##fileformat=VCFv4.1
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AB,Number=1,Type=Float,Description="Allele balance for each het genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
##FORMAT=<ID=MQ0,Number=1,Type=Integer,Description="Number of Mapping Quality Zero Reads per sample">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=GenotypeGVCFs,Version=3.2-2-gec30cee,Date="Wed Sep 03 16:15:40 EDT 2014",Epoch=1409775340906,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=/ifs/e63data/offitlab/ngstools/variantcallers/gatk/ravichav_mskcc.org.key tag=NA read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=8 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/ifs/e63data/offitlab/Lymphoma/OnelALL/Project_4843/Sample_CGRBG2432/CGRBG2432_TGACCA_baserecal_maxAltAlleles_322.raw.snps.indels.g.vcf)])] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub includeNonVariantSites=false annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=20 input_prior=[] sample_ploidy=2 annotation=[InbreedingCoeff, FisherStrand, QualByDepth, ChromosomeCounts, GenotypeSummaries] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine=<ID=HaplotypeCaller,Version=3.2-2-gec30cee,Date="Wed Sep 03 11:57:08 EDT 2014",Epoch=1409759828736,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[CGRBG2432_TGACCA_baserecal.bam] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=/ifs/e63data/offitlab/ngstools/variantcallers/gatk/ravichav_mskcc.org.key tag=NA read_filter=[] intervals=[/ifs/e63data/offitlab/ngstools/BED_files/AgilentCaptureBaitFiles/SureSelect_AllExon_V5_wo_chr_split/SureSelect_AllExon_V5_wo_chr.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=LINEAR variant_index_parameter=128000 logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN graphOutput=null bamOutput=null bam_compression=null disable_bam_indexing=null generate_md5=null simplifyBAM=null bamWriterType=CALLED_HAPLOTYPES dbsnp=(RodBinding name=dbsnp source=/ifs/e63data/offitlab/ngstools/REF/GATK_resourcebundle_b37/dbsnp_137.b37.vcf) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[ClippingRankSumTest, DepthPerSampleHC, StrandBiasBySample] excludeAnnotation=[SpanningDeletions, TandemRepeatAnnotator, ChromosomeCounts, FisherStrand, QualByDepth] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF annotateNDA=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=-0.0 max_alternate_alleles=20 input_prior=[] sample_ploidy=2 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingTails=false consensus=false GVCFGQBands=[5, 20, 60] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 minPruning=2 gcpHMM=10 includeUmappedReads=false useAllelesTrigger=false phredScaledGlobalReadMismappingRate=45 maxNumHaplotypesInPopulation=128 mergeVariantsViaLD=false pair_hmm_implementation=VECTOR_LOGLESS_CACHING keepRG=null justDetermineActiveRegions=false dontGenotype=false errorCorrectKmers=false debugGraphTransformations=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false allowCyclesInKmerGraphToGeneratePaths=false noFpga=false errorCorrectReads=false kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 pcr_indel_model=CONSERVATIVE activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine=<ID=VariantAnnotator,Version=3.2-2-gec30cee,Date="Sun Sep 14 00:41:49 EDT 2014",Epoch=1410669709705,CommandLineOptions="analysis_type=VariantAnnotator input_file=[] showFullBamList=false read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[] intervals=[/home/pcingola/workspace/SnpEff/tests/integration/test_gatk.vcf] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/home/pcingola/snpEff/data/genomes/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=/home/pcingola/workspace/SnpEff/tests/integration/test_gatk.vcf) snpEffFile=(RodBinding name=snpEffFile