ=missense_variant|gCc/gTc|A/V|ENSG00000102076|OPN1LW|ENST00000442922|1/4|benign(0.009)||37/164|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102076|OPN1LW|ENST00000463296|3/4||||processed_transcript,missense_variant|gCc/gTc|A/V|ENSG00000102076|OPN1LW|ENST00000369951|3/6|benign(0.009)||174/364|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:140,0 .:0,0:.:.:. chrX 153418541 . T G 177.64 my_snp_filter AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=205;MLEAC=1;MLEAF=1;MQ=36.67;MQ0=0;NCC=2;QD=25.38;SOR=2.584;set=FilteredInAll;CSQ=missense_variant|Tct/Gct|S/A|ENSG00000102076|OPN1LW|ENST00000369951|3/6|benign(0.006)||180/364|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102076|OPN1LW|ENST00000463296|3/4||||processed_transcript,missense_variant|Tct/Gct|S/A|ENSG00000102076|OPN1LW|ENST00000442922|1/4|benign(0.014)||43/164|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,7:7:99:205,0 .:0,0:.:.:. chrX 153558418 . A G 288.64 PASS AC=1;AF=1;AN=1;DP=13;FS=0;GQ_MEAN=316;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=22.2;SOR=0.836;set=variant2;CSQ=downstream_gene_variant|||ENSG00000007350|TKTL1|ENST00000482044|||||processed_transcript,downstream_gene_variant|||ENSG00000007350|TKTL1|ENST00000465168|||||processed_transcript,3_prime_UTR_variant|||ENSG00000007350|TKTL1|ENST00000369915|13/13|||-/596|protein_coding,downstream_gene_variant|||ENSG00000007350|TKTL1|ENST00000217905||||-/336|protein_coding,downstream_gene_variant|||ENSG00000231830|XX-FW83128A1.2|ENST00000433825|||||antisense,downstream_gene_variant|||ENSG00000007350|TKTL1|ENST00000463884|||||processed_transcript,3_prime_UTR_variant|||ENSG00000007350|TKTL1|ENST00000369912|12/12|||-/540|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,13:13:99:316,0 .:0,0:.:.:. chrX 153609616 . G C 508.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=1.04;ClippingRankSum=-0.116;DP=22;FS=0;GQ_MEAN=322;GQ_STDDEV=306.88;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=1.27;NCC=1;QD=33.91;ReadPosRankSum=-1.042;SOR=1.179;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102119|EMD|ENST00000485261|||||retained_intron,downstream_gene_variant|||ENSG00000102119|EMD|ENST00000468294|||||retained_intron,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102119|EMD|ENST00000428228|6/6|||-/21|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000102119|EMD|ENST00000369842|6/6|||-/254|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000471965|2/2||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000486738|4/4||||retained_intron,3_prime_UTR_variant|||ENSG00000102119|EMD|ENST00000369835|5/5|||-/219|protein_coding,downstream_gene_variant|||ENSG00000102119|EMD|ENST00000494443|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000492448|5/5||||processed_transcript GT:AD:DP:GQ:PL 1:1,14:15:99:539,0 .:0,0:.:.:. 0:3,0:3:99:0,105 chrX 153609617 . C T 508.63 PASS AC=1;AF=0.5;AN=2;BaseQRankSum=-0.579;ClippingRankSum=-0.116;DP=22;FS=0;GQ_MEAN=322;GQ_STDDEV=306.88;MLEAC=1;MLEAF=0.5;MQ=60;MQ0=0;MQRankSum=-1.273;NCC=1;QD=33.91;ReadPosRankSum=-1.504;SOR=1.179;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000102119|EMD|ENST00000369842|6/6|||-/254|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102119|EMD|ENST00000428228|6/6|||-/21|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102119|EMD|ENST00000468294|||||retained_intron,downstream_gene_variant|||ENSG00000102119|EMD|ENST00000485261|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000486738|4/4||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000471965|2/2||||retained_intron,downstream_gene_variant|||ENSG00000102119|EMD|ENST00000494443|||||retained_intron,3_prime_UTR_variant|||ENSG00000102119|EMD|ENST00000369835|5/5|||-/219|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102119|EMD|ENST00000492448|5/5||||processed_transcript GT:AD:DP:GQ:PL 1:1,14:15:99:539,0 .:0,0:.:.:. 0:3,0:3:99:0,105 chrX 153629155 . A G 1051.64 PASS AC=3;AF=1;AN=3;DP=28;FS=0;GQ_MEAN=359.67;GQ_STDDEV=221.06;MLEAC=3;MLEAF=1;MQ=40;MQ0=0;NCC=0;QD=32;SOR=1.863;set=variant2;CSQ=intron_variant|||ENSG00000147403|RPL10|ENST00000428169||||-/91|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000489200|3/3||||retained_intron,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000309585||||-/302|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000485196|5/5||||retained_intron,missense_variant|aAt/aGt|N/S|ENSG00000147403|RPL10|ENST00000424325|7/7|benign(0.007)||202/214|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000451865||||-/208|protein_coding,intron_variant|||ENSG00000147403|RPL10|ENST00000449494||||-/28|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000393638||||-/302|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000369809||||-/302|protein_coding,missense_variant|aAt/aGt|N/S|ENSG00000147403|RPL10|ENST00000406022|6/6|benign(0.007)||151/163|protein_coding,downstream_gene_variant|||ENSG00000207165|SNORA70|ENST00000384436|||||snoRNA,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000432135||||-/26|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000424626||||-/103|protein_coding,intron_variant|||ENSG00000147403|RPL10|ENST00000427682||||-/131|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000369807||||-/302|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000412184||||-/62|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000436473||||-/200|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000491035|5/5||||retained_intron,missense_variant|Atc/Gtc|I/V|ENSG00000147403|RPL10|ENST00000458500|6/6|benign(0.031)||148/181|protein_coding,missense_variant|aAt/aGt|N/S|ENSG00000147403|RPL10|ENST00000344746|6/6|benign(0.007)||202/214|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000014935||||-/302|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000482732|2/2||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000467168|5/5||||retained_intron,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000497242|||||retained_intron,missense_variant|aAt/aGt|N/S|ENSG00000147403|RPL10|ENST00000369817|8/8|benign(0.007)||202/214|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000369808||||-/302|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000147403|RPL10|ENST00000492572|4/4||||retained_intron,intron_variant|||ENSG00000147403|RPL10|ENST00000451365||||-/108|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000479366|||||processed_transcript,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000447892||||-/85|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000474786|||||retained_intron GT:AD:DP:GQ:PL 1:0,14:14:99:545,0 1:0,3:3:99:115,0 1:0,11:11:99:419,0 chrX 153633359 . G C 3746.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=1.65;ClippingRankSum=-0.26;DP=121;FS=3.504;GQ_MEAN=1258;GQ_STDDEV=583.92;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.173;NCC=0;QD=30.96;ReadPosRankSum=1.21;SOR=0.607;set=variant2;CSQ=intron_variant|||ENSG00000013563|DNASE1L1|ENST00000447892||||-/85|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000474786|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000451365||||-/108|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000492572|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000467168|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000369817||||-/214|protein_coding,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000497242|||||retained_intron,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000369808|3/8|||67/302|protein_coding,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000014935|4/9|||67/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000482732|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000458500||||-/181|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000412184||||-/62|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000436473||||-/200|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000491035|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000344746||||-/214|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000427682||||-/131|protein_coding,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000369807|3/8|||67/302|protein_coding,downstream_gene_variant|||ENSG00000207165|SNORA70|ENST00000384436|||||snoRNA,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000424626|5/6|||67/103|protein_coding,downstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000432135||||-/26|protein_coding,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000369809|5/10|||67/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000406022||||-/163|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000449494||||-/28|protein_coding,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000393638|3/8|||67/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000424325||||-/214|protein_coding,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000451865|3/7|||67/208|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000489200|||||retained_intron,synonymous_variant|ccC/ccG|P|ENSG00000013563|DNASE1L1|ENST00000309585|4/9|||67/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000485196|||||retained_intron,intron_variant|||ENSG00000147403|RPL10|ENST00000428169||||-/91|protein_coding GT:AD:DP:GQ:PL 1:1,39:40:99:1305,0 1:0,26:26:99:652,0 1:0,55:55:99:1817,0 chrX 153633953 . T C 1374.64 PASS AC=3;AF=1;AN=3;DP=43;FS=0;GQ_MEAN=467.33;GQ_STDDEV=196.93;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.97;SOR=1.775;set=variant2;CSQ=downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000489200|||||retained_intron,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000309585|3/9|||-/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000485196|||||retained_intron,intron_variant|||ENSG00000147403|RPL10|ENST00000428169||||-/91|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000449494||||-/28|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000393638|2/8|||-/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000424325||||-/214|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000451865|2/7|||-/208|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000406022||||-/163|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000369809|4/10|||-/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000427682||||-/131|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000369807|2/8|||-/302|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000424626|4/6|||-/103|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000432135|4/4|||-/26|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000491035|||||retained_intron,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000412184|1/2|||-/62|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000436473||||-/200|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000458500||||-/181|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000344746||||-/214|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000467168|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000369817||||-/214|protein_coding,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000497242|||||retained_intron,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000369808|2/8|||-/302|protein_coding,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000014935|3/9|||-/302|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000482732|||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000451365||||-/108|protein_coding,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000492572|||||retained_intron,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000447892||||-/85|protein_coding GT:AD:DP:GQ:PL 1:0,18:18:99:691,0 1:0,13:13:99:320,0 1:0,12:12:99:391,0 chrX 153637305 . T C 215.64 PASS AC=2;AF=1;AN=2;DP=6;FS=0;GQ_MEAN=121.5;GQ_STDDEV=3.54;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=31.88;SOR=3.912;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000351413||||-/278|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000455296||||-/95|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000369790||||-/248|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476307|||||retained_intron,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000447892||||-/85|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476800|||||retained_intron,5_prime_UTR_variant|||ENSG00000013563|DNASE1L1|ENST00000369808|1/8|||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000433313||||-/95|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000426231||||-/34|nonsense_mediated_decay,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000424626||||-/103|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000432135||||-/26|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000439735||||-/184|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000369793|||||retained_intron,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000309585||||-/302|protein_coding,intron_variant|||ENSG00000147403|RPL10|ENST00000428169||||-/91|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000393638||||-/302|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000451865||||-/208|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000454722||||-/196|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000470127|||||processed_transcript,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476679|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000445994||||-/95|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000412184||||-/62|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000426834||||-/170|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000014935||||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000369776||||-/262|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000350743||||-/262|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000369809||||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000479875|||||processed_transcript,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000369807||||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483674|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483780|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000475699||||-/265|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000465540|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000299328||||-/292|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000480812|||||retained_intron GT:AD:DP:GQ:PL 1:0,3:3:99:124,0 .:0,0:.:.:. 