source=/home/pcingola/workspace/SnpEff/tests/integration/test_gatk.eff.vcf) dbsnp=(RodBinding name= source=UNBOUND) comp=[] resource=[] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub annotation=[SnpEff] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GATKCommandLine=<ID=VariantAnnotator,Version=3.2-2-gec30cee,Date="Wed Sep 03 16:36:18 EDT 2014",Epoch=1409776578169,CommandLineOptions="analysis_type=VariantAnnotator input_file=[CGRBG2432_TGACCA_baserecal.bam] showFullBamList=false read_buffer_size=null phone_home=NO_ET gatk_key=/ifs/e63data/offitlab/ngstools/variantcallers/gatk/ravichav_mskcc.org.key tag=NA read_filter=[] intervals=[/ifs/e63data/offitlab/ngstools/BED_files/AgilentCaptureBaitFiles/SureSelect_AllExon_V5_wo_chr_split/SureSelect_AllExon_V5_wo_chr.bed] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/ifs/e63data/offitlab/Human_Decoy_REF/hs37d5.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=LENIENT_VCF_PROCESSING disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=8 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 logging_level=INFO log_to_file=null help=false version=false variant=(RodBinding name=variant source=CGRBG2432_TGACCA_bwa_withmaxallele_322.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/ifs/e63data/offitlab/ngstools/REF/GATK_resourcebundle_b37/dbsnp_137.b37.vcf) comp=[] resource=[] out=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.gatk.engine.io.stubs.VariantContextWriterStub annotation=[QualByDepth, HaplotypeScore, MappingQualityRankSumTest, ReadPosRankSumTest, FisherStrand, InbreedingCoeff, Coverage, AlleleBalance, AlleleBalanceBySample, BaseCounts, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, DepthPerAlleleBySample, GCContent, HardyWeinberg, HomopolymerRun, LowMQ, MappingQualityZero, MappingQualityZeroBySample, NBaseCount, QualByDepth, RMSMappingQuality, ReadPosRankSumTest, SpanningDeletions, TandemRepeatAnnotator, VariantType] excludeAnnotation=[] group=[] expression={} useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive)
##INFO=<ID=ABHet,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
##INFO=<ID=ABHom,Number=1,Type=Float,Description="Allele Balance for homs (A/(A+O))">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseCounts,Number=4,Type=Integer,Description="Counts of each base">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=CCC,Number=1,Type=Integer,Description="Number of called chromosomes">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=GC,Number=1,Type=Integer,Description="GC content around the variant (see docs for window size details)">
##INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">
##INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HW,Number=1,Type=Float,Description="Phred-scaled p-value for Hardy-Weinberg violation">
##INFO=<ID=HWP,Number=1,Type=Float,Description="P value from test of Hardy Weinberg Equilibrium">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=LowMQ,Number=3,Type=Float,Description="3-tuple: <fraction of reads with MQ=0>,<fraction of reads with MQ<=10>,<total number of reads>">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">
##INFO=<ID=OND,Number=1,Type=Float,Description="Overall non-diploid ratio (alleles/(alleles+non-alleles))">
##INFO=<ID=PercentNBaseSolid,Number=1,Type=Float,Description="Percentage of N bases in the pileup (counting only SOLiD reads)">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SNPEFF_AMINO_ACID_CHANGE,Number=1,Type=String,Description="Old/New amino acid for the highest-impact effect resulting from the current variant (in HGVS style)">
##INFO=<ID=SNPEFF_CODON_CHANGE,Number=1,Type=String,Description="Old/New codon for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_EFFECT,Number=1,Type=String,Description="The highest-impact effect resulting from the current variant (or one of the highest-impact effects, if there is a tie)">
##INFO=<ID=SNPEFF_EXON_ID,Number=1,Type=String,Description="Exon ID for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_FUNCTIONAL_CLASS,Number=1,Type=String,Description="Functional class of the highest-impact effect resulting from the current variant: [NONE, SILENT, MISSENSE, NONSENSE]">
##INFO=<ID=SNPEFF_GENE_BIOTYPE,Number=1,Type=String,Description="Gene biotype for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_GENE_NAME,Number=1,Type=String,Description="Gene name for the highest-impact effect resulting from the current variant">
##INFO=<ID=SNPEFF_IMPACT,Number=1,Type=String,Description="Impact of the highest-impact effect resulting from the current variant [MODIFIER, LOW, MODERATE, HIGH]">
##INFO=<ID=SNPEFF_TRANSCRIPT_ID,Number=1,Type=String,Description="Transcript ID for the highest-impact effect resulting from the current variant">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=VariantType,Number=1,Type=String,Description="Variant type description">
##OriginalSnpEffCmd="SnpEff  -o gatk GRCh37.75 /home/pcingola/workspace/SnpEff/tests/integration/test_gatk.vcf "
##OriginalSnpEffVersion="4.0e (build 2014-09-13), by Pablo Cingolani"
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##reference=file:///home/pcingola/snpEff/data/genomes/hs37d5.fa
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CGRBG2432_TGACCA
1	762273	rs3115849	G	A	1720.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=71,0,0,0;DB;DP=71;Dels=0.00;FS=0.000;GC=62.38;GQ_MEAN=153.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.1972,0.1972,71;MLEAC=2;MLEAF=1.00;MQ=26.35;MQ0=14;NCC=0;PercentNBaseSolid=0.0000;QD=33.74;SNPEFF_CODON_CHANGE=715;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=LINC01128;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000445118;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,71:51:99:14:1749,153,0
1	762320	rs75333668	C	T	717.77	.	ABHet=0.457;AC=1;AF=0.500;AN=2;BaseCounts=0,26,0,29;BaseQRankSum=-3.235;ClippingRankSum=0.044;DB;DP=55;Dels=0.00;FS=0.000;GC=59.41;GQ_MEAN=639.00;HRun=1;HaplotypeScore=0.6651;LowMQ=0.0727,0.0727,55;MLEAC=1;MLEAF=0.500;MQ=39.40;MQ0=4;MQRankSum=0.518;NCC=0;PercentNBaseSolid=0.0000;QD=15.60;ReadPosRankSum=0.479;SNPEFF_CODON_CHANGE=668;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=lincRNA;SNPEFF_GENE_NAME=LINC01128;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000445118;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.470:26,29:46:99:4:746,0,639
1	865694	rs9988179	C	T	1272.77	.	ABHet=0.512;AC=1;AF=0.500;AN=2;BaseCounts=1,44,0,43;BaseQRankSum=-4.285;ClippingRankSum=0.072;DB;DP=88;Dels=0.00;FS=12.588;GC=63.37;GQ_MEAN=1301.00;HRun=0;HaplotypeScore=0.9995;LowMQ=0.0000,0.0000,88;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.498;NCC=0;PercentNBaseSolid=0.0000;QD=15.15;ReadPosRankSum=0.597;SNPEFF_AMINO_ACID_CHANGE=H78Y;SNPEFF_CODON_CHANGE=Cac/Tac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000420190;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.510:44,43:84:99:0:1301,0,1472
1	871215	rs28419423	C	G	1478.77	.	ABHet=0.471;AC=1;AF=0.500;AN=2;BaseCounts=0,42,49,0;BaseQRankSum=5.055;ClippingRankSum=0.832;DB;DP=91;Dels=0.00;FS=2.705;GC=61.39;GQ_MEAN=1183.00;HRun=1;HaplotypeScore=1.5757;LowMQ=0.0000,0.0000,91;MLEAC=1;MLEAF=0.500;MQ=59.44;MQ0=0;MQRankSum=1.220;NCC=0;PercentNBaseSolid=0.0000;QD=17.40;ReadPosRankSum=1.144;SNPEFF_AMINO_ACID_CHANGE=P123;SNPEFF_CODON_CHANGE=ccC/ccG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=5;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000420190;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.460:42,49:85:99:0:1507,0,1183