1:0,3:3:99:119,0 chrX 153640060 . CT C 958.64 PASS AC=3;AF=1;AN=3;DP=25;FS=0;GQ_MEAN=328.67;GQ_STDDEV=115.77;MLEAC=3;MLEAF=1;MQ=60.98;MQ0=0;NCC=0;QD=33.76;SOR=1.893;set=variant;CSQ=5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000426834|1/5|||-/170|protein_coding,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000014935||||-/302|protein_coding,5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000454722|1/7|||-/196|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000470127|||||processed_transcript,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476679|||||retained_intron,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102125|TAZ|ENST00000445994|1/4|||-/95|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000465540|1/3||||retained_intron,5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000299328|1/11|||-/292|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000480812|1/2||||retained_intron,5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000350743|1/10|||-/262|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000369776||||-/262|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000369809||||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000479875|||||processed_transcript,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000369807||||-/302|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483780|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000475699||||-/265|protein_coding,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483674|||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476800|||||retained_intron,upstream_gene_variant|||ENSG00000013563|DNASE1L1|ENST00000369808||||-/302|protein_coding,5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000351413|1/10|||-/278|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102125|TAZ|ENST00000455296|1/10|||-/95|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000369790|1/9|||-/248|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000476307|1/6||||retained_intron,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000439735||||-/184|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000309585||||-/302|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000369793|1/8||||retained_intron,downstream_gene_variant|||ENSG00000147403|RPL10|ENST00000428169||||-/91|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000393638||||-/302|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000451865||||-/208|protein_coding,5_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102125|TAZ|ENST00000433313|1/7|||-/95|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102125|TAZ|ENST00000426231||||-/34|nonsense_mediated_decay,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000432135||||-/26|protein_coding,intron_variant|||ENSG00000013563|DNASE1L1|ENST00000424626||||-/103|protein_coding GT:AD:DP:GQ:PL 1:0,9:9:99:355,0 1:0,5:5:99:202,0 1:0,11:11:99:429,0 chrX 153649813 . G C 358.64 PASS AC=2;AF=1;AN=2;DP=14;FS=0;GQ_MEAN=193;GQ_STDDEV=156.98;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=25.62;SOR=0.976;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000369793|8/8||||retained_intron,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000439735||||-/184|protein_coding,3_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000299328|11/11|||-/292|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000498029|||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102125|TAZ|ENST00000494912|5/5||||retained_intron,3_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000369776|7/7|||-/262|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000433313||||-/95|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000350743|10/10|||-/262|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000426231||||-/34|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000475699||||-/265|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483674|||||retained_intron,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000483780|||||retained_intron,3_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000351413|10/10|||-/278|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000454722||||-/196|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102125|TAZ|ENST00000455296|10/10|||-/95|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000470127|||||processed_transcript,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476679|||||retained_intron,3_prime_UTR_variant|||ENSG00000102125|TAZ|ENST00000369790|9/9|||-/248|protein_coding,downstream_gene_variant|||ENSG00000102125|TAZ|ENST00000476307|||||retained_intron GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,12:12:99:304,0 1:0,2:2:82:82,0 chrX 153657083 . A G 1750.64 PASS AC=3;AF=1;AN=3;DP=53;FS=0;GQ_MEAN=592.67;GQ_STDDEV=347.33;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.03;SOR=0.981;set=variant2;CSQ=synonymous_variant&NMD_transcript_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000446552|1/3|||15/134|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000071553|ATP6AP1|ENST00000484908|||||processed_transcript,upstream_gene_variant|||ENSG00000197180|BX936347.1|ENST00000360656|||||pseudogene,synonymous_variant&NMD_transcript_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000455205|1/10|||14/133|nonsense_mediated_decay,synonymous_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000369762|1/10|||15/470|protein_coding,synonymous_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000449556|1/7|||15/230|protein_coding,upstream_gene_variant|||ENSG00000071553|ATP6AP1|ENST00000429585||||-/128|nonsense_mediated_decay,synonymous_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000422890|1/6|||15/273|protein_coding,upstream_gene_variant|||ENSG00000071553|ATP6AP1|ENST00000491569|||||retained_intron,synonymous_variant&NMD_transcript_variant|cgA/cgG|R|ENSG00000071553|ATP6AP1|ENST00000439372|1/3|||15/134|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:0,19:19:99:680,0 1:0,8:8:99:210,0 1:0,26:26:99:888,0 chrX 153693811 . C T 1373.87 PASS AC=2;AF=0.667;AN=3;DP=50;FS=0;GQ_MEAN=506;GQ_STDDEV=442.66;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=29.23;SOR=0.919;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000493546|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000480645|||||processed_transcript,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000495040|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000478236|||||retained_intron,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000467463|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000491066|||||retained_intron,synonymous_variant|ttC/ttT|F|ENSG00000130827|PLXNA3|ENST00000369682|12/33|||763/1871|protein_coding,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000482598|||||retained_intron GT:AD:DP:GQ:PL 1:0,29:29:99:985,0 1:0,18:18:99:421,0 0:3,0:3:99:0,112 chrX 153694334 . C G 2999.87 PASS AC=2;AF=0.667;AN=3;DP=91;FS=0;GQ_MEAN=1048;GQ_STDDEV=1222.41;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=34.09;SOR=0.997;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000497802|||||retained_intron,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000480645|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000493546|||||processed_transcript,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000482598|||||retained_intron,missense_variant|gaC/gaG|D/E|ENSG00000130827|PLXNA3|ENST00000369682|14/33|benign(0)||863/1871|protein_coding,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000491066|||||retained_intron,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000495040|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000478236|||||retained_intron,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000467463|||||processed_transcript GT:AD:DP:GQ:PL 1:0,66:66:99:2431,0 1:0,22:22:99:601,0 0:3,0:3:99:0,112 chrX 153695908 . G T 484.87 PASS AC=2;AF=0.667;AN=3;DP=21;FS=0;GQ_MEAN=217.33;GQ_STDDEV=124.86;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=28.52;SOR=1.371;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000491066|||||retained_intron,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000478236|||||retained_intron,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000467463|||||processed_transcript,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000482598|||||retained_intron,synonymous_variant|gcG/gcT|A|ENSG00000130827|PLXNA3|ENST00000369682|20/33|||1154/1871|protein_coding,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000493546|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000497802|||||retained_intron,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000480645|||||processed_transcript GT:AD:DP:GQ:PL 1:0,10:10:99:361,0 1:0,7:7:99:156,0 0:4,0:4:99:0,135 chrX 153696247 . G C 1739.87 PASS AC=2;AF=0.667;AN=3;DP=62;FS=0;GQ_MEAN=635.67;GQ_STDDEV=465.73;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=30.52;SOR=1.047;set=variant2;CSQ=upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000497802|||||retained_intron,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000480645|||||processed_transcript,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000493546|||||processed_transcript,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000482598|||||retained_intron,synonymous_variant|gcG/gcC|A|ENSG00000130827|PLXNA3|ENST00000369682|21/33|||1241/1871|protein_coding,upstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000491066|||||retained_intron,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000478236|||||retained_intron,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000467463|||||processed_transcript GT:AD:DP:GQ:PL 1:0,29:29:99:1056,0 1:0,28:28:99:716,0 0:4,0:4:99:0,135 chrX 153706264 . C G 973.87 PASS AC=2;AF=0.667;AN=3;DP=33;FS=0;GQ_MEAN=372;GQ_STDDEV=466.85;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.46;SOR=1.143;set=variant2;CSQ=3_prime_UTR_variant|||ENSG00000196976|LAGE3|ENST00000357360|3/3|||-/143|protein_coding,downstream_gene_variant|||ENSG00000130827|PLXNA3|ENST00000369682||||-/1871|protein_coding,3_prime_UTR_variant|||ENSG00000196976|LAGE3|ENST00000407062|2/2|||-/106|protein_coding GT:AD:DP:GQ:PL 1:0,27:27:99:911,0 1:0,3:3:95:95,0 0:3,0:3:99:0,110 chrX 153712888 . C T 127.64 PASS AC=1;AF=1;AN=1;DP=7;FS=0;GQ_MEAN=155;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=21.27;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393587||||-/477|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393586||||-/532|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000369653||||-/180|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000481237|||||retained_intron,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000477777|||||processed_transcript,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000417913||||-/103|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000263512||||-/477|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102178|UBL4A|ENST00000421431|3/3|||-/33|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000369649||||-/448|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000453912||||-/218|protein_coding,3_prime_UTR_variant|||ENSG00000102178|UBL4A|ENST00000369660|4/4|||-/157|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,6:6:99:155,0 .:0,0:.:.:. chrX 153713167 . G A 601.64 PASS AC=1;AF=1;AN=1;BaseQRankSum=-1.733;ClippingRankSum=0.391;DP=31;FS=0;GQ_MEAN=629;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;MQRankSum=0.615;NCC=2;QD=19.41;ReadPosRankSum=-0.168;SOR=0.346;set=variant2;CSQ=downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000481237|||||retained_intron,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000369653||||-/180|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393586||||-/532|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393587||||-/477|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000417913||||-/103|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000477777|||||processed_transcript,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102178|UBL4A|ENST00000421431|3/3|||-/33|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000263512||||-/477|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000453912||||-/218|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000369649||||-/448|protein_coding,3_prime_UTR_variant|||ENSG00000102178|UBL4A|ENST00000369660|4/4|||-/157|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:1,30:31:99:629,0 .:0,0:.:.:. chrX 153713451 . C T 192.87 PASS AC=2;AF=0.667;AN=3;DP=11;FS=0;GQ_MEAN=109.67;GQ_STDDEV=35.84;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=24.11;SOR=0.693;set=variant2;CSQ=downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000453912||||-/218|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000369649||||-/448|protein_coding,3_prime_UTR_variant|||ENSG00000102178|UBL4A|ENST00000369660|4/4|||-/157|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102178|UBL4A|ENST00000421431|3/3|||-/33|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000263512||||-/477|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000477777|||||processed_transcript,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000417913||||-/103|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000369653||||-/180|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393587||||-/477|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393586||||-/532|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000481237|||||retained_intron GT:AD:DP:GQ:PL 1:0,2:2:77:77,0 1:0,6:6:99:148,0 0:3,0:3:99:0,104 chrX 153713787 . C T 1569.87 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=1.14;ClippingRankSum=0.884;DP=55;FS=0;GQ_MEAN=584.33;GQ_STDDEV=820.81;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=1.34;NCC=0;QD=30.78;ReadPosRankSum=0.227;SOR=1.112;set=variant2;CSQ=3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102178|UBL4A|ENST00000421431|3/3|||-/33|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000263512||||-/477|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000369649||||-/448|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000453912||||-/218|protein_coding,3_prime_UTR_variant|||ENSG00000102178|UBL4A|ENST00000369660|4/4|||-/157|protein_coding,missense_variant|cGt/cAt|R/H|ENSG00000102178|UBL4A|ENST00000369653|5/5|benign(0)||142/180|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393587||||-/477|protein_coding,downstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393586||||-/532|protein_coding,downstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000481237|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000102178|UBL4A|ENST00000477777|2/2||||processed_transcript,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000102178|UBL4A|ENST00000417913|4/4|||-/103|nonsense_mediated_decay