1	876499	rs4372192	A	G	742.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,23,0;DB;DP=23;Dels=0.00;FS=0.000;GC=67.33;GQ_MEAN=63.00;HRun=6;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,23;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=31.57;SNPEFF_CODON_CHANGE=984;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000466827;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,23:21:63:0:771,63,0
1	877715	rs6605066	C	G	1670.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,50,0;DB;DP=50;Dels=0.00;FS=0.000;GC=76.24;GQ_MEAN=135.00;HRun=3;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,50;MLEAC=2;MLEAF=1.00;MQ=57.75;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=24.79;SNPEFF_CODON_CHANGE=1869;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,50:45:99:0:1699,135,0
1	877831	rs6672356	T	C	2217.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,62,0,0;DB;DP=62;Dels=0.00;FS=0.000;GC=71.29;GQ_MEAN=183.00;HRun=2;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,62;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.65;SNPEFF_AMINO_ACID_CHANGE=W343R;SNPEFF_CODON_CHANGE=Tgg/Cgg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=10;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=SAMD11;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000342066;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,62:61:99:0:2246,183,0
1	879364	rs201551514	G	A	1834.77	.	ABHet=0.522;AC=1;AF=0.500;AN=2;BaseCounts=56,0,60,0;BaseQRankSum=4.865;ClippingRankSum=-2.880e-01;DB;DP=116;Dels=0.00;FS=4.952;GC=69.31;GQ_MEAN=1863.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,116;MLEAC=1;MLEAF=0.500;MQ=59.36;MQ0=0;MQRankSum=0.986;NCC=0;PercentNBaseSolid=0.0000;QD=15.95;ReadPosRankSum=1.666;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.520:60,56:115:99:0:1863,0,1894
1	880238	rs3748592	A	G	1735.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,45,0;DB;DP=45;Dels=0.00;FS=0.000;GC=37.62;GQ_MEAN=135.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,45;MLEAC=2;MLEAF=1.00;MQ=59.07;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.37;SNPEFF_CODON_CHANGE=461;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000496938;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,45:45:99:0:1764,135,0
1	881627	rs2272757	G	A	491.77	.	ABHet=0.360;AC=1;AF=0.500;AN=2;BaseCounts=16,0,9,0;BaseQRankSum=-2.916;ClippingRankSum=0.142;DB;DP=25;Dels=0.00;FS=0.000;GC=64.36;GQ_MEAN=298.00;HRun=1;HaplotypeScore=0.7340;LowMQ=0.0000,0.0000,25;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.047;NCC=0;PercentNBaseSolid=0.0000;QD=19.67;ReadPosRankSum=0.764;SNPEFF_AMINO_ACID_CHANGE=L615;SNPEFF_CODON_CHANGE=Ctg/Ttg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=16;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.360:9,16:25:99:0:520,0,298
1	883625	rs4970378	A	G	1417.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,39,0;DB;DP=39;Dels=0.00;FS=0.000;GC=67.33;GQ_MEAN=114.00;HRun=2;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,39;MLEAC=2;MLEAF=1.00;MQ=57.71;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=27.40;SNPEFF_CODON_CHANGE=2683;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000496938;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,39:38:99:0:1446,114,0
1	887560	rs3748595	A	C	743.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,21,0,0;DB;DP=21;Dels=0.00;FS=0.000;GC=56.44;GQ_MEAN=60.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,21;MLEAC=2;MLEAF=1.00;MQ=58.89;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=26.55;SNPEFF_CODON_CHANGE=2246;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=processed_transcript;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487214;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,21:20:60:0:772,60,0
1	887801	rs3828047	A	G	466.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,14,0;DB;DP=14;Dels=0.00;FS=0.000;GC=62.38;GQ_MEAN=39.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,14;MLEAC=2;MLEAF=1.00;MQ=55.15;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=31.97;SNPEFF_AMINO_ACID_CHANGE=T394;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=10;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,14:13:39:0:495,39,0
1	888639	rs3748596	T	C	4834.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,133,0,0;DB;DP=133;Dels=0.00;FS=0.000;GC=58.42;GQ_MEAN=381.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,133;MLEAC=2;MLEAF=1.00;MQ=54.25;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.04;SNPEFF_AMINO_ACID_CHANGE=E306;SNPEFF_CODON_CHANGE=gaA/gaG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=9;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,133:127:99:0:4863,381,0
1	888659	rs3748597	T	C	5310.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,145,0,0;DB;DP=145;Dels=0.00;FS=0.000;GC=60.40;GQ_MEAN=415.00;HRun=1;HaplotypeScore=0.9665;LowMQ=0.0000,0.0000,145;MLEAC=2;MLEAF=1.00;MQ=55.55;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=29.36;SNPEFF_AMINO_ACID_CHANGE=I300V;SNPEFF_CODON_CHANGE=Atc/Gtc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=9;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000327044;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,145:138:99:0:5339,415,0
1	894573	rs13303010	G	A	1127.77	.	ABHet=0.633;AC=1;AF=0.500;AN=2;BaseCounts=41,0,64,0;BaseQRankSum=3.018;ClippingRankSum=-1.455e+00;DB;DP=105;Dels=0.00;FS=0.000;GC=65.35;GQ_MEAN=1156.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,105;MLEAC=1;MLEAF=0.500;MQ=59.12;MQ0=0;MQRankSum=0.807;NCC=0;PercentNBaseSolid=0.0000;QD=11.51;ReadPosRankSum=0.173;SNPEFF_CODON_CHANGE=1394;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.610:64,41:98:99:0:1156,0,2072
1	897325	rs4970441	G	C	6202.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,167,0,0;DB;DP=167;Dels=0.00;FS=0.000;GC=65.35;GQ_MEAN=483.00;HRun=1;HaplotypeScore=0.9997;LowMQ=0.0000,0.0000,167;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=31.76;SNPEFF_AMINO_ACID_CHANGE=A203;SNPEFF_CODON_CHANGE=gcG/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=4;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,167:161:99:0:6231,483,0
1	897564	rs13303229	T	C	6422.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,172,1,0;DB;DP=173;Dels=0.00;FS=0.000;GC=63.37;GQ_MEAN=502.00;HRun=1;HaplotypeScore=1.9886;LowMQ=0.0000,0.0000,173;MLEAC=2;MLEAF=1.00;MQ=58.54;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=29.96;SNPEFF_CODON_CHANGE=543;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=nonsense_mediated_decay;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000466300;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,172:167:99:0:6451,502,0
1	898323	rs6605071	T	C	3799.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,99,0,0;DB;DP=99;Dels=0.00;FS=0.000;GC=66.34;GQ_MEAN=286.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,99;MLEAC=2;MLEAF=1.00;MQ=59.53;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=24.93;SNPEFF_CODON_CHANGE=4485;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=NOC2L;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000477976;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,99:95:99:0:3828,286,0
1	902128	rs28499371	C	T	1404.77	.	ABHet=0.534;AC=1;AF=0.500;AN=2;BaseCounts=0,56,0,50;BaseQRankSum=-7.051;ClippingRankSum=-4.730e-01;DB;DP=106;Dels=0.00;FS=0.000;GC=73.27;GQ_MEAN=1433.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,106;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.565;NCC=0;PercentNBaseSolid=0.0000;QD=13.64;ReadPosRankSum=-1.312;SNPEFF_AMINO_ACID_CHANGE=A43V;SNPEFF_CODON_CHANGE=gCt/gTt;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=2;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379410;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.530:56,50:103:99:0:1433,0,1929