GT:AD:DP:GQ:PL 1:2,47:49:99:1531,0 1:0,2:2:71:71,0 0:4,0:4:99:0,151 chrX 153718976 . A C 52.64 PASS AC=1;AF=1;AN=1;DP=2;FS=0;GQ_MEAN=80;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=26.32;SOR=0.693;set=variant2;CSQ=upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000369653||||-/180|protein_coding,upstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000393586||||-/532|protein_coding,5_prime_UTR_variant|||ENSG00000126903|SLC10A3|ENST00000393587|1/3|||-/477|protein_coding,upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000481237|||||retained_intron,upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000477777|||||processed_transcript,upstream_gene_variant|||ENSG00000264783|BX664739.1|ENST00000582532|||||miRNA,upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000417913||||-/103|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000421431||||-/33|nonsense_mediated_decay,5_prime_UTR_variant|||ENSG00000126903|SLC10A3|ENST00000263512|1/2|||-/477|protein_coding,5_prime_UTR_variant|||ENSG00000126903|SLC10A3|ENST00000453912|1/2|||-/218|protein_coding,upstream_gene_variant|||ENSG00000126903|SLC10A3|ENST00000369649||||-/448|protein_coding,upstream_gene_variant|||ENSG00000102178|UBL4A|ENST00000369660||||-/157|protein_coding GT:AD:DP:GQ:PL 1:0,2:2:80:80,0 .:0,0:.:.:. .:0,0:.:.:. chrX 153734787 . T A 223.64 PASS AC=1;AF=1;AN=1;DP=11;FS=0;GQ_MEAN=251;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=20.33;SOR=0.859;set=variant2;CSQ=downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000457212||||-/53|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000442929||||-/21|protein_coding,3_prime_UTR_variant|||ENSG00000071889|FAM3A|ENST00000359889|10/10|||-/230|protein_coding,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000426266||||-/163|protein_coding,3_prime_UTR_variant|||ENSG00000071889|FAM3A|ENST00000369643|10/10|||-/230|protein_coding,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000416319||||-/77|nonsense_mediated_decay,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000071889|FAM3A|ENST00000469041|6/6||||retained_intron,3_prime_UTR_variant|||ENSG00000071889|FAM3A|ENST00000447601|9/9|||-/230|protein_coding,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000393572||||-/192|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000071889|FAM3A|ENST00000419205|9/9|||-/70|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000475657|||||retained_intron,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000492763|||||processed_transcript,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000369641||||-/237|protein_coding,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000421517||||-/70|nonsense_mediated_decay,3_prime_UTR_variant|||ENSG00000071889|FAM3A|ENST00000434658|8/8|||-/213|protein_coding,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000449971||||-/70|nonsense_mediated_decay,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000071889|FAM3A|ENST00000322269|10/10|||-/70|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000412894||||-/39|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000440318||||-/51|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000071889|FAM3A|ENST00000497506|||||processed_transcript GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,11:11:99:251,0 .:0,0:.:.:. chrX 153759858 . T C 503.64 PASS AC=2;AF=1;AN=2;DP=16;FS=0;GQ_MEAN=265.5;GQ_STDDEV=214.25;MLEAC=2;MLEAF=1;MQ=60;MQ0=0;NCC=1;QD=31.48;SOR=2.049;set=variant2;CSQ=downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000439227||||-/338|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000393564||||-/515|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000440967||||-/320|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000497281|||||processed_transcript,3_prime_UTR_variant|||ENSG00000160211|G6PD|ENST00000393562|13/13|||-/545|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000488434|||||retained_intron,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000433845||||-/256|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000489497|||||retained_intron,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000369620||||-/561|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000490651|||||retained_intron GT:AD:DP:GQ:PL 1:0,3:3:99:114,0 1:0,13:13:99:417,0 .:0,0:.:.:. chrX 153760654 . G A 3181.86 PASS AC=2;AF=0.667;AN=3;BaseQRankSum=-0.646;ClippingRankSum=1.53;DP=111;FS=0;GQ_MEAN=1109.67;GQ_STDDEV=1113.76;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;MQRankSum=0.595;NCC=0;QD=30.3;ReadPosRankSum=-1.474;SOR=0.799;set=variant2;CSQ=downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000433845||||-/256|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000488434|||||retained_intron,synonymous_variant|taC/taT|Y|ENSG00000160211|G6PD|ENST00000393562|11/13|||467/545|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000440967||||-/320|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000497281|||||processed_transcript,synonymous_variant|taC/taT|Y|ENSG00000160211|G6PD|ENST00000393564|11/13|||437/515|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000439227||||-/338|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000160211|G6PD|ENST00000490651|2/3||||retained_intron,synonymous_variant|taC/taT|Y|ENSG00000160211|G6PD|ENST00000369620|11/13|||483/561|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000489497|||||retained_intron GT:AD:DP:GQ:PL 1:1,66:67:99:2313,0 1:0,38:38:99:901,0 0:3,0:3:99:0,115 chrX 153762634 . G A 2098.87 PASS AC=2;AF=0.667;AN=3;DP=70;FS=0;GQ_MEAN=748.67;GQ_STDDEV=805.39;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=31.33;SOR=1.41;set=variant2;CSQ=missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000393562|6/13|benign(0.034)|deleterious(0)|218/545|protein_coding,missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000433845|6/7|benign(0.058)|deleterious_low_confidence(0)|188/256|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000488434|||||retained_intron,missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000393564|6/13|benign(0.058)|deleterious(0)|188/515|protein_coding,missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000439227|6/9|||189/338|protein_coding,missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000440967|6/9|possibly_damaging(0.697)|deleterious(0)|189/320|protein_coding,downstream_gene_variant|||ENSG00000160211|G6PD|ENST00000497281|||||processed_transcript,missense_variant|tCc/tTc|S/F|ENSG00000160211|G6PD|ENST00000369620|6/13|benign(0.029)|deleterious(0.01)|188/561|protein_coding,upstream_gene_variant|||ENSG00000160211|G6PD|ENST00000490651|||||retained_intron,upstream_gene_variant|||ENSG00000160211|G6PD|ENST00000489497|||||retained_intron GT:AD:DP:GQ:PL 1:0,47:47:99:1655,0 1:0,20:20:99:476,0 0:3,0:3:99:0,115 chrX 153880830 . A C 3521.64 PASS AC=3;AF=1;AN=3;DP=113;FS=0;GQ_MEAN=1183;GQ_STDDEV=711.06;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=31.16;SOR=0.903;set=variant2;CSQ=upstream_gene_variant|||ENSG00000224882|IKBKGP1|ENST00000453062|||||unprocessed_pseudogene,synonymous_variant|ccT/ccG|P|ENSG00000126890|CTAG2|ENST00000247306|2/2|||115/210|protein_coding,upstream_gene_variant|||ENSG00000226141|AF277315.13|ENST00000442033|||||unprocessed_pseudogene,synonymous_variant|ccT/ccG|P|ENSG00000126890|CTAG2|ENST00000369585|2/3|||115/180|protein_coding GT:AD:DP:GQ:PL 1:0,44:44:99:1423,0 1:0,15:15:99:383,0 1:0,54:54:99:1743,0 chrX 153881525 . G C 5445.64 PASS AC=3;AF=1;AN=3;BaseQRankSum=2.13;ClippingRankSum=-0.276;DP=183;FS=0;GQ_MEAN=1824.33;GQ_STDDEV=918.24;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;MQRankSum=1.22;NCC=0;QD=29.92;ReadPosRankSum=0.6;SOR=0.761;set=variant2;CSQ=upstream_gene_variant|||ENSG00000226141|AF277315.13|ENST00000442033|||||unprocessed_pseudogene,missense_variant|Cag/Gag|Q/E|ENSG00000126890|CTAG2|ENST00000369585|1/3|benign(0.061)||89/180|protein_coding,missense_variant|Cag/Gag|Q/E|ENSG00000126890|CTAG2|ENST00000247306|1/2|benign(0.011)||89/210|protein_coding,upstream_gene_variant|||ENSG00000224882|IKBKGP1|ENST00000453062|||||unprocessed_pseudogene GT:AD:DP:GQ:PL 1:2,74:76:99:2456,0 1:0,30:30:99:771,0 1:0,76:76:99:2246,0 chrX 153881773 . T C 106.64 PASS AC=2;AF=1;AN=2;DP=4;FS=0;GQ_MEAN=67;GQ_STDDEV=1.41;MLEAC=2;MLEAF=1;MQ=40;MQ0=0;NCC=1;QD=26.66;SOR=3.258;set=variant2;CSQ=missense_variant|cAg/cGg|Q/R|ENSG00000126890|CTAG2|ENST00000247306|1/2|unknown(0)||6/210|protein_coding,missense_variant|cAg/cGg|Q/R|ENSG00000126890|CTAG2|ENST00000369585|1/3|unknown(0)||6/180|protein_coding,upstream_gene_variant|||ENSG00000226141|AF277315.13|ENST00000442033|||||unprocessed_pseudogene GT:AD:DP:GQ:PL 1:0,2:2:66:66,0 .:0,0:.:.:. 1:0,2:2:68:68,0 chrX 153904473 . C T 617.64 PASS AC=1;AF=1;AN=1;DP=26;FS=0;GQ_MEAN=645;MLEAC=1;MLEAF=1;MQ=60;MQ0=0;NCC=2;QD=23.76;SOR=2.303;set=variant2;CSQ=downstream_gene_variant|||ENSG00000160219|GAB3|ENST00000475685|||||processed_transcript,3_prime_UTR_variant|||ENSG00000160219|GAB3|ENST00000369568|9/9|||-/548|protein_coding,3_prime_UTR_variant|||ENSG00000160219|GAB3|ENST00000369575|10/10|||-/586|protein_coding,downstream_gene_variant|||ENSG00000160219|GAB3|ENST00000424127||||-/587|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000160219|GAB3|ENST00000496390|9/9||||processed_transcript,downstream_gene_variant|||ENSG00000160219|GAB3|ENST00000454973||||-/150|protein_coding GT:AD:DP:GQ:PL .:0,0:.:.:. 1:0,26:26:99:645,0 .:0,0:.:.:. chrX 153994596 . G T 2522.64 PASS AC=3;AF=1;AN=3;DP=76;FS=0;GQ_MEAN=850;GQ_STDDEV=685.26;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=33.19;SOR=0.984;set=variant2;CSQ=synonymous_variant|acG/acT|T|ENSG00000130826|DKC1|ENST00000413910|5/9|||123/258|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130826|DKC1|ENST00000473552|5/5||||processed_transcript,synonymous_variant&NMD_transcript_variant|acG/acT|T|ENSG00000130826|DKC1|ENST00000452771|4/7|||109/169|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000130826|DKC1|ENST00000475423|||||retained_intron,synonymous_variant|acG/acT|T|ENSG00000130826|DKC1|ENST00000437719|4/7|||109/229|protein_coding,synonymous_variant|acG/acT|T|ENSG00000130826|DKC1|ENST00000369550|5/15|||123/514|protein_coding,upstream_gene_variant|||ENSG00000206948|SNORA36A|ENST00000384221|||||snoRNA,upstream_gene_variant|||ENSG00000130826|DKC1|ENST00000426673||||-/208|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000130826|DKC1|ENST00000412124||||-/76|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000130826|DKC1|ENST00000484317|||||retained_intron,upstream_gene_variant|||ENSG00000130826|DKC1|ENST00000475966|||||processed_transcript GT:AD:DP:GQ:PL 1:0,43:43:99:1428,0 1:0,5:5:93:93,0 1:0,28:28:99:1029,0 chrX 154005148 . G A 1241.87 PASS AC=1;AF=0.333;AN=3;DP=49;FS=0;GQ_MEAN=503;GQ_STDDEV=667.71;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=31.05;SOR=0.793;set=variant2;CSQ=downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000413259||||-/436|protein_coding,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000453245||||-/205|protein_coding,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000439370||||-/68|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000482757|||||retained_intron,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130826|DKC1|ENST00000492372|3/3||||processed_transcript,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000369534||||-/466|protein_coding,3_prime_UTR_variant|||ENSG00000130826|DKC1|ENST00000369550|15/15|||-/514|protein_coding,downstream_gene_variant|||ENSG00000130826|DKC1|ENST00000481062|||||retained_intron,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000393531||||-/446|protein_coding,downstream_gene_variant|||ENSG00000130826|DKC1|ENST00000426673||||-/208|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000130830|MPP1|ENST00000491955|||||retained_intron,downstream_gene_variant|||ENSG00000206693|SNORA56|ENST00000383966|||||snoRNA,downstream_gene_variant|||ENSG00000130826|DKC1|ENST00000412124||||-/76|nonsense_mediated_decay,downstream_gene_variant|||ENSG00000130826|DKC1|ENST00000475966|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,114 0:5,0:5:99:0,121 1:0,40:40:99:1274,0 chrX 154020114 . C A 2288.87 PASS AC=2;AF=0.667;AN=3;DP=73;FS=0;GQ_MEAN=808.67;GQ_STDDEV=1064.24;MLEAC=2;MLEAF=0.667;MQ=60;MQ0=0;NCC=0;QD=32.7;SOR=1.512;set=variant2;CSQ=non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130830|MPP1|ENST00000488694|2/5||||processed_transcript,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130830|MPP1|ENST00000471821|3/3||||processed_transcript,intron_variant&non_coding_transcript_variant|||ENSG00000130830|MPP1|ENST00000494170|||||retained_intron,intron_variant|||ENSG00000130830|MPP1|ENST00000428488||||-/156|protein_coding,synonymous_variant|acG/acT|T|ENSG00000130830|MPP1|ENST00000393529|3/8|||39/241|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000130830|MPP1|ENST00000462825|||||processed_transcript,synonymous_variant|acG/acT|T|ENSG00000130830|MPP1|ENST00000369534|3/12|||85/466|protein_coding,intron_variant&non_coding_transcript_variant|||ENSG00000130830|MPP1|ENST00000475943|||||retained_intron,synonymous_variant|acG/acT|T|ENSG00000130830|MPP1|ENST00000393531|3/12|||85/446|protein_coding,synonymous_variant|acG/acT|T|ENSG00000130830|MPP1|ENST00000369531|3/5|||68/131|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000130830|MPP1|ENST00000417435|4/7|||-/89|nonsense_mediated_decay,intron_variant|||ENSG00000130830|MPP1|ENST00000453245||||-/205|protein_coding,synonymous_variant|acG/acT|T|ENSG00000130830|MPP1|ENST00000413259|4/13|||55/436|protein_coding,3_prime_UTR_variant&NMD_transcript_variant|||ENSG00000130830|MPP1|ENST00000439370|4/13|||-/68|nonsense_mediated_decay,upstream_gene_variant|||ENSG00000130830|MPP1|ENST00000488754|||||processed_transcript GT:AD:DP:GQ:PL 1:0,58:58:99:2033,0 1:0,12:12:99:288,0 0:3,0:3:99:0,105 chrX 154158201 . T G 688.87 PASS AC=1;AF=0.333;AN=3;DP=25;FS=0;GQ_MEAN=310;GQ_STDDEV=355.95;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=29.27;SOR=0.793;set=variant2;CSQ=synonymous_variant|tcA/tcC|S|ENSG00000185010|F8|ENST00000360256|14/26|||1288/2351|protein_coding GT:AD:DP:GQ:PL 0:3,0:3:99:0,108 0:3,0:3:99:0,101 1:0,19:19:99:721,0 chrX 154456747 . A G 2287.64 PASS AC=3;AF=1;AN=3;DP=75;FS=0;GQ_MEAN=771.67;GQ_STDDEV=51.83;MLEAC=3;MLEAF=1;MQ=60;MQ0=0;NCC=0;QD=30.5;SOR=1.402;set=variant2;CSQ=missense_variant|Atg/Gtg|M/V|ENSG00000155959|VBP1|ENST00000286428|4/6|benign(0)||123/197|protein_coding,missense_variant|Atg/Gtg|M/V|ENSG00000155959|VBP1|ENST00000535916|5/7|benign(0)||118/192|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000155959|VBP1|ENST00000460509|2/4||||processed_transcript GT:AD:DP:GQ:PL 1:0,22:22:99:761,0 1:0,33:33:99:828,0 1:0,20:20:99:726,0 chrX 154507173 . T G 979.87 PASS AC=1;AF=0.333;AN=3;DP=34;FS=0;GQ_MEAN=405.33;GQ_STDDEV=525.4;MLEAC=1;MLEAF=0.333;MQ=60;MQ0=0;NCC=0;QD=24.82;SOR=1.101;set=variant2;CSQ=downstream_gene_variant|||ENSG00000155962|CLIC2|ENST00000491205|||||processed_transcript,downstream_gene_variant|||ENSG00000155962|CLIC2|ENST00000321926||||-/133|protein_coding,3_prime_UTR_variant|||ENSG00000155962|CLIC2|ENST00000369449|6/6|||-/247|protein_coding,downstream_gene_variant|||ENSG00000155962|CLIC2|ENST00000465553|||||processed_transcript GT:AD:DP:GQ:PL 0:3,0:3:99:0,99 0:4,0:4:99:0,105 1:0,27:27:99:1012,0 cyvcf2-0.30.14/cyvcf2/tests/issue_44.vcf0000644000175000017500000000111414154107376017103 0ustar nileshnilesh##fileformat=VCFv4.1 ##FILTER= ##log_file=shapeit_18022017_21h52m25s_134fb6d8-5a8f-4ddb-ab2a-84d25a7828e0.log ##FORMAT= ##contig= ##contig= ##bcftools_viewVersion=1.4-19-g1802ff3+htslib-1.4-29-g42bfe70 ##bcftools_viewCommand=view cyvcf2/tests/issue_44.vcf; Date=Mon May 1 08:52:21 2017 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SSC00089 2 176938646 . A G . PASS . GT ./. 