1	906272	rs28507236	A	C	1114.77	.	ABHet=0.566;AC=1;AF=0.500;AN=2;BaseCounts=50,39,0,0;BaseQRankSum=3.527;ClippingRankSum=-5.000e-03;DB;DP=89;Dels=0.00;FS=0.858;GC=69.31;GQ_MEAN=1143.00;HRun=4;HaplotypeScore=0.9867;LowMQ=0.0000,0.0000,89;MLEAC=1;MLEAF=0.500;MQ=58.43;MQ0=0;MQRankSum=1.480;NCC=0;PercentNBaseSolid=0.0000;QD=13.43;ReadPosRankSum=0.392;SNPEFF_AMINO_ACID_CHANGE=A206;SNPEFF_CODON_CHANGE=gcA/gcC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=5;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379409;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.560:50,39:83:99:0:1143,0,1463
1	907609	rs79890672	T	C	1843.77	.	ABHet=0.430;AC=1;AF=0.500;AN=2;BaseCounts=0,64,1,52;BaseQRankSum=3.875;ClippingRankSum=0.146;DB;DP=117;Dels=0.00;FS=0.000;GC=74.26;GQ_MEAN=1316.00;HRun=0;HaplotypeScore=1.3670;LowMQ=0.0000,0.0000,117;MLEAC=1;MLEAF=0.500;MQ=56.58;MQ0=0;MQRankSum=2.172;NCC=0;PercentNBaseSolid=0.0000;QD=18.44;ReadPosRankSum=-0.416;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.450:52,64:100:99:0:1872,0,1316
1	907622	rs59928984	G	C	2065.77	.	ABHet=0.390;AC=1;AF=0.500;AN=2;BaseCounts=0,70,54,1;BaseQRankSum=-1.098;ClippingRankSum=-7.210e-01;DB;DP=125;Dels=0.00;FS=0.759;GC=72.28;GQ_MEAN=1153.00;HRun=0;HaplotypeScore=20.5481;LowMQ=0.0000,0.0000,125;MLEAC=1;MLEAF=0.500;MQ=55.83;MQ0=0;MQRankSum=0.512;NCC=0;PercentNBaseSolid=0.0000;QD=20.66;ReadPosRankSum=1.645;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.440:54,70:100:99:0:2094,0,1153
1	908275	rs145574509	G	A	684.77	.	ABHet=0.560;AC=1;AF=0.500;AN=2;BaseCounts=22,0,30,0;BaseQRankSum=-1.397;ClippingRankSum=0.479;DB;DP=52;Dels=0.00;FS=1.188;GC=68.32;GQ_MEAN=713.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,52;MLEAC=1;MLEAF=0.500;MQ=58.66;MQ0=0;MQRankSum=-0.225;NCC=0;PercentNBaseSolid=0.0000;QD=13.70;ReadPosRankSum=-0.577;SNPEFF_AMINO_ACID_CHANGE=G346D;SNPEFF_CODON_CHANGE=gGc/gAc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=11;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379410;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.580:30,22:50:99:0:713,0,976
1	908414	rs28504611	C	T	544.77	.	ABHet=0.620;AC=1;AF=0.500;AN=2;BaseCounts=0,32,0,19;BaseQRankSum=2.119;ClippingRankSum=-3.600e-01;DB;DP=51;Dels=0.00;FS=4.127;GC=64.36;GQ_MEAN=573.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,51;MLEAC=1;MLEAF=0.500;MQ=59.55;MQ0=0;MQRankSum=-0.939;NCC=0;PercentNBaseSolid=0.0000;QD=10.90;ReadPosRankSum=0.839;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.630:32,19:50:99:0:573,0,1020
1	909768	rs2340593	A	G	4446.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,127,0;DB;DP=127;Dels=0.00;FS=0.000;GC=61.39;GQ_MEAN=358.00;HRun=2;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,127;MLEAC=2;MLEAF=1.00;MQ=59.42;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=31.79;SNPEFF_CODON_CHANGE=811;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000433179;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,127:119:99:0:4475,358,0
1	911595	rs7417106	A	G	1839.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,52,0;DB;DP=52;Dels=0.00;FS=0.000;GC=71.29;GQ_MEAN=147.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,52;MLEAC=2;MLEAF=1.00;MQ=59.11;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.92;SNPEFF_AMINO_ACID_CHANGE=V683A;SNPEFF_CODON_CHANGE=gTg/gCg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=5;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000433179;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,52:49:99:0:1868,147,0