2 176938647 . A G . PASS . GT . 2 176938648 . A G . PASS . GT .|. 2 176938649 . A G . PASS . GT 0|0 cyvcf2-0.30.14/cyvcf2/tests/test_reader.py0000644000175000017500000011537314154107376017634 0ustar nileshnileshfrom __future__ import print_function import os.path import tempfile import sys import os import atexit try: from pathlib import Path except ImportError: from pathlib2 import Path # python 2 backport import warnings import numpy as np import pytest from ..cyvcf2 import VCF, Variant, Writer HERE = os.path.dirname(__file__) VCF_PATH = os.path.join(HERE, "test.vcf.gz") VCF_PATH2 = os.path.join(HERE, "test.snpeff.vcf") VCF_PATH3 = os.path.join(HERE, "test.mnp.vcf") VCF_PHASE_PATH = os.path.join(HERE, "test.comp_het.3.vcf") VCF_ALTFREQ_PATH = os.path.join(HERE, "test_gt_alt_freqs.vcf") try: basestring except NameError: basestring = (str, bytes) def test_init(): # string v = VCF(VCF_PATH) assert v expected_count = sum(1 for _ in v) v.close() # Path v = VCF(Path(VCF_PATH)) value = sum(1 for _ in v) assert value == expected_count # file descriptor with open(VCF_PATH) as fp: fd = fp.fileno() v = VCF(fd) assert sum(1 for _ in v) == expected_count v.close() # this should not close the file descriptor originally opened # file-like object with open(VCF_PATH) as fp: v = VCF(fp) assert sum(1 for _ in v) == expected_count v.close() # this should not close the file descriptor originally opened def test_type(): vcf = VCF(VCF_PATH) for v in vcf: if len(v.REF) == 1 and len(v.ALT[0]) == 1: assert v.var_type == 'snp' elif v.ALT[0][0] != "<": assert v.var_type == 'indel' else: print(v.var_type, v.REF, v.ALT) def test_type_mnp(): vcf = VCF(VCF_PATH3) for v in vcf: if len(v.ALT) == 1: if (v.REF, v.ALT[0]) in [("CGT","CGG"), ("AGG","CGA")]: assert v.var_type == 'mnp' if (v.REF, v.ALT[0]) in [("GCA","GA")]: assert v.var_type == 'indel' if len(v.ALT) == 2: if (v.REF, v.ALT[0], v.ALT[1]) in [("TCGGT","GCGGG","GCGGT")]: assert v.var_type == 'mnp' if (v.REF, v.ALT[0], v.ALT[1]) in [("ATTAC","ATAC","AATAC")]: assert v.var_type == 'indel' if len(v.ALT) == 3: if (v.REF, v.ALT[0], v.ALT[1], v.ALT[2]) in [("GCC","TCC","GCA","GCG")]: assert v.var_type == 'mnp' def test_format_str(): vcf = VCF(os.path.join(HERE, "test-format-string.vcf")) f = next(vcf).format("RULE") assert list(f) == ['F', 'G'] f = next(vcf).format("RULE") assert list(f) == ['F2,F3,F4', 'G2,G3,G4'] def test_missing_samples(): samples = ['101976-101976', 'sample_not_in_vcf'] with warnings.catch_warnings(record=True) as w: vcf = VCF(VCF_PATH, gts012=True, samples=samples) assert len(w) == 1 assert "not all requested samples found" in str(w[-1].message) assert len(vcf.samples) == 1 vcf.close() samples = '101976-101976,sample_not_in_vcf' with warnings.catch_warnings(record=True) as w: vcf = VCF(VCF_PATH, gts012=True, samples=samples) assert len(w) == 1 assert "not all requested samples found" in str(w[-1].message) assert len(vcf.samples) == 1 def test_ibd(): samples = ['101976-101976', '100920-100920', '100231-100231'] vcf = VCF(VCF_PATH, gts012=True, samples=samples) res = vcf.ibd() assert len(res) == 3, (len(res)) arr = res[('101976-101976', '100920-100920')] assert len(arr) > 0 def test_relatedness(): vcf = VCF(VCF_PATH, gts012=True) with warnings.catch_warnings(record=True) as w: warnings.simplefilter("ignore", category=DeprecationWarning) df = vcf.relatedness(gap=0, linkage_max=2) assert len(w) == 1 assert "tested:" in str(w[-1].message) assert "ibs0" in df, df assert "rel" in df #vcf = VCF(VCF_PATH, gts012=True) #for r in viter: # print r['pair'], r['ibs0'], r['ibs2'], r['ibs2*'] def test_pls(): vcf = VCF(VCF_PATH) v = next(vcf) assert v.gt_phred_ll_homref[0] == 0, v.gt_phred_ll_homref[0] assert v.gt_phred_ll_het[0] == 7, v.gt_phred_ll_het[0] assert v.gt_phred_ll_homalt[0] == 922, v.gt_phred_ll_homalt[0] import numpy as np imax = np.iinfo(np.int32(0)).max # missing assert v.gt_phred_ll_homref[1] == imax, v.gt_phred_ll_homref[1] assert v.gt_phred_ll_het[1] == imax, v.gt_phred_ll_het[1] assert v.gt_phred_ll_homalt[1] == imax, v.gt_phred_ll_homalt[1] def test_gt_alt_freqs(): vcf = VCF(VCF_ALTFREQ_PATH) v = next(vcf) assert v.gt_alt_freqs[0] == 0.2 assert v.gt_alt_freqs[1] == 1.0 v = next(vcf) assert v.gt_alt_freqs[0] == 0.5 assert v.gt_alt_freqs[1] == 0.9 v = next(vcf) assert v.gt_alt_freqs[0] == 0.0 assert v.gt_alt_freqs[1] == 0.0 v = next(vcf) assert v.gt_alt_freqs[0] == 0.0 assert v.gt_alt_freqs[1] == 1.0 v = next(vcf) assert v.gt_alt_freqs[0] == 0.0 assert v.gt_alt_freqs[1] == 0.0 v = next(vcf) assert v.gt_alt_freqs[0] == -1 assert v.gt_alt_freqs[1] == -1 def test_str(): vcf = VCF(VCF_PATH, lazy=True) v = next(vcf) s = str(v) assert "10172\t.\tCCCTAA\t" in s assert "fitcons_float=0.1266" in s def test_region(): vcf = VCF(VCF_PATH) start = 12783 end = 13783 k = 0 reg = '1:%d-%d' % (start, end) for var in vcf(reg): k += 1 assert var.start <= end, var assert var.end >= start, var assert isinstance(var.REF, basestring) assert isinstance(var.ALT, list) assert k == 28, k def test_empty_info(): for v in VCF(VCF_PHASE_PATH): dict(v.INFO) def test_phases(): vcf = VCF(VCF_PHASE_PATH) v = next(vcf) assert all(v.gt_phases), v.gt_phases v = next(vcf) assert all(v.gt_phases) v = next(vcf) assert all(v.gt_phases[1::2]) assert not any(v.gt_phases[0::2]) v = next(vcf) assert not any(v.gt_phases[:-1]) assert v.gt_phases[-1] v = next(vcf) assert not any(v.gt_phases) def test_bad_init(): with pytest.raises(Exception): VCF("XXXXX") def test_samples(): v = VCF(VCF_PATH) assert len(v.samples) == 189 def test_next(): v = VCF(VCF_PATH) variant = next(v) assert isinstance(variant, Variant) def test_variant(): with pytest.raises(TypeError): Variant() def test_info_dict(): v = VCF(VCF_PATH) variant = next(v) d = dict(variant.INFO) assert d != {}, d toks = _get_line_for(variant) info = toks[7].split(";") keys = [x.split('=')[0] for x in info] for k in keys: assert k in d, (k, info) def test_attrs(): # 1 10172 . CCCTAA C 92.0 PASS v = VCF(VCF_PATH) variant = next(v) assert variant.POS == 10172 assert variant.CHROM == "1" assert variant.ID is None, variant.ID assert variant.start == 10171 assert variant.end == 10177, variant.end assert variant.FILTER is None assert variant.QUAL == 92.0 assert variant.REF == "CCCTAA" assert variant.ALT == ["C"] def test_empty(): p = os.path.join(HERE, "empty.vcf") assert os.path.exists(p) with pytest.raises(IOError): VCF(p) def test_format_field(): vcf = VCF(VCF_PATH) for v in vcf: assert isinstance(v.FORMAT, list) def test_writer_from_string(): header = """##fileformat=VCFv4.1 ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT samplea """ w = Writer.from_string("out.vcf", header) w.write_header() v = w.variant_from_string("chr1\t234\t.\tA\tC\t40\tPASS\t.\tGT\t0/0") w.write_record(v) w.close() def test_isa(): vcf = VCF(os.path.join(HERE, "test.isa.vcf")) for i, v in enumerate(vcf): if i in {0, 1, 2, 3}: assert v.is_indel assert not v.is_snp if i in {4}: assert v.is_snp def run_writer(writer, filename, rec): rec.INFO["AC"] = "3" rec.FILTER = ["LowQual"] writer.write_record(rec) rec.FILTER = ["LowQual", "VQSRTrancheSNP99.90to100.00"] writer.write_record(rec) rec.FILTER = "PASS" writer.write_record(rec) writer.close() expected = ["LowQual", "LowQual;VQSRTrancheSNP99.90to100.00", None] for i, variant in enumerate(VCF(filename)): assert variant.FILTER == expected[i], (variant.FILTER, expected[i]) def test_writer(): v = VCF(VCF_PATH) f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) rec = next(v) # string run_writer(Writer(f, v), f, rec) # Path path = Path(f) run_writer(Writer(path, v), f, rec) # file descriptor with open(VCF_PATH) as fp: fd = fp.fileno() run_writer(Writer(fd, v), f, rec) # file-like object with open(VCF_PATH) as fp: run_writer(Writer(fp, v), f, rec) def test_filters(): v = VCF(VCF_PATH) f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) rec = next(v) writer = Writer(f, v) rec.INFO["AC"] = "3" rec.FILTER = ["LowQual"] writer.write_record(rec) rec.FILTER = ["LowQual", "VQSRTrancheSNP99.90to100.00"] writer.write_record(rec) rec.FILTER = "PASS" writer.write_record(rec) rec.FILTER = [] writer.write_record(rec) writer.close() expected_filter = ["LowQual", "LowQual;VQSRTrancheSNP99.90to100.00", None, None] expected_filters = [["LowQual"], ["LowQual", "VQSRTrancheSNP99.90to100.00"], ["PASS"], []] for i, variant in enumerate(VCF(f)): assert variant.FILTER == expected_filter[i], (variant.FILTER, expected_filter[i]) assert variant.FILTERS == expected_filters[i], (variant.FILTERS, expected_filters[i]) def test_add_info_to_header(): v = VCF(VCF_PATH) v.add_info_to_header({'ID': 'abcdefg', 'Description': 'abcdefg', 'Type':'Character', 'Number': '1'}) # NOTE that we have to add the info to the header of the reader, # not the writer because the record will be associated with the reader f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) w = Writer(f, v) import sys rec = next(v) rec.INFO["abcdefg"] = "XXX" w.write_record(rec) w.close() v = next(VCF(f)) ret = v.INFO["abcdefg"] if isinstance(ret, bytes): ret = ret.decode() assert ret == "XXX", (dict(v.INFO), v.INFO["abcdefg"]) def test_read_flag(): vcf = VCF(VCF_PATH) for v in vcf: assert ("in_exac_flag" in str(v)) == v.INFO.get('in_exac_flag', False) def test_add_flag(): vcf = VCF(VCF_PATH) vcf.add_info_to_header({'ID': 'myflag', 'Description': 'myflag', 'Type':'Flag', 'Number': '0'}) # NOTE that we have to add the info to the header of the reader, # not the writer because the record will be associated with the reader f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) w = Writer(f, vcf) rec = next(vcf) rec.INFO["myflag"] = True w.write_record(rec) w.close() fh = VCF(f) v = next(fh) fh.close() assert v.INFO["myflag"] is True, dict(v.INFO) f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) w = Writer(f, vcf) rec.INFO["myflag"] = False w.write_record(rec) w.close() fh = VCF(f) v = next(fh) fh.close() with pytest.raises(KeyError): v.INFO["myflag"] def test_issue198(): vcf = VCF(os.path.join(HERE, "issue_198.vcf"), strict_gt=True) for v in vcf: assert all(v.gt_types == [2]), v.gt_types vcf = VCF(os.path.join(HERE, "issue_198.vcf"), strict_gt=False) for v in vcf: assert all(v.gt_types == [0]), v.gt_types def test_constants(): v = VCF(VCF_PATH) assert v.HOM_REF == 0 assert v.HET == 1 assert v.UNKNOWN == 2 assert v.HOM_ALT == 3 v = VCF(VCF_PATH, gts012=True) assert v.HOM_REF == 0 assert v.HET == 1 assert v.HOM_ALT == 2 assert v.UNKNOWN == 3 def test_add_filter_to_header(): v = VCF(VCF_PATH) # NOTE that we have to add the filter to the header of the reader, # not the writer because the record will be associated with the reader v.add_filter_to_header({'ID': 'abcdefg', 'Description': 'abcdefg'}) f = tempfile.mktemp(suffix=".vcf") atexit.register(os.unlink, f) w = Writer(f, v) rec = next(v) rec.FILTER = ["abcdefg"] w.write_record(rec) w.close() v = next(VCF(f)) ret = v.FILTER if isinstance(ret, bytes): ret = ret.decode() assert ret == "abcdefg", v.FILTER def test_seqnames(): v = VCF(VCF_PATH) assert v.seqnames == [u'1', u'2', u'3', u'4', u'5', u'6', u'7', u'8', u'9', u'10', u'11', u'12', u'13', u'14', u'15', u'16', u'17', u'18', u'19', u'20', u'21', u'22', u'X', u'Y', u'MT', u'GL000207.1', u'GL000226.1', u'GL000229.1', u'GL000231.1', u'GL000210.1', u'GL000239.1', u'GL000235.1', u'GL000201.1', u'GL000247.1', u'GL000245.1', u'GL000197.1', u'GL000203.1', u'GL000246.1', u'GL000249.1', u'GL000196.1', u'GL000248.1', u'GL000244.1', u'GL000238.1', u'GL000202.1', u'GL000234.1', u'GL000232.1', u'GL000206.1', u'GL000240.1', u'GL000236.1', u'GL000241.1', u'GL000243.1', u'GL000242.1', u'GL000230.1', u'GL000237.1', u'GL000233.1', u'GL000204.1', u'GL000198.1', u'GL000208.1', u'GL000191.1', u'GL000227.1', u'GL000228.1', u'GL000214.1', u'GL000221.1', u'GL000209.1', u'GL000218.1', u'GL000220.1', u'GL000213.1', u'GL000211.1', u'GL000199.1', u'GL000217.1', u'GL000216.1', u'GL000215.1', u'GL000205.1', u'GL000219.1', u'GL000224.1', u'GL000223.1', u'GL000195.1', u'GL000212.1', u'GL000222.1', u'GL000200.1', u'GL000193.1', u'GL000194.1', u'GL000225.1', u'GL000192.1', u'NC_007605', u'hs37d5', u'phix'], v.seqnames b = VCF('{}/test.snpeff.bcf'.format(HERE), threads=3) assert b.seqnames[0] == 'chr1', b.seqnames assert b.seqnames[-1] == 'chrY', b.seqnames def test_different_index(): b = VCF('{}/test.snpeff.bcf'.format(HERE), threads=3) b.set_index("{}/test-diff.csi".format(HERE)) s = 0 for r in b("chr1:69427-69429"): s += 1 assert s == 1 def test_var_type(): v = VCF(VCF_PATH) variant = next(v) assert variant.var_type == "indel", variant.var_type # 1 10172 . CCCTAA C 92.0 PASS for variant in v: if variant.POS == 10478: break else: raise Exception