1	912049	rs9803103	T	C	1468.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,43,0,0;DB;DP=43;Dels=0.00;FS=0.000;GC=71.29;GQ_MEAN=120.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,43;MLEAC=2;MLEAF=1.00;MQ=58.81;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=26.67;SNPEFF_CODON_CHANGE=28;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000479361;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,43:40:99:0:1497,120,0
1	914333	rs13302979	C	G	2787.77	.	ABHom=1.000;AC=2;AF=1.00;AN=2;BaseCounts=0,0,78,0;DB;DP=78;Dels=0.00;FS=0.000;GC=77.23;GQ_MEAN=219.00;HRun=2;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,78;MLEAC=2;MLEAF=1.00;MQ=59.17;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.69;SNPEFF_AMINO_ACID_CHANGE=E579Q;SNPEFF_CODON_CHANGE=Gag/Cag;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000341290;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,78:73:99:0:2816,219,0
1	914852	rs13303368	G	C	4399.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,103,0,0;DB;DP=103;Dels=0.00;FS=0.000;GC=70.30;GQ_MEAN=307.00;HRun=0;HaplotypeScore=0.5784;LowMQ=0.0000,0.0000,103;MLEAC=2;MLEAF=1.00;MQ=59.69;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.05;SNPEFF_AMINO_ACID_CHANGE=Q406E;SNPEFF_CODON_CHANGE=Cag/Gag;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000341290;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,103:99:99:0:4428,307,0
1	914876	rs13302983	T	C	4735.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,116,0,0;DB;DP=116;Dels=0.00;FS=0.000;GC=66.34;GQ_MEAN=334.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,116;MLEAC=2;MLEAF=1.00;MQ=59.52;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=28.52;SNPEFF_AMINO_ACID_CHANGE=S398G;SNPEFF_CODON_CHANGE=Agc/Ggc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000341290;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,116:111:99:0:4764,334,0
1	914940	rs13303033	T	C	4725.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,123,0,0;DB;DP=123;Dels=0.00;FS=0.000;GC=65.35;GQ_MEAN=364.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,123;MLEAC=2;MLEAF=1.00;MQ=59.25;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=33.06;SNPEFF_AMINO_ACID_CHANGE=A376;SNPEFF_CODON_CHANGE=gcA/gcG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000341290;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,123:121:99:0:4754,364,0
1	915227	rs13303355	A	G	2876.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,82,0;DB;DP=82;Dels=0.00;FS=0.000;GC=57.43;GQ_MEAN=226.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,82;MLEAC=2;MLEAF=1.00;MQ=55.45;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=24.01;SNPEFF_AMINO_ACID_CHANGE=L281;SNPEFF_CODON_CHANGE=Ttg/Ctg;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=3;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000341290;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,82:75:99:0:2905,226,0
1	916549	rs6660139	A	G	4649.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,1,132,0;DB;DP=133;Dels=0.00;FS=0.000;GC=67.33;GQ_MEAN=376.00;HRun=0;HaplotypeScore=1.2434;LowMQ=0.0000,0.0000,133;MLEAC=2;MLEAF=1.00;MQ=59.06;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=27.57;SNPEFF_AMINO_ACID_CHANGE=W20R;SNPEFF_CODON_CHANGE=Tgg/Cgg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=2;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf170;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000433179;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,132:125:99:0:4678,376,0
1	935222	rs2298214	C	A	1848.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=53,1,0,0;DB;DP=54;Dels=0.00;FS=0.000;GC=83.17;GQ_MEAN=153.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,54;MLEAC=2;MLEAF=1.00;MQ=56.94;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.21;SNPEFF_AMINO_ACID_CHANGE=R44S;SNPEFF_CODON_CHANGE=agG/agT;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=1;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=HES4;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000428771;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:1,53:51:99:0:1877,153,0