assert variant.var_type == "snp", variant.var_type def _get_line_for(v): import gzip with gzip.open(VCF_PATH) as f: for i, line in enumerate(f, start=1): line = line.decode() if line[0] == "#": continue toks = line.strip().split("\t") if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue if toks[3] != v.REF: continue if toks[4] not in v.ALT: continue return toks else: raise Exception("not found") def _get_samples(v): import numpy as np def _get_gt(s): if not ":" in s: return 2 s = s.split(":", 1)[0] if s in ("0/0", "0|0", "0/.", "./0", "0|."): return 0 if s in ("0/1", "0|1", "1/.", "./1", "1/."): return 1 if s in ("1/1", "1|1"): return 3 return 2 toks = _get_line_for(v) samples = toks[9:] return np.array([_get_gt(s) for s in samples], np.int32) def test_header_info(): v = VCF(VCF_PATH) csq = v['CSQ'] assert csq['ID'] == "CSQ" assert "Description" in csq with pytest.raises(KeyError): v[b'XXXXX'] def test_snpeff_header(): v = VCF(VCF_PATH2) f = v['SnpEffVersion'] assert f != {}, f assert 'SnpEffVersion' in f #def test_info_update(): # vcf = VCF(VCF_PATH) # v = next(vcf) # ret = v.INFO.update({'k': 22}) #print ret #assert v.INFO['k'] == 22 #assert ret == 0, ret def test_gt_types(): v = VCF(VCF_PATH) for variant in v: gt_types = variant.gt_types o = _get_samples(variant) assert (gt_types == o).all(), (variant, variant.CHROM, variant.POS, zip(gt_types, o)) def test_raw_header(): v = VCF(VCF_PATH) h = v.raw_header.strip().split("\n") s = h[0] assert s == "##fileformat=VCFv4.1", s assert len(h) == 185, len(h) def test_iterate(): for i, v in enumerate(VCF(VCF_PATH), start=1): pass assert i == 115, i def test_empty_call(): for i, v in enumerate(VCF(VCF_PATH)(), start=1): pass assert i == 115, i del i for i, v in enumerate(VCF(VCF_PATH)(''), start=1): pass assert i == 115, i def test_haploid(): for (gts012, (HOM_REF, HOM_ALT, UNKNOWN)) in ((False, [0, 3, 2]), (True, [0, 2, 3])): vcf = VCF("%s/test-haploidX.vcf" % HERE, gts012=gts012) for i, v in enumerate(vcf): assert not any("/" in b for b in v.gt_bases), (v.start + 1, v.gt_bases) if i == 0: assert (v.gt_types == [HOM_ALT, HOM_ALT, HOM_ALT]).all(), v.gt_types elif v.start == 2800676: assert (v.gt_types == [UNKNOWN, HOM_ALT, UNKNOWN]).all(), v.gt_types elif v.start == 2832771: assert (v.gt_types == [HOM_REF, HOM_ALT, HOM_ALT]).all(), v.gt_types break if v.start == 2700156: assert (v.gt_bases == ['A', 'A', 'A']).all(), v.gt_bases break def test_diploid(): vcf = VCF("%s/test.comp_het.3.vcf" % HERE) for v in vcf: if v.start == 17362: assert (v.gt_bases == ['TTCT|TTCT', 'TTCT|TTCT', 'TTCT|TTCT', 'TTCT|TTCT', 'TTCT|TTCT', 'TTCT|TTCT', 'TTCT|T', 'TTCT|T', 'TTCT|TTCT', 'TTCT|T', 'TTCT|T', 'TTCT|TTCT']).all(), v.gt_bases def test_format(): vcf = VCF('{}/test.vcf.gz'.format(HERE)) for v in vcf: a = v.format('PL', int) assert a.shape == (189, 3) a = v.format('SB', int) assert a is None a = v.format('DP', int) assert a.shape == (189, 1) def test_header_stuff(): vcf = VCF('{}/test.vcf.gz'.format(HERE)) import sys seen_formats, seen_infos = 0, 0 for h in vcf.header_iter(): i = h.info(extra=True) assert isinstance(i, dict) seen_formats += i['HeaderType'] == 'FORMAT' seen_infos += i['HeaderType'] == 'INFO' assert seen_formats == 9, seen_formats assert seen_infos == 73, seen_infos def test_bcf(): vcf = VCF('{}/test.snpeff.bcf'.format(HERE)) l = sum(1 for _ in vcf) assert l == 10, l # NOTE: this is 0 becuase we don't SEEK. l = sum(1 for _ in vcf()) assert l == 0, l viter = vcf("1:69260-69438") sys.stderr.write("\nOK\n") sys.stderr.flush() with warnings.catch_warnings(record=True) as w: l = list(viter) assert len(w) == 1 assert "no intervals found" in str(w[-1].message) assert len(l) == 0, len(l) iter = vcf("chr1:69260-69438") l = list(iter) assert len(l) == 2, len(l) def test_vcf_no_intervals(): vcf = VCF('{}/test.vcf.gz'.format(HERE)) viter = vcf("not_a_chrom") with warnings.catch_warnings(record=True) as w: l = list(viter) assert len(w) == 1 assert "no intervals found" in str(w[-1].message) assert len(l) == 0, len(l) def test_issue12(): fields = "ADP_ALL ADPD ADPO ADP_PASS ADPR AFR AMBIG BMF_PASS BMF_QUANT AF_FAILED FA_FAILED FM_FAILED FP_FAILED FR_FAILED MD_FAILED IMPROPER MQ_FAILED OVERLAP PV_FAILED QSS".split() vcf = VCF('{}/bug.vcf.gz'.format(HERE)) for v in vcf: for f in fields: vals = v.format(f) if vals is not None: assert vals.dtype in (np.int32, np.float32), (f, vals.dtype) vals = v.format("RVF") assert vals.dtype in (np.float32, np.float64) with pytest.raises(KeyError): v.format("RULE") def test_gt_bases_nondiploid(): """Ensure gt_bases works with more complex base representations. """ vcf = VCF('{}/test_gt_bases.vcf.gz'.format(HERE)) expected = {0: ['C/C', 'C/C'], 1: ['C/T', 'C'], 2: ['C', 'C/T'], 3: ['C', 'C']} for i, v in enumerate(vcf): assert v.gt_bases.tolist() == expected[i], (v.gt_bases.tolist(), expected[i]) def fmap(fn, a): return list(map(fn, a)) def allclose(a, b): return np.allclose(np.array(a, dtype=float), np.array(b, dtype=float)) def test_set_format_float(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="PS", Number=1, Type="Float", Description="PS example")) == 0 v = next(vcf) v.set_format("PS", np.array([0.555, 1.111], dtype=np.float32)) assert allclose(fmap(float, get_gt_str(v, "PS")), np.array([0.555, 1.111])) v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) assert allclose(fmap(float, get_gt_str(v, "PS")), [8.555, 11.111]) v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) obs = fmap(float, get_gt_str(v, "PS")) assert allclose(obs, [9998.555, 99911.111]), obs def test_set_format_int_a(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="PI", Number=1, Type="Integer", Description="Int example")) == 0 v = next(vcf) v.set_format("PI", np.array([5, 1], dtype=int)) assert allclose(fmap(float, get_gt_str(v, "PI")), [5, 1]) def test_set_format_int_b(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="PI", Number=1, Type="Integer", Description="Int example")) == 0 v = next(vcf) v.set_format("PI", np.array([855, 11], dtype=np.int64)) assert allclose(fmap(float, get_gt_str(v, "PI")), [855, 11]) def test_set_format_int_c(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="PI", Number=1, Type="Integer", Description="Int example")) == 0 v = next(vcf) v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) obs = fmap(float, get_gt_str(v, "PI")) assert allclose(obs, [9998, 99911]), obs def test_set_format_int3(): "test that we can handle multiple (in this case 3) values per sample" vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="P3", Number=3, Type="Integer", Description="Int example")) == 0 v = next(vcf) exp = np.array([[1, 11, 111], [2, 22, 222]], dtype=int) v.set_format("P3", exp) res = get_gt_str(v, "P3") assert res == ["1,11,111", "2,22,222"], (res, str(v)) assert np.allclose(v.format("P3"), exp) def test_set_format_str_bytes_second_longer(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="STR", Number=1, Type="String", Description="String example")) == 0 v = next(vcf) v.set_format("STR", np.array([b'foo', b'barbaz'])) assert np.all(v.format('STR') == np.array(['foo', 'barbaz'])) def test_set_format_str_bytes_first_longer(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="STR", Number=1, Type="String", Description="String example")) == 0 v = next(vcf) v.set_format("STR", np.array([b'foobar', b'baz'])) assert np.all(v.format('STR') == np.array(['foobar', 'baz'])) def test_set_format_str_bytes_number3(): # Confirm currently not supported vcf = VCF('{}/test-format-string.vcf'.format(HERE)) assert vcf.add_format_to_header(dict(ID="STR", Number=3, Type="String", Description="String example")) == 0 v = next(vcf) contents = np.array([[b'foo', b'barbaz', b'biz'], [b'blub', b'bloop', b'blop']]) with pytest.raises(Exception): v.set_format("STR", contents) def test_set_gts(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) v = next(vcf) v.genotypes = [[1, 1, True], [0, 0, False]] assert get_gt_str(v) == ["1|1", "0/0"] v.genotypes = [[-1, 1, False], [-1, 0, False]] assert get_gt_str(v) == ["./1", "./0"] v.genotypes = [[-1, -1, False], [0, 0, True]] assert get_gt_str(v) == ["./.", "0|0"] v.genotypes = [[2, 2, True], [0, 2, True]] assert get_gt_str(v) == ["2|2", "0|2"] v.genotypes = [[0, 1, 2, False], [1, 2, True]] s = get_gt_str(v) assert s == ["0/1/2", "1|2"] v.genotypes = [[1, 2, False], [0, 1, 2, True]] assert get_gt_str(v) == ["1/2", "0|1|2"] v.genotypes = [[0, 1, 2, False], [0, 1, 2, True]] assert get_gt_str(v) == ["0/1/2", "0|1|2"] def test_info_del(): vcf = VCF(os.path.join(HERE, "test-hemi.vcf")) v = next(vcf) d = str(v) assert ";DP=" in d del v.INFO["DP"] d = str(v) assert not ";DP=" in d def test_filter_id(): vcf = VCF(os.path.join(HERE, "test-hemi.vcf")) v = next(vcf) assert v.ID == "ID1" assert v.FILTER == "FAIL" def get_gt_str(variant, key="GT"): idx = variant.FORMAT.index(key) return [x.split(":")[idx] for x in str(variant).strip().split("\t")[9:]] def test_access_gts(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) """ 7 55086956 . C G 0 . . GT:ADP_ALL:RULE 0/0:6728,1:F 1|1:22,1:G 7 55086957 . T A,C,G 0 . . GT:ADP_ALL:RULE 1/2:6768,2,2,1:F2,F3,F4 2|3:1,2,3,4:G2,G3,G4 7 55086958 . T G 0 . . GT:ADP_ALL:RULE 0/1/.:6768,2,2,1:F2,F3,F4 0:1,2,3,4:G2,G3,G4 7 55086959 . T G,T 0 . . GT:ADP_ALL:RULE . 0|2:1,2,3,4:G2,G3,G4 """ v = next(vcf) gts = v.genotypes assert gts == [[0, 0, False], [1, 1, True]], gts v = next(vcf) assert v.genotypes == [[1, 2, False], [2, 3, True]], v.genotypes v = next(vcf) assert v.genotypes == [[0, 1, -1, False], [0, True]], v.genotypes v = next(vcf) assert v.genotypes == [[-1, True], [0, 2, True]], v.genotypes def test_access_genotype(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) v = next(vcf) gts = v.genotype #print(str(v), file=sys.stderr) # indexing directly gives a list of Allele objects (for diploid, the list # has length 2) alleles = gts[0] assert alleles[0].value == 0 assert alleles[1].value == 0 assert alleles[0].phased == False alleles = gts[1] assert alleles[0].value == 1 assert alleles[1].value == 1 assert alleles[1].phased == True assert np.all(gts.array()[:, :2] == np.array([[0, 0], [1, 1]])) assert np.all(gts.array()[:, 2] == np.array([False, True])) assert alleles[1].phased == True alleles[1].phased = False assert alleles[1].phased == False alleles = gts[1] assert alleles[1].phased == False assert np.all(gts.array()[:, 2] == np.array([False, False])) # can also just get the phased stats of the nth sample: assert gts.phased(0) == False # note this got updated above assert gts.phased(1) == False # and the alleles of the nth sample. assert gts.alleles(0) == [0, 0] #print(gts.alleles(1), file=sys.stderr) assert gts.alleles(1) == [1, 1] alleles = gts[0] assert alleles[0].value == 0 alleles[0].value = 1 assert alleles[0].value == 1 alleles = gts[0] assert alleles[0].value == 1 assert alleles[0].phased == False assert np.all(gts.array()[:, :2] == np.array([[1, 0], [1, 1]])) gts[1][0].value = 0 assert np.all(gts.array()[:, :2] == np.array([[1, 0], [0, 1]])) # update the varint v.genotype = gts assert "1/0:6728,1:F 0/1:22,1:G" in str(v) def test_access_genotype_array(): vcf = VCF('{}/test-format-string.vcf'.format(HERE)) """ 7 55086956 . C G 0 . . GT:ADP_ALL:RULE 0/0:6728,1:F 1|1:22,1:G 7 55086957 . T A,C,G 0 . . GT:ADP_ALL:RULE 1/2:6768,2,2,1:F2,F3,F4 2|3:1,2,3,4:G2,G3,G4 7 55086958 . T G 0 . . GT:ADP_ALL:RULE 0/1/.:6768,2,2,1:F2,F3,F4 0:1,2,3,4:G2,G3,G4 7 55086959 . T G,T 0 . . GT:ADP_ALL:RULE . 0|2:1,2,3,4:G2,G3,G4 """ v = next(vcf) np.testing.assert_array_equal( v.genotype.array(), np.array([[0, 0, 0], [1, 1, 1]], dtype=np.int16) ) v = next(vcf) np.testing.assert_array_equal( v.genotype.array(), np.array([[1, 2, 0], [2, 3, 1]], dtype=np.int16) ) v = next(vcf) np.testing.assert_array_equal( v.genotype.array(), np.array([[0, 1, -1, 0], [0, -2, -2, 1]], dtype=np.int16) ) v = next(vcf) np.testing.assert_array_equal( v.genotype.array(), np.array([[-1, -2, 1], [0, 2, 1]], dtype=np.int16) ) # test fill value np.testing.assert_array_equal( v.genotype.array(fill=-9), np.array([[-1, -9, 1], [0, 2, 1]], dtype=np.int16) ) def test_alt_homozygous_gt(): vcf = VCF(os.path.join(HERE, "test-multiallelic-homozygous-alt.vcf.gz")) assert vcf is not None v = next(vcf) assert v assert v.gt_bases[0] == '<*:DEL>/<*:DEL>' vcf = VCF(os.path.join(HERE, "test-multiallelic-homozygous-alt.vcf.gz"), gts012=True) assert vcf is not None v = next(vcf) assert v assert v.gt_bases[0] == '<*:DEL>/<*:DEL>' def test_write_missing_contig(): input_vcf = VCF('{}/seg.vcf.gz'.format(HERE)) output_vcf = Writer('/dev/null', input_vcf) for v in input_vcf: v.genotypes = [[1,1,False]] output_vcf.write_record(v) output_vcf.close() def test_set_samples(): vcf = VCF(VCF_PATH) assert len(vcf.samples) == 189, len(vcf.samples) vcf.set_samples([vcf.samples[2]]) assert len(vcf.samples) == 1 v = next(vcf) assert len(v.gt_types) == 1 def test_hrec(): vcf = VCF(VCF_PATH) for item in vcf.header_iter(): info = item.info() if info['HeaderType'] != 'GENERIC': assert 'ID' in info def test_issue44(): vcf = VCF('{}/issue_44.vcf'.format(HERE)) w = Writer('__o.vcf', vcf) for v in vcf: tmp = v.genotypes #print(tmp, file=sys.stderr) v.genotypes = tmp w.write_record(v) w.close() # "./." "." ".