1	948921	rs15842	T	C	6115.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=1,165,0,0;DB;DP=166;Dels=0.00;FS=0.000;GC=61.39;GQ_MEAN=484.00;HRun=0;HaplotypeScore=0.6651;LowMQ=0.0000,0.0000,166;MLEAC=2;MLEAF=1.00;MQ=58.74;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.17;SNPEFF_CODON_CHANGE=33;SNPEFF_EFFECT=UTR_5_PRIME;SNPEFF_EXON_ID=1;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ISG15;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000379389;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,165:161:99:0:6144,484,0
1	949654	rs8997	A	G	6099.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,156,0;DB;DP=156;Dels=0.00;FS=0.000;GC=62.38;GQ_MEAN=457.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,156;MLEAC=2;MLEAF=1.00;MQ=59.85;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=26.33;SNPEFF_AMINO_ACID_CHANGE=V98;SNPEFF_CODON_CHANGE=gtA/gtG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=2;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=ISG15;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379389;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,156:152:99:0:6128,457,0
1	978603	rs138543546	CCT	C	1759.77	.	AC=2;AF=1.00;AN=2;BaseCounts=0,42,0,0;DB;DP=42;FS=0.000;GC=70.30;GQ_MEAN=120.00;HRun=0;LowMQ=0.0000,0.0000,42;MLEAC=2;MLEAF=1.00;MQ=60.51;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.44;SNPEFF_CODON_CHANGE=2175;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000479707;VariantType=DELETION.NumRepetitions_1.EventLength_2.RepeatExpansion_CT	GT:AD:DP:GQ:MQ0:PL	1/1:0,40:40:99:0:1788,120,0
1	978850	.	T	G	141.77	.	ABHet=0.781;AC=1;AF=0.500;AN=2;BaseCounts=2,2,55,64;BaseQRankSum=-5.249;ClippingRankSum=-2.070e-01;DP=123;Dels=0.00;FS=48.312;GC=69.31;GQ_MEAN=170.00;HRun=3;HaplotypeScore=11.9426;LowMQ=0.0000,0.0000,123;MLEAC=1;MLEAF=0.500;MQ=54.10;MQ0=0;MQRankSum=-2.474;NCC=0;PercentNBaseSolid=0.0000;QD=1.94;ReadPosRankSum=-0.888;SNPEFF_CODON_CHANGE=1929;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000479707;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.540:64,55:73:99:0:170,0,3797
1	978852	.	A	G	141.77	.	ABHet=0.805;AC=1;AF=0.500;AN=2;BaseCounts=97,1,27,2;BaseQRankSum=-2.272;ClippingRankSum=0.367;DP=127;Dels=0.00;FS=0.000;GC=68.32;GQ_MEAN=170.00;HRun=4;HaplotypeScore=15.1559;LowMQ=0.0000,0.0000,127;MLEAC=1;MLEAF=0.500;MQ=54.30;MQ0=0;MQRankSum=-0.586;NCC=0;PercentNBaseSolid=0.0000;QD=1.84;ReadPosRankSum=-2.387;SNPEFF_CODON_CHANGE=1927;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000479707;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.780:97,27:77:99:0:170,0,3797
1	981087	rs3128098	A	G	4692.77	.	ABHom=1.000;AC=2;AF=1.00;AN=2;BaseCounts=0,0,133,0;DB;DP=133;Dels=0.00;FS=0.000;GC=65.35;GQ_MEAN=370.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,133;MLEAC=2;MLEAF=1.00;MQ=59.34;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=33.63;SNPEFF_CODON_CHANGE=1494;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000466223;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,133:123:99:0:4721,370,0
1	981931	rs2465128	A	G	5051.77	.	ABHom=0.993;AC=2;AF=1.00;AN=2;BaseCounts=2,1,140,0;BaseQRankSum=1.707;ClippingRankSum=-4.910e-01;DB;DP=143;Dels=0.00;FS=0.000;GC=69.31;GQ_MEAN=393.00;HRun=0;HaplotypeScore=5.6725;LowMQ=0.0000,0.0000,143;MLEAC=2;MLEAF=1.00;MQ=59.35;MQ0=0;MQRankSum=-0.336;NCC=0;OND=7.463e-03;PercentNBaseSolid=0.0000;QD=33.69;ReadPosRankSum=0.611;SNPEFF_AMINO_ACID_CHANGE=S1022;SNPEFF_CODON_CHANGE=tcA/tcG;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=