|." "0|0" expected = [[-1, -1, False], [-1, False], [-1, -1, True], [0, 0, True]] #print("", file=sys.stderr) for i, v in enumerate(VCF('__o.vcf')): #print(v.genotypes, file=sys.stderr) assert v.genotypes == [expected[i]], (i, v.genotypes, expected[i]) os.unlink("__o.vcf") def test_id_field_updates(): # 1 10172 . CCCTAA C 92.0 PASS v = VCF(VCF_PATH) variant = next(v) assert variant.ID is None, variant.ID variant.ID = 'foo' assert variant.ID == 'foo', variant.ID variant.ID = 100 assert variant.ID == '100', variant.ID variant.ID = 100.1 assert variant.ID == '100.1', variant.ID variant.ID = '.' assert variant.ID is None, variant.ID variant.ID = None assert variant.ID is None, variant.ID def test_set_pos(): test_vcf = '{}/test-strict-gt-option-flag.vcf.gz'.format(HERE) vcf = VCF(test_vcf, gts012=False) v = next(vcf) orig_pos, orig_start = v.POS, v.start v.set_pos(22) assert v.start == 22 assert v.POS == 23 def test_set_chrom_when_contig_not_in_header(): test_vcf = '{}/test-strict-gt-option-flag.vcf.gz'.format(HERE) new_chrom = "NEW" vcf = VCF(test_vcf, gts012=False) original_seqnames = vcf.seqnames assert new_chrom not in original_seqnames v = next(vcf) with warnings.catch_warnings(record=True) as w: v.CHROM = new_chrom assert len(w) == 1 assert "added new contig" in str(w[-1].message) assert v.CHROM == new_chrom expected_seqnames = sorted(original_seqnames + [new_chrom]) assert vcf.seqnames == expected_seqnames def test_set_chrom_after_contig_is_added_to_header(): test_vcf = '{}/test-strict-gt-option-flag.vcf.gz'.format(HERE) new_chrom = "NEW" vcf = VCF(test_vcf, gts012=False) original_seqnames = vcf.seqnames vcf.add_to_header("##contig=".format(new_chrom)) expected_seqnames = sorted(original_seqnames + [new_chrom]) assert vcf.seqnames == expected_seqnames v = next(vcf) v.CHROM = new_chrom assert v.CHROM == new_chrom def test_set_qual(): v = VCF(VCF_PATH) variant = next(v) assert variant.QUAL == 92.0 variant.QUAL = 30.0 assert variant.QUAL == 30.0 with pytest.raises(TypeError): variant.QUAL = "30.0" variant.QUAL = None assert variant.QUAL is None, 'variant.QUAL is {}'.format(variant.QUAL) def test_strict_gt_option_flag(): test_vcf = '{}/test-strict-gt-option-flag.vcf.gz'.format(HERE) #T, C #0/0 1/1 0/1 1/0 1/. ./1 0/. ./0 ./. truth_gt_bases = ('T/T', 'C/C', 'T/C', 'C/T', 'C/.', './C', 'T/.', './T', './.') truth_genotypes = ( [0, 0, False], [1, 1, False], [0, 1, False], [1, 0, False], [1, -1, False], [-1, 1, False], [0, -1, False], [-1, 0, False], [-1, -1, False], ) vcf = VCF(test_vcf, gts012=False) variant = next(vcf) msg = "VCF(gts012=False, strict_gt=False) not working" truth_gt_types = (0, 3, 1, 1, 1, 1, 0, 0, 2) print(variant.gt_bases.tolist(), file=sys.stderr) print(variant.gt_types.tolist(), file=sys.stderr) assert bool(tuple(variant.gt_bases.tolist()) == truth_gt_bases), '{} [gt_bases]'.format(msg) """ assert bool(tuple(variant.gt_types.tolist()) == truth_gt_types), '{} [gt_types]'.format(msg) assert bool(tuple(variant.genotypes) == truth_genotypes), '{} (genotypes)'.format(msg) vcf = VCF(test_vcf, gts012=False, strict_gt=True) variant = next(vcf) msg = "VCF(gts012=False, strict_gt=True) not working" truth_gt_types = (0, 3, 1, 1, 2, 2, 2, 2, 2) assert bool(tuple(variant.gt_bases.tolist()) == truth_gt_bases), '{} [gt_bases]'.format(msg) assert bool(tuple(variant.gt_types.tolist()) == truth_gt_types), '{} [gt_types]'.format(msg) assert bool(tuple(variant.genotypes) == truth_genotypes), '{} (genotypes)'.format(msg) vcf = VCF(test_vcf, gts012=True) variant = next(vcf) msg = "VCF(gts012=True, strict_gt=False) not working" truth_gt_types = (0, 2, 1, 1, 1, 1, 0, 0, 3) assert tuple(variant.gt_bases.tolist()) == truth_gt_bases, '{} [gt_bases]'.format(msg) #sys.stderr.write("\nobs:%s\n" % variant.gt_types.tolist()) #sys.stderr.write("exp:%s\n" % list(truth_gt_types)) assert tuple(variant.gt_types.tolist()) == truth_gt_types, '{} [gt_types]'.format(msg) assert tuple(variant.genotypes) == truth_genotypes, '{} (genotypes)'.format(msg) vcf = VCF(test_vcf, gts012=True, strict_gt=True) variant = next(vcf) msg = "VCF(gts012=True, strict_gt=True) not working" truth_gt_types = (0, 2, 1, 1, 3, 3, 3, 3, 3) assert tuple(variant.gt_bases.tolist()) == truth_gt_bases, '{} [gt_bases]'.format(msg) assert tuple(variant.gt_types.tolist()) == truth_gt_types, '{} [gt_types]'.format(msg) assert tuple(variant.genotypes) == truth_genotypes, '{} (genotypes)'.format(msg) """ def test_alt_repr(): v = os.path.join(HERE, "test-alt-repr.vcf") vcf = VCF(v, gts012=True, strict_gt=False) v = next(vcf) assert np.all(v.gt_types == np.array([0, 1, 2, 0, 1, 3])) v = os.path.join(HERE, "test-alt-repr.vcf") vcf = VCF(v, gts012=False, strict_gt=False) v = next(vcf) assert np.all(v.gt_types == np.array([0, 1, 3, 0, 1, 2])) """ def test_seqlens(): v = VCF(VCF_PATH) assert v.seqlens == [249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569, 4262, 15008, 19913, 27386, 27682, 33824, 34474, 36148, 36422, 36651, 37175, 37498, 38154, 38502, 38914, 39786, 39929, 39939, 40103, 40531, 40652, 41001, 41933, 41934, 42152, 43341, 43523, 43691, 45867, 45941, 81310, 90085, 92689, 106433, 128374, 129120, 137718, 155397, 159169, 161147, 161802, 164239, 166566, 169874, 172149, 172294, 172545, 174588, 179198, 179693, 180455, 182896, 186858, 186861, 187035, 189789, 191469, 211173, 547496, 171823, 35477943, 5386], v.seqlens """ def test_closed_iter(): path = os.path.join(HERE, "test-alt-repr.vcf") vcf = VCF(path, gts012=True, strict_gt=False) vcf.close() with pytest.raises(Exception): next(vcf) def test_issue72(): path = os.path.join(HERE, "test-alt-repr.vcf") vcf = VCF(path, gts012=True, strict_gt=False) v = next(vcf) assert v.INFO['DQ'] == 1 assert v.format('DQ') is not None def test_is_transition(): vcf = VCF(VCF_ALTFREQ_PATH) for r in vcf: assert r.is_transition def test_decomposed(): vcf = VCF(os.path.join(HERE, "decomposed.vcf")) v = next(vcf) #0/. ./0 1/. ./1 ./. assert np.all(v.gt_types == np.array([vcf.HOM_REF, vcf.HOM_REF, vcf.HET, vcf.HET, vcf.UNKNOWN])) def test_fd(): fh = open(os.path.join(HERE, "decomposed.vcf")) fn = fh.fileno() vcf = VCF(fn) v = next(vcf) assert np.all(v.gt_types == np.array([vcf.HOM_REF, vcf.HOM_REF, vcf.HET, vcf.HET, vcf.UNKNOWN])) fh.close() vcf.close() def test_set_reference(): fh = open(os.path.join(HERE, "decomposed.vcf")) fn = fh.fileno() vcf = VCF(fn) for v in vcf: v.REF = "CCCCA" assert "CCCCA" in str(v) def test_set_alternates(): fh = open(os.path.join(HERE, "decomposed.vcf")) fn = fh.fileno() vcf = VCF(fn) for v in vcf: v.ALT = "TTT,GGG" assert "TTT,GGG" in str(v) v.ALT = ["AAAC", "CCCA"] assert "AAAC,CCCA" in str(v) def test_no_seqlen(): vcf_path = os.path.join(HERE, "no-seq-len.vcf") vcf = VCF(vcf_path) assert vcf.seqnames == ["3"] with pytest.raises(AttributeError): vcf.seqlens def test_set_unknown_format(): vcf = VCF(VCF_PATH) vcf.add_format_to_header({'ID':'NEW', 'Type':'Float', 'Number':1, 'Description':'...'}) v = next(vcf) arr = np.array([[1.1] for s in vcf.samples]) arr[-1][0] = np.nan v.set_format('NEW', arr) record = str(v) parts = record.split() assert parts[-1][-1] == '.' assert parts[-2][-3:] == '1.1' def test_invalid_header(): # htslib produces the error "Empty sample name: trailing spaces/tabs in the header line?" p = os.path.join(HERE, "test-invalid-header.vcf") assert os.path.exists(p) with pytest.raises(Exception): VCF(p) def test_genotypes(): """ . 1 ./. ./1 ./. 1 0/1 0 0 0/1 """ exp_array = [[-1, 0], [-1, -1, 0], [-1, -1, 0], [0, 1, 0], [0, -2, 1], ] non_strict_exp_num = [ [0, 0, 1, 1], [0, 1, 1, 0], [0, 0, 1, 1], [1, 1, 0, 0], [1, 1, 0, 0], ] strict_exp_num = [x[:] for x in non_strict_exp_num] strict_exp_num[1] = [0, 0, 2, 0] # both unknown for strict_gt in (False, True): vcf = VCF(os.path.join(HERE, "test-genotypes.vcf"), strict_gt=strict_gt) exp_num = strict_exp_num if strict_gt else non_strict_exp_num for i, v in enumerate(vcf): #if i != 3: continue obs = [v.num_hom_ref, v.num_het, v.num_unknown, v.num_hom_alt] assert obs == exp_num[i], ("error with num_*") a = v.genotype.array()[0] # only 0'th item print("i:", i, " a:", v.genotype.array()[0], " exp:", exp_array[i]) assert (a == exp_array[i]).all(), " error with array" cyvcf2-0.30.14/cyvcf2/tests/test-alt-repr.vcf0000644000175000017500000000477314154107376020165 0ustar nileshnilesh##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT samplea sampleb samplec sampled samplee samplef 1 17363 . C T 62 PASS AC=2;AF=0.083;AN=24;DQ=1 GT:AD:GQ:DQ 0/0:20,0:10:0 0/1:20,20:10:. 1/1:0,20:10 0/.:20,0:. ./1:0,20:10 ./.:0,0:0:. cyvcf2-0.30.14/cyvcf2/tests/test_gt_alt_freqs.vcf0000644000175000017500000005114114154107376021162 0ustar nileshnilesh##fileformat=VCFv4.2 ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= 0.5 && (DP < 4 && %QUAL < 50))"> ##FILTER= ##FILTER= ##FILTER= ##FILTER==14)"> ##FILTER= ##FILTER= ##FILTER= 0.05, thus not somatic"> ##FILTER= ##FILTER== 4.25, thus likely false positive"> ##FILTER= 0.01/5**vd2"> ##FILTER= 0.9"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= 0.35) and low p-value for somatic (SPV < 0.05)"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##GATKCommandLine= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= 1 indicates MSI"> ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##PEDIGREE= ##SAMPLE= ##SnpEffCmd="SnpEff -cancer -i vcf -o vcf -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/vardict/PairedBatch2-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/vardict/PairedBatch2.vcf.gz " ##SnpEffVersion="4.2 (build 2015-12-05), by Pablo Cingolani" ##bcftools_annotateCommand=annotate -x FMT/DPR ##bcftools_annotateVersion=1.3+htslib-1.3 ##bcftools_filterCommand=filter -m + -s REJECT -e 'STATUS !~ ".*Somatic"' ##bcftools_filterVersion=1.3+htslib-1.3 ##bcftools_viewCommand=view ##bcftools_viewVersion=1.3+htslib-1.3 ##commandline="/usr/local/bin/freebayes -f /home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --genotype-qualities --strict-vcf --ploidy 2 --targets /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/freebayes/chr22/PairedBatch2-chr22_0_400-regions-glimit.bed --min-repeat-entropy 1 --no-partial-observations --min-alternate-fraction 0.05 --pooled-discrete --pooled-continuous --report-genotype-likelihood-max --allele-balance-priors-off /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/c-tumor2/c-tumor2-sort.bam /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/align/c-normal/c-normal-sort.bam" ##contig= ##contig= ##fileDate=20160630 ##phasing=none ##reference=file:///home/chapmanb/bio/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa ##source=freeBayes v1.0.2-29-g41c1313 ##INFO= ##SnpEffCmd="SnpEff -cancer -i vcf -o vcf -s /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/PairedBatch2-ensemble-decompose-effects-stats.html hg19 /home/chapmanb/bio/bcbio-nextgen/tests/test_automated_output/gemini/PairedBatch2-ensemble-decompose.vcf.gz " ##INFO= ##INFO= ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT c-tumor2 c-normal chr22 16060 . C T . PASS . GT:AD:BQ:DP:FREQ 0/1:8,2:30:21:0.381 0/0:0,20:.:28:0.607 chr22 16061 . C T . PASS . GT:AD:BQ:DP:FREQ 0/0:5,5:30:21:0.381 0/0:1,9:.:28:0.607 chr22 16062 . C T . PASS . GT:AD:BQ:DP:FREQ 0/0:13:30:21:0.381 ./.:0,0:.:28:0.607 chr22 16063 . C T . PASS . GT:AD:BQ:DP:FREQ 0/0:13:30:21:0.381 ./.:0,1:.:28:0.607 chr22 16064 . C T . PASS . GT:AD:BQ:DP:FREQ 0/0:13:30:21:0.381 ./.:1,0:.:28:0.607 chrM 15011 . T C . PASS . GT:GQ:DP:RO:QR:AO:QA:GL 1:160:970:0:0:968:31792:-2860.58,0 1:160:970:0:0:968:31792:-2860.58,0 cyvcf2-0.30.14/cyvcf2/tests/test-hemi.vcf0000644000175000017500000004712414154107376017356 0ustar nileshnilesh##fileformat=VCFv4.1 ##FILTER= ##FILTER= ##fileDate=20151105 ##source=freeBayes v0.9.21-17-g06ea37a ##reference=/var/reference_sequences/MiSeq/genome.fa ##phasing=none ##commandline="freebayes --report-genotype-likelihood-max --no-population-priors --use-duplicate-reads -r chr1 -F 0.15 -C 5 --min-coverage 10 -m 20 -q 20 -E 1 -f /var/reference_sequences/MiSeq/genome.fa -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G15594_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G15631_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G16714_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17401_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17765_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17766_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17874_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17881_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17882_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17965_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17976_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G17977_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18041_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18042_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18046_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18160_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18300_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18302_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18358_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18365_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18404_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18424_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18444_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18637_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18726_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18897_PE_sorted.bam -b /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/Alignments/raw/15G18915_PE_sorted.bam" ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##bcftools_concatVersion=1.2+htslib-1.2.1 ##bcftools_concatCommand=concat /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr1_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr2_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr3_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr4_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr5_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr6_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr7_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr8_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr9_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr10_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr11_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr12_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr13_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr14_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr15_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr16_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr17_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr18_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr19_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr20_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr21_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chr22_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chrX_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chrY_freebayes.vcf.gz /home/chris/analysis_dir/151027_M00755_0464_000000000-AHN5P/genesis_analysis/VCFs/chrM_freebayes.vcf.gz ##INFO= ##INFO= ##VEP=v82 cache=/var/NGS_annotation/VEP/homo_sapiens/82_GRCh37 db=. polyphen=2.2.2 sift=sift5.2.2 COSMIC=71 ESP=20141103 gencode=GENCODE 19 HGMD-PUBLIC=20152 genebuild=2011-04 regbuild=13 assembly=GRCh37.p13 dbSNP=144 ClinVar=201507 ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 15G15594 15G15631 15G16714 15G17401 15G17765 15G17766 15G17874 15G17881 15G17882 15G17965 15G17976 15G17977 15G18041 15G18042 15G18046 15G18160 15G18300 15G18302 15G18358 15G18365 15G18404 15G18424 15G18444 15G18637 15G18726 15G18897 15G18915 chr19 11210912 ID1 C T 18759.5 FAIL AB=0.259215,0.471042;ABP=1273.55,10.556;AC=2,1;AF=0.047619,0.0238095;AN=42;AO=671,491;CIGAR=1X,1X;DP=10979;DPB=10979;DPRA=3.73489,1.2339;EPP=795.954,1017.72;EPPR=15750.2;GTI=1;LEN=1,1;MEANALT=2.16667,2.75;MQM=59.9553,60;MQMR=59.9844;NS=21;NUMALT=2;ODDS=1.91924;PAIRED=1,1;PAIREDR=0.999896;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=20523,18198;QR=353946;RO=9649;RPL=88,6;RPP=795.954,1017.72;RPPR=15750.2;RPR=583,485;RUN=1,1;SAF=671,491;SAP=1460.07,1069.2;SAR=0,0;SRF=9649;SRP=20955.5;SRR=0;TYPE=snp,snp;technology.M00755=1,1;OLD_MULTIALLELIC=chr19:11210912:C/T/G;CSQ=synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000558013|2/18|||27/858|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000545707|2/16|||27/682|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130164|LDLR|ENST00000557958|2/3||||retained_intron,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000535915|2/17|||27/819|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000455727|2/16|||27/692|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130164|LDLR|ENST00000560502|2/2||||retained_intron,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000252444|2/18|||112/945|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000558518|2/18|||27/860|protein_coding,synonymous_variant|tgC/tgT|C|ENSG00000130164|LDLR|ENST00000557933|2/18|||27/948|protein_coding GT:DP:RO:QR:AO:QA:GL 0/0:1:1:32:0:0:0,-0.30103,-3.19931 0/0:1:1:39:0:0:0,-0.30103,-3.89656 0/0:1:1:38:0:0:0,-0.30103,-3.79727 .:.:.:.:.:.:. 0/0:860:842:30243:2:69:0,-247.85,-2714.28 0/1:605:324:11537:255:7581:-507.835,0,-863.6 .:.:.:.:.:.:. 0/0:801:790:29718:4:147:0,-225.744,-2659.56 0/0:474:463:16725:1:35:0,-136.519,-1501.31 .:.:.:.:.:.:. .:.:.:.:.:.:. 0/0:712:709:26635:3:114:0,-203.701,-2385.19 0/0:315:310:11093:1:20:0,-91.8423,-995.931 0/0:288:279:9886:0:0:0,-83.9874,-889.336 0/0:1081:1065:38763:2:55:0,-316.244,-3481.8 0/0:1122:1119:41998:1:39:0,-333.583,-3773.75 0/.:1036:544:20369:3:91:-1316.91,-1473.38,-3140.64 0/0:415:409:14792:0:0:0,-123.121,-1330.66 0/0:267:265:9659:0:0:0,-79.7729,-868.955 .:.:.:.:.:.:. .:.:.:.:.:.:. 0/0:226:221:8050:1:37:0,-63.4761,-720.835 0/0:250:242:8539:0:0:0,-72.8493,-768.134 0/0:198:190:6753:0:0:0,-57.1957,-607.561 0/1:882:458:16605:396:12263:-846.078,0,-1236.63 0/0:1029:1016:38005:2:72:0,-299.952,-3411.73 0/0:415:400:14467:0:0:0,-120.412,-1301.4 chr19 11210912 . C G 18759.5 . AB=0.259215,0.471042;ABP=1273.55,10.556;AC=2,1;AF=0.047619,0.0238095;AN=42;AO=671,491;CIGAR=1X,1X;DP=10979;DPB=10979;DPRA=3.73489,1.2339;EPP=795.954,1017.72;EPPR=15750.2;GTI=1;LEN=1,1;MEANALT=2.16667,2.75;MQM=59.9553,60;MQMR=59.9844;NS=21;NUMALT=2;ODDS=1.91924;PAIRED=1,1;PAIREDR=0.999896;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=20523,18198;QR=353946;RO=9649;RPL=88,6;RPP=795.954,1017.72;RPPR=15750.2;RPR=583,485;RUN=1,1;SAF=671,491;SAP=1460.07,1069.2;SAR=0,0;SRF=9649;SRP=20955.5;SRR=0;TYPE=snp,snp;technology.M00755=1,1;OLD_MULTIALLELIC=chr19:11210912:C/T/G;CSQ=missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000558013|2/18|probably_damaging(1)|deleterious(0)|27/858|protein_coding,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000545707|2/16|probably_damaging(1)|deleterious(0)|27/682|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130164|LDLR|ENST00000557958|2/3||||retained_intron,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000535915|2/17|probably_damaging(1)|deleterious(0)|27/819|protein_coding,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000455727|2/16|probably_damaging(1)|deleterious(0)|27/692|protein_coding,non_coding_transcript_exon_variant&non_coding_transcript_variant|||ENSG00000130164|LDLR|ENST00000560502|2/2||||retained_intron,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000252444|2/18|probably_damaging(1)|deleterious(0)|112/945|protein_coding,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000558518|2/18|probably_damaging(1)|deleterious(0)|27/860|protein_coding,missense_variant|tgC/tgG|C/W|ENSG00000130164|LDLR|ENST00000557933|2/18|probably_damaging(1)|deleterious(0)|27/948|protein_coding GT:DP:RO:QR:AO:QA:GL 0/0:1:1:32:0:0:0,-0.30103,-3.19931 0/0:1:1:39:0:0:0,-0.30103,-3.89656 0/0:1:1:38:0:0:0,-0.30103,-3.79727 .:.:.:.:.:.:. 0/0:860:842:30243:0:0:0,-253.467,-2720.49 0/.:605:324:11537:0:0:-507.835,-605.369,-1545.66 .:.:.:.:.:.:. 0/0:801:790:29718:1:37:0,-234.777,-2669.45 0/0:474:463:16725:0:0:0,-139.377,-1504.45 .:.:.:.:.:.:. .:.:.:.:.:.:. 0/0:712:709:26635:0:0:0,-213.43,-2395.44 0/0:315:310:11093:1:32:0,-90.7328,-994.851 0/0:288:279:9886:0:0:0,-83.9874,-889.336 0/0:1081:1065:38763:0:0:0,-320.597,-3486.75 0/0:1122:1119:41998:0:0:0,-336.853,-3777.26 0/1:1036:544:20369:488:18095:-1316.91,0,-1521.35 0/0:415:409:14792:0:0:0,-123.121,-1330.66 0/0:267:265:9659:0:0:0,-79.7729,-868.955 .:.:.:.:.:.:. .:.:.:.:.:.:. 0/0:226:221:8050:0:0:0,-66.5276,-724.163 0/0:250:242:8539:0:0:0,-72.8493,-768.134 0/0:198:190:6753:1:34:0,-54.4245,-604.502 0/.:882:458:16605:0:0:-846.078,-983.95,-2339.7 0/0:1029:1016:38005:0:0:0,-305.846,-3418.2 0/0:415:400:14467:0:0:0,-120.412,-1301.4 cyvcf2-0.30.14/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz0000644000175000017500000000050714154107376024524 0ustar nileshnileshBC*POk0???EQIE0BjnבҴ4_y={w MW ?Vy2 Ӓ/?,Р}!mc >/TSPʍDXbOE.dyYEey oϾ ;N"Ε۠n}<^ŁPӧI01XW«`ث"k$w=L!Nr]@9uS6e0 %9lJ`l#BCcyvcf2-0.30.14/cyvcf2/tests/bug.vcf.gz0000644000175000017500000001241514154107376016646 0ustar nileshnileshBC\rɑ}|Ee7uC6#cFHDze`Dh\$_uo48;":}2dV^?tӯ0xqzū>{ϣ7z?mū_OjӮtno~鹿˳WO޽}>^WOŦkW\>Eum|fڬ@Y3dQ;7CЎt8ǫ+I{58zݮN/ֻb6na.nlߴzsOs}zhO2nns Y~mWӧ_[nfs?_7vY;ۧji{{}=#v^ď}3_/Cs/W?Zu\Yo f<ݝa9 mnWYXN[qa{CSl[]?7~OS3v]7?nii%ߢɯ&a ]}ɇf_߷8|pzuzr훟˷)zǧw 8Ew<s<ǏY}wtquvUv>⊚5g_q^;̯.c|QnlO }EB1}l_ د8tq=a_p>a@wzu~/[8~~_c~,;Mwׂ2柿xG?9x{ztĻQr}t}\~1GJ1GG1QL6&I u1Aq7I:h5$GIa&5LV'hL/&i#Ob& ǹr!'cU| _?Xu :R)Ocn%|"e{yt2z=: nFqD ȿ%Du;CF"%8 5ս.vJtHUG5V IR R&*# L=(A?%B'+((4[AayX V4ZhHxvZZ\K״ߑE]C壹׈hܱP(k-! "-&JjꛃCϏETaׇq !" DP cV&B-7a aY NfEvp[|a*8 +E:"``YxCW7B OpJMj TxQXV]TQF22VT+c>PE%XC %3b%I~Do#X9BRBۤJhu j& InJ0CMщ˔`0M UESP3J F<@#[U3EBո F(+?Bo-TI ,a٤V\E6v&x #E!4"0XA3,9bI8!('ə0M-Ԉw^.G3IȞgJ6= JWPꁨW^``P>@i*(-%Xb&b7CD;USe1Is K*(1gocYIF~X$"w9~IkYhUU݆M1V%!t] i#cջ3,;sn_Cp)n |&RnFt2dUls`W3s%T%4,]aʅ cx#0:h[@B-Ͳ$ QӅ(`[- PΪ=hɲF(cO8j N>cUXeQ.3Fv|H!H3pFBT*V aR28,};}pI wB^RaiM0pR BY% VD92O"3RBQ4:5EHJUHrP I=wIH"0YR875ftXj*̧,>Ymm UNL |Yܩ8X<*tE Y4 j $# Ʈ&2R?)FeG74nFǡs U.N& UC2j |`h,w@@39_d !.2cg"4;z.UAkbi(G@IT4uBbj׊aXAQeh( V[U4U8h=ES#yA)[<,'z@42"(@Uh}`FNwhiB H~&ILhu.W*S;lLSΫA3, D\#T{eQPQ;GnmǧFC$ Hf(9ka;ܣӦ8keZk ))sxjYH~p "o fO(B\#b Ђ@.I ` MZP  -B@jtPn_^jZ Zl1{j2Ɩ=Mk]ho.5`K!s`J5JXbQ|R⒄(H^wXR2PQ`m¯P)Mmu$)h)g*ژ~R* bUHll(´Io> X[ QؚlB6I@.tprgJΩypVxLXX!ŠުRX1:nyΔat](S(] qWf3YqE!Mp4`㯤TY&:)F$N-YDzbW%AR#)iaP찔i찀8,P/a8BBd89^,){;UqE5v.mϺ Z{I' ⏴A,+sGˁC#-gШdBO8+a }wf'd(rh$.B}t2.󤨇e ~UǠKgB[gx\:@/e`8Qv/&l"ΩZ'Ey·!A$.=թ j"e僨xN)0lHJ ~9;IPɃIdJ+l50G`HDŽJ4P\| Q$!?F(U%:]̔X(8Ǡ[ l0ls$ϼV lg#6ueX>Ql%4 Bi(U ŠI!MF^Rq>nz2mVU7:SzF}`m',j|+h94AI?ctUQ4ASQ6%{P5bJ9tQRz'xJ%a&B[G' K2FKvC3&-U,T'ֱ0YΒdv= v5պ TY?Cg蜴ᢓ1my$,H>猄1rSJSM-) ^;8Cɣ(Zl9B17ud8+i3jN57elblXPFɇLVJm7^w9{*ƩN{SEdƱ& mӹk]b -VV/EOFQXdbj2j(>vvHWI,u[QҦRmmgI&x L;`³`ZaD]y-:M:ˁ2~x9.TU;s K43{)LqorUփUJ/1ѬNr6}{N=+xS@o8[gBS]E0 =j'zVVk!UCj,5WzKT`-u Zup *cF(~ B*3%U [<4%+T:r%"9:bBCcyvcf2-0.30.14/cyvcf2/tests/test.snpeff.vcf0000644000175000017500000004154614154107376017720 0ustar nileshnilesh##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/all.conc.on.pos.dedup.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##reference=file:///home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa ##SnpEffVersion="SnpEff 3.1b (build 2012-11-14), by Pablo Cingolani" ##SnpEffCmd="SnpEff GRCh37.68 -c /Users/arq5x/src/other/snpEff_3_1/snpEff.config -i vcf -o vcf rs-exome.all.raw.nobaq.2012-Nov-15.vcf " ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1094PC0005 1094PC0009 1094PC0012 1094PC0013 chr1 30548 . T G 50.09 . AC=6;AF=0.429;AN=14;BaseQRankSum=0.000;DP=7;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=29.00;MQ0=0;MQRankSum=-0.550;QD=16.70;ReadPosRankSum=0.937;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),EXON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|1),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) GT:AD:DP:GQ:PL ./. ./. ./. ./. chr1 30860 . G C 54.3 . AC=3;AF=0.058;AN=52;BaseQRankSum=2.815;DP=61;Dels=0.00;FS=2.403;HRun=0;HaplotypeScore=0.6396;InbreedingCoeff=-0.0048;MQ=36.25;MQ0=0;MQRankSum=0.396;QD=13.57;ReadPosRankSum=2.148;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) GT:AD:DP:GQ:PL 0/0:7,0:7:15.04:0,15,177 0/0:2,0:2:3.01:0,3,39 0/0:6,0:6:12.02:0,12,143 0/0:4,0:4:9.03:0,9,119 chr1 30867 . CCT C 49.48 . AC=6;AF=0.107;AN=56;BaseQRankSum=0.900;DP=65;FS=0.000;HRun=0;HaplotypeScore=12.2055;InbreedingCoeff=-0.1167;MQ=36.09;MQ0=0;MQRankSum=1.148;QD=3.81;ReadPosRankSum=0.124;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) GT:AD:DP:GQ:PL 0/0:8,0:8:18.06:0,18,283 0/0:3,0:3:6.01:0,6,60 0/1:5,1:6:17.12:17,0,215 0/0:5,0:5:9.03:0,9,142 chr1 30895 . T C 51.79 . AC=4;AF=0.069;AN=58;BaseQRankSum=-0.230;DP=63;Dels=0.00;FS=11.041;HRun=0;HaplotypeScore=0.2091;InbreedingCoeff=-0.0237;MQ=36.09;MQ0=0;MQRankSum=1.212;QD=3.98;ReadPosRankSum=0.230;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) GT:AD:DP:GQ:PL 0/1:7,1:8:8.58:9,0,188 0/1:1,2:3:29.23:33,0,29 0/0:6,0:6:18.04:0,18,206 0/0:5,0:5:12.03:0,12,139 chr1 30923 . G T 601.49 . AC=30;AF=1.000;AN=30;DP=17;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;InbreedingCoeff=-0.1858;MQ=35.61;MQ0=0;QD=35.38;EFF=DOWNSTREAM(MODIFIER||||85|FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000469289|1),INTRON(MODIFIER|||||MIR1302-10|antisense|NON_CODING|ENST00000473358|2),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|) GT:AD:DP:GQ:PL ./. ./. ./. ./. chr1 69270 . A G 2971.02 . AC=53;AF=0.946;AN=56;BaseQRankSum=1.675;DP=100;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0340;InbreedingCoeff=0.1553;MQ=31.06;MQ0=0;MQRankSum=-0.742;QD=31.61;ReadPosRankSum=-1.925;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcG|S60|305|OR4F5|protein_coding|CODING|ENST00000335137|) GT:AD:DP:GQ:PL ./. ./. 1/1:0,3:3:9.03:106,9,0 1/1:0,6:6:18.05:203,18,0 chr1 69428 . T G 938.56 . AC=3;AF=0.0283;AN=106;BaseQRankSum=-0.638;DP=5013;DS;Dels=0.00;FS=2.607;HRun=0;HaplotypeScore=2.5603;InbreedingCoeff=0.3557;MQ=29.79;MQ0=0;MQRankSum=-5.524;QD=18.40;ReadPosRankSum=4.047;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tGt|F113C|305|OR4F5|protein_coding|CODING|ENST00000335137|) GT:AD:DP:GQ:PL 0/0:2,0:2:6.01:0,6,62 0/0:79,0:79:99:0,201,1853 0/0:87,0:87:99:0,243,2236 0/0:107,0:107:99:0,294,2744 chr1 69511 . A G 101944.44 . AC=79;AF=0.878;AN=90;BaseQRankSum=-1.592;DP=3853;DS;Dels=0.00;FS=20.586;HRun=0;HaplotypeScore=3.0494;InbreedingCoeff=0.1357;MQ=33.24;MQ0=0;MQRankSum=-12.858;QD=26.51;ReadPosRankSum=-1.756;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aca/Gca|T141A|305|OR4F5|protein_coding|CODING|ENST00000335137|) GT:AD:DP:GQ:PL ./. ./. 0/1:2,4:6:15.70:16,0,40 0/1:2,2:4:21.59:22,0,40 chr1 69761 . A T 1026.71 . AC=8;AF=0.091;AN=88;BaseQRankSum=1.333;DP=574;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.3806;InbreedingCoeff=0.5887;MQ=32.18;MQ0=0;MQRankSum=-2.342;QD=21.39;ReadPosRankSum=-3.271;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D224V|305|OR4F5|protein_coding|CODING|ENST00000335137|) GT:AD:DP:GQ:PL 0/0:1,0:1:3.01:0,3,33 0/1:6,1:7:12.39:12,0,177 0/0:12,0:12:36.11:0,36,442 0/0:9,0:9:27.08:0,27,324 chr1 69871 . G A 82.97 . AC=2;AF=0.025;AN=80;BaseQRankSum=-0.646;DP=154;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.1095;InbreedingCoeff=0.1693;MQ=31.10;MQ0=0;MQRankSum=-0.154;QD=20.74;ReadPosRankSum=-0.292;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D261N|305|OR4F5|protein_coding|CODING|ENST00000335137|) GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12.02:0,12,129 0/0:2,0:2:6.02:0,6,67 0/0:2,0:2:6.02:0,6,73 cyvcf2-0.30.14/cyvcf2/tests/test.bug.117.vcf0000644000175000017500000000066614154107376017521 0ustar nileshnilesh##fileformat=VCFv4.0 ##phasing=partial ##contig= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 chr1 4 . T C 9.6 . . GT:HQ ./.:51,51 0|0:51,51 1/1:51,51 chr1 5 . A GA 10 . . GT:HQ 0|0:10,10 0|0:10,10 0|0:3,3 chr1 25 . AACG GA 10 . . GT:HQ 0|0:10,10 1/1:10,10 0|0:3,3 cyvcf2-0.30.14/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi0000644000175000017500000000015014154107376025273 0ustar nileshnileshBCK qddd```b P7B%P)m0kD8 Hj0DBCcyvcf2-0.30.14/cyvcf2/tests/test-genotypes.vcf0000644000175000017500000000102514154107376020437 0ustar nileshnilesh##fileformat=VCFv4.1 ##FORMAT= ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT samplea sampleb 1 8466747 . A C . PASS . GT:PL .:. 1:36,0 1 8466747 . A C . PASS . GT:PL ./.:. ./1:36,0,40 1 8466747 . A T . PASS . GT:PL ./.:. 1:36,0 1 8466747 . A T . PASS . GT 0/1 0 1 8466747 . A T . PASS . GT 0 0/1 cyvcf2-0.30.14/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi0000644000175000017500000000014714154107376023757 0ustar nileshnileshBCJ qddd```b P}CžB%{r !`$6tq8 PB@BCcyvcf2-0.30.14/cyvcf2/tests/empty.vcf0000644000175000017500000000000014154107376016573 0ustar nileshnileshcyvcf2-0.30.14/cyvcf2/tests/test.mnp.vcf0000644000175000017500000002551714154107376017231 0ustar nileshnilesh##fileformat=VCFv4.2 ##fileDate=20200122 ##source=freeBayes v1.3.1-dirty ##reference=assembly/scaffolds.fasta ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##phasing=none ##commandline="freebayes -p 1 -f assembly/scaffolds.fasta mappings/evol1.sorted.dedup.q20.bam" ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown NODE_1_length_348724_cov_30.410613 146999 . TCGGT GCGGG,GCGGT 0 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=1;AO=2,2;CIGAR=1X3M1X,1X4M;DP=33;DPB=33;DPRA=0,0;EPP=7.35324,7.35324;EPPR=3.0103;GTI=0;LEN=5,1;MEANALT=3,3;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=180.296;PAIRED=1,1;PAIREDR=1;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=51,26;QR=928;RO=28;RPL=0,0;RPP=7.35324,7.35324;RPPR=3.32051;RPR=2,2;RUN=1,1;SAF=0,0;SAP=7.35324,7.35324;SAR=2,2;SRF=15;SRP=3.32051;SRR=13;TYPE=complex,snp GT:DP:AD:RO:QR:AO:QA:GL 0:33:28,2,2:28:928:2,2:51,26:0,-79.0317,-81.2895 NODE_5_length_164027_cov_28.935175 46218 . CGT CGG 9.34428e-16 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=3;CIGAR=2M1X;DP=38;DPB=38.6667;DPRA=0;EPP=9.52472;EPPR=13.4954;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=227.003;PAIRED=1;PAIREDR=1;PAO=0.5;PQA=12.5;PQR=12.5;PRO=0.5;QA=61;QR=1175;RO=35;RPL=0;RPP=9.52472;RPPR=10.5174;RPR=3;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=19;SRP=3.56868;SRR=16;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 0:38:35,3:35:1175:3:61:0,-100.335 NODE_12_length_115292_cov_29.218192 69322 . GCC TCC,GCA,GCG 4.33994e-15 . AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=1;AO=2,5,2;CIGAR=1X2M,2M1X,2M1X;DP=33;DPB=35;DPRA=0,0,0;EPP=3.0103,13.8677,7.35324;EPPR=3.40511;GTI=0;LEN=1,1,1;MEANALT=5,5,5;MQM=21,60,60;MQMR=55.5909;NS=1;NUMALT=3;ODDS=124.05;PAIRED=1,1,1;PAIREDR=1;PAO=0,1,1;PQA=0,35.3333,35.3333;PQR=35.3333;PRO=1;QA=29,95,60;QR=714;RO=22;RPL=1,4,2;RPP=3.0103,6.91895,7.35324;RPPR=12.8806;RPR=1,1,0;RUN=1,1,1;SAF=0,4,2;SAP=7.35324,6.91895,7.35324;SAR=2,1,0;SRF=16;SRP=12.8806;SRR=6;TYPE=snp,snp,snp GT:DP:AD:RO:QR:AO:QA:GL 0:33:22,2,5,2:22:714:2,5,2:29,95,60:0,-61.2863,-55.0685,-58.2018 NODE_22_length_87915_cov_29.488718 87208 . GCA GA 0 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=2;CIGAR=1M1D1M;DP=34;DPB=33.3333;DPRA=0;EPP=3.0103;EPPR=5.45321;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=206.136;PAIRED=1;PAIREDR=0.96875;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=1091;RO=32;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=13;SRP=5.45321;SRR=19;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 0:34:32,2:32:1091:2:74:0,-91.4633 NODE_31_length_46922_cov_30.386978 253 . AGG CGA 1.10297e-14 . AB=0;ABP=0;AC=0;AF=0;AN=1;AO=6;CIGAR=1X1M1X;DP=49;DPB=49;DPRA=0;EPP=4.45795;EPPR=4.27278;GTI=0;LEN=3;MEANALT=1;MQM=38.1667;MQMR=58.7209;NS=1;NUMALT=1;ODDS=265.514;PAIRED=0.833333;PAIREDR=0.976744;PAO=0;PQA=0;PQR=0;PRO=0;QA=202;QR=1477;RO=43;RPL=5;RPP=8.80089;RPPR=3.0608;RPR=1;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=25;SRP=5.48477;SRR=18;TYPE=complex GT:DP:AD:RO:QR:AO:QA:GL 0:49:43,6:43:1477:6:202:0,-116.271 NODE_69_length_1317_cov_64.516129 720 . ATTAC ATAC,AATAC 6.69002e-15 . AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=1;AO=2,2;CIGAR=1M1D3M,1M1X3M;DP=18;DPB=17.6;DPRA=0,0;EPP=3.0103,7.35324;EPPR=5.49198;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=60;NS=1;NUMALT=2;ODDS=79.4694;PAIRED=1,1;PAIREDR=0.928571;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=69,30;QR=467;RO=14;RPL=2,1;RPP=7.35324,3.0103;RPPR=5.49198;RPR=0,1;RUN=1,1;SAF=1,1;SAP=3.0103,3.0103;SAR=1,1;SRF=8;SRP=3.63072;SRR=6;TYPE=del,snp GT:DP:AD:RO:QR:AO:QA:GL 0:18:14,2,2:14:467:2,2:69,30:0,-35.8718,-39.4036 cyvcf2-0.30.14/cyvcf2/tests/decomposed.vcf0000644000175000017500000000071014154107376017567 0ustar nileshnilesh##fileformat=VCFv4.1 ##ALT= ##ALT= ##FORMAT= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 3 81262 . G A 1826147.32 . . GT 0/. ./0 1/. ./1 ./. cyvcf2-0.30.14/cyvcf2/tests/no-seq-names.vcf0000644000175000017500000000063214154107376017753 0ustar nileshnilesh##fileformat=VCFv4.1 ##ALT= ##ALT= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2 sample3 sample4 sample5 3 81262 . G A 1826147.32 . . GT 0/. ./0 1/. ./1 ./. cyvcf2-0.30.14/cyvcf2/tests/__init__.py0000644000175000017500000000000214154107376017050 0ustar nileshnilesh# cyvcf2-0.30.14/cyvcf2/tests/test.vcf.gz.tbi0000644000175000017500000000014714154107376017624 0ustar nileshnileshBCJ qddd```b P7B!P)#@^ ŋP^i_F~BCcyvcf2-0.30.14/cyvcf2/tests/test-diff.csi0000644000175000017500000000016514154107376017336 0ustar nileshnileshBCXsdc```eX fb/!GZ1F{-LH@"  !2"S? > BCcyvcf2-0.30.14/cyvcf2/tests/test_cli.py0000644000175000017500000000051614154107376017131 0ustar nileshnileshfrom cyvcf2 import VCF import os.path from click.testing import CliRunner from cyvcf2.cli import cyvcf2 HERE = os.path.dirname(__file__) VCF_PATH = os.path.join(HERE, "test.vcf.gz") #Sanity check for cli def test_version(): runner = CliRunner() result = runner.invoke(cyvcf2, [VCF_PATH]) assert result.exit_code == 0 cyvcf2-0.30.14/cyvcf2/tests/test_gt_bases.vcf.gz0000644000175000017500000001405414154107376020720 0ustar nileshnileshBC]N݅w Ǔоn>M؋R/ W*qB";Ion<;9Lc;p v}Ut>$Ityc҄1%^UT:4 )d2OO:4p4GJ' |xs>mir4%ޚvɹ>I|y.ׯQmcn?|S޼y:?+2UOT62\saJ0H<f̭R/!)|}B|{m %QxwGAR v(Ah H!DZ0%N goУgn׈gA^X%JO`.ϕgIgnB5Px >@K ,c0oFvyG_r Tлu4p9q@aۆ!7"%;~ޑdX'>.#}^'@7%uG-"m޶.[UZ=> m(݋n-(tzqu}ѹ|4 X挜D{e/7/6x sOmMgkGʁR@`%)M҄}ŝQMGb{V %+{ |9Lmx?~CY 0kĦ3B-,G4N?YL6<ͫ4 EA6?R8?y!v[WݠCmIR E(yEݟ {sB2V`Whzg7frhlF`rVsZ6ѭhn&@`FS&4@PÝI+>D7Ѽ`]L>ji}Nȷ6( qph`AABXBVUDF:0/ ,s]{?Ōá xјdRM ͭi' ] ,lhKP`?ꉀ@‰ lpԚ@ j+HIF3Ǔl R^[Qnb{g>v3l(kj%ܐa5e{5znX@QXh;#d°oi`8Q̘nMeoNZ,X @4^`Kxkp8n" XXXL&m瓅aѨmb Vo{-1-l­g@:AY36Mo(EJ)]3}:Y`Rdj@]* ;ꃝαg[G&&01%3D77ǝ\d.<KѺ@@w̅YBPδ̭\j7#{g#@ǛFY>£Ed ̳0h>j?t PۥS`Ă+\K";pyw,!Z3A>Bkɭ5gRq{D{ރB샃]@qMUDVQGeCI\EhMa:xg(iR<{(ŝvk`J>+GwH-]B$U@&G7]_ؤYd3LՑZ z¸% #h']RaXm—DSNC2K9T\/ɝx#M$B9!_%{ ?h = ]s1BG*a\0 / c`ЋAk?{S.(v%MUj%ț_ d9'po.$$ɋOH =oj)g  + f[+36ocǙY uu,(amnZCN_,Fp%;g9Ssru4i}\9b_7X]'_Xk>< a og/#` y?hNӟr&}l-thǧYF녱}}17LQ7fkK{y"^g0Eb`508έ 8;+,M[iVaiSL) C<<{Ok5GihA)v -L ?Bhkcr$NRD~aXJgD7ܠcMW>[?wCJfܕ9[)Q֋Jt17g-#M;a'7:ᒞN,ېǛgR`Ё%oN[D:Æ(p%WF=[ucϖ5$;#6d0.ҲA~ |CXCŠ/q'|c@ ;;36$ha!߄ND ËJ Vʣ=&Ha"3(# *AX)Tz!땺bt p Z =*^8PH 5CHV>.^73>|N;`shD&c)uA臛=>`Gho6^s"P2xd }.Bye#˘e8GlYsckr`h^v.{$DrnDĒH!'yٍGL|Rt,DyO9aBn]@ґԖt40W~Hzb!r?^94 T\-Ѳw"}!_ghUmJH^_oDڑf %?"T*1y>ÇG!8#%UsMv+hcJW:Һz>}QB9+F^C/1=Z҂Ԏ74}x:"m|<(@hķ!D[q=P9 @r 嗦+pr"$X`ePLB`e:vCI'R7)\^v#am66QS/;o0n?h(N?TFZVc!%~̔˶mƈI €kn-TQw-u-m.TGmr}acd\]~{+6K"` B%=./%{JY@i"l>|zg1?㿫s=2{?0zv.;Wgw^33Q`s6rۀ:Br^O>z75ǚf& 5:{rNxFk3熦|é<6~ 61@Wv 9w_x8_]eM]nşNoi7..Av~׼vYcLm]Ѿ*]{h][ jtd|WmE~z)_(ڸQwuqmry :- f`.9UƯ Ӆ1v)8@ִ*l\J6"fG}<Ն+t-xUm*'5]P&:ʥV(Q uC;.30LI1Ƽ{ktuwG3Īt*K\׭ԺTUC1 3[TBCcyvcf2-0.30.14/cyvcf2/tests/test_writer.py0000644000175000017500000000523714154107376017703 0ustar nileshnileshfrom io import StringIO from ..cyvcf2 import Writer try: from pathlib import Path except ImportError: from pathlib2 import Path # python 2 backport class TestFileModeInference: def test_defaultModeWithVcfFname_returnsUncompressedVcf(self): fname = "test.vcf" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_defaultModeWithBcfFname_returnsCompressedBcf(self): fname = "test.bcf" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "wb" assert actual == expected def test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf(self): fname = "test.bcf" mode = "wbu" actual = Writer._infer_file_mode(fname, mode) expected = mode assert actual == expected def test_defaultModeWithCompressedBcfFname_returnsCompressedBcf(self): fname = "test.bcf.gz" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "wb" assert actual == expected def test_defaultModeWithCompressedVcfFname_returnsCompressedVcf(self): fname = "test.vcf.gz" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "wz" assert actual == expected def test_defaultModeWithStdOut_returnsUncompressedVcf(self): fname = "-" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_defaultModeWithNonVcfName_returnsUncompressedVcf(self): fname = "foo" mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_defaultModeWithIntFname_returnsUncompressedVcf(self): fname = 1 mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_defaultModeWithHandle_returnsUncompressedVcf(self): fname = StringIO() mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_defaultModeWithPosixPath_returnsUncompressedVcf(self): fname = Path("test.vcf") mode = None actual = Writer._infer_file_mode(fname, mode) expected = "w" assert actual == expected def test_explicitMode_doesNotInferFromFname(self): fname = "test.vcf.gz" mode = "wb4" actual = Writer._infer_file_mode(fname, mode) expected = "wb4" assert actual == expected cyvcf2-0.30.14/cyvcf2/__main__.py0000644000175000017500000000050614154107376015700 0ustar nileshnileshimport sys from .cli import cyvcf2 as cli """ cyvcf2.__main__ ~~~~~~~~~~~~~~~~~~~~~ The main entry point for the command line interface. Invoke as ``cyvcf2`` (if installed) or ``python -m cyvcf2`` (no install required). """ if __name__ == "__main__": # exit using whatever exit code the CLI returned sys.exit(cli())cyvcf2-0.30.14/cyvcf2/helpers.h0000644000175000017500000000031514154107376015417 0ustar nileshnilesh#include #include int as_gts(int *gts, int num_samples, int ploidy, int strict_gt, int HOM_ALT, int UNKNOWN); int32_t* bcf_hdr_seqlen(const bcf_hdr_t *hdr, int32_t *nseq); cyvcf2-0.30.14/cyvcf2/__init__.py0000644000175000017500000000023614154107376015717 0ustar nileshnileshfrom .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, par_het) Reader = VCFReader = VCF __version__ = "0.30.14" cyvcf2-0.30.14/cyvcf2/helpers.c0000644000175000017500000000522614154107376015420 0ustar nileshnilesh#include #define MAX(x, y) (((x) > (y)) ? (x) : (y)) int as_gts(int32_t *gts, int num_samples, int ploidy, int strict_gt, int HOM_ALT, int UNKNOWN) { int j = 0, i, k; int missing= 0, found=0; for (i = 0; i < ploidy * num_samples; i += ploidy){ missing = 0; found = 0; for (k = 0; k < ploidy; k++) { if bcf_gt_is_missing(gts[i+k]) { missing += 1; } } if (missing == ploidy) { gts[j++] = UNKNOWN; // unknown continue; } else if ( (missing != 0) && (strict_gt == 1) ) { gts[j++] = UNKNOWN; // unknown continue; } if(ploidy == 1 || gts[i+1] == bcf_int32_vector_end) { int a = bcf_gt_allele(gts[i]); if (a == 0) { gts[j++] = 0; } else if (a == 1) { gts[j++] = HOM_ALT; } else { gts[j++] = UNKNOWN; } continue; } int a = bcf_gt_allele(gts[i]); int b = bcf_gt_allele(gts[i+1]); if((a == 0) && (b == 0)) { gts[j++] = 0; // HOM_REF continue; } //fprintf(stderr, "i: %d\tmissing:%d\ta:%d\tb:%d\n", i/ploidy, missing, a, b); if ((missing > 0) && ((a == 0) || (b == 0))) { // if a single allele is missing e.g 0/. it's still encoded as hom ref because it has no alts gts[j++] = 0; // HOM_REF continue; } else if((a == 1) && (b == 1)) { gts[j] = HOM_ALT; // HOM_ALT } else if((a != b)) { gts[j] = 1; // HET } else if((a == b)) { gts[j] = HOM_ALT; // HOM_ALT } else { gts[j] = UNKNOWN; // unknown } j++; } return j; } KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t) typedef khash_t(vdict) vdict_t; // this is taken directly from atks/vt int32_t* bcf_hdr_seqlen(const bcf_hdr_t *hdr, int32_t *nseq) { vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_CTG]; int tid, m = kh_size(d); int32_t *lens = (int32_t*) malloc(m*sizeof(int32_t)); khint_t k; int found = 0; for (k=kh_begin(d); k 0 && sscanf(kh_val(d, k).hrec[0]->vals[lens[tid]],"%d",&j) ) lens[tid] = j; if(lens[tid] > 0){ found++; } } *nseq = m; // found is used to check that we actually got the lengths. if(found == 0){ *nseq = -1; } return lens; } cyvcf2-0.30.14/cyvcf2/relatedness.h0000644000175000017500000001423614154107376016275 0ustar nileshnilesh#include #include #define _HOM_REF 0 #define _HET 1 #define _HOM_ALT 2 #define _UNKNOWN 3 // internal calculate of alternate allele frequency. static inline float aaf(int *gt_types, int32_t n_samples){ float af = 0; int i, n_called = 0; for (i = 0; i < n_samples; i++){ if(gt_types[i] == _UNKNOWN){ continue; } af += gt_types[i]; n_called += 1; } return af / (float)(2 * n_called); } int pow2(uint32_t v) { int r = 0; // r will be lg(v) while (v >>= 1) { r++; } return r; } // calculate a bins of IBD between 2 pairs of samples. // returns 0 starting a new run-length and run_length + 1 if continuing. // *bins are filled in powers of 2 so that we have a bins of, e.g.: // (0, 1), (2, 3), (4, 7), (8, 15), (16, 31) ... // this should be called iteratively, sending the return value in as the new // run_length. int ibd(int agt, int bgt, int run_length, float pi, int *bins, int32_t n_bins) { if(agt == bgt) { if (agt != _UNKNOWN) { run_length++; } return run_length; } // skip unknown. if (agt == _UNKNOWN || bgt == _UNKNOWN) { return run_length; } // if they arent equal genotypes, we only stop the run if they have a lowish relatedness float val = (agt - 2 * pi) * (bgt - 2 * pi); // end this block. if (val < -0.8) { int b = pow2(run_length); b = (b >= n_bins) ? n_bins : b; bins[b]++; run_length = 0; } else if (val > 0) { // only increment if any info run_length += 1; } return run_length; } // related takes an array of genotypes (0=_HOM_REF, 1=_HET, 2=HOMALT, 3=_UNKNOWN) and updates asum and N // which are used to calculate relatedness between samples j, k as asum[j, k] / N[j, k]. // The result value should be ~1 for self and idential twins, ~0.5 for sibs and parent off-spring. // This should be called on few hundred to a few thousand variants that are // not in linkage and have an aaf > 1 / n_samples (or so). // asum and N are of length n_samples * n_samples and assumed to be in C order. // http://www.nature.com/ng/journal/v42/n7/full/ng.608.html int related(int *gt_types, double *asum, int32_t *N, int32_t *ibs0, int32_t *ibs2, int32_t n_samples) { int idx, uidx, n_used = 0; int32_t j, k; float pi = aaf(gt_types, n_samples); //if(pi < 0.1 || pi > 0.6) { return 0; } float numer, val; float gtj, gtk; float denom = 2.0 * pi * (1.0 - pi); if(denom == 0) { return 0; } for(j=0; j 2.5) { // ibs2* ibs2[uidx]+=1; } else if (val > 2.5) { ibs2[idx] += (gtj == gtk && gtk != _HET); } // heuristic to avoid too-large values /* if(val > 30.0) { fprintf(stderr, "pos: %.1f\taaf: %.4f\tgtj, gtk: %f,%f\n", val, pi, gtj, gtk); val = 30.0; } else if (val < -2.0){ val = -2.0; fprintf(stderr, "negative: %.1f\n", val); } */ asum[idx] += val; N[idx]+= 1; } } return n_used; } // returns 1 if this is a usable site. static inline int ab_ok(double ab, int ab_missing) { if (ab_missing) { return 1; } return ab >= 0.2 && ab <= 0.8; } // implementation of the relatedness calculation in king. // ibs is n_samples * n_samples. the lower diag stores ibs0, the lower diag stores number of shared hets // n is n_samples * n_samples. lower stores the number of times that each pair was used. // upper diag stores the ibs2. // hets is n_samples it counts the number of hets per sample. // IBS0: (AA, aa) and (aa, AA) // IBS1: 1 _HET, 1 HOM_{REF,ALT} : not calculated (shared-hets is used instead) // IBS2: samples are same (even unphased hets) int krelated(int32_t *gt_types, int32_t *ibs, int32_t *n, int32_t *hets, int32_t n_samples, double *ab) { int32_t j, k; int n_used = 0; int32_t gtj, gtk; int is_het = 0; // check if we have any values with an AB. If not, then the site can still be usable. int ab_missing = 1; for (j = 0; j = 0) { ab_missing = 0; break; } } hets[n_samples - 1] += (gt_types[n_samples -1] == _HET && ab_ok(ab[n_samples - 1], ab_missing)); for(j=0; j 0) { return cov/sqrt(vAB); } return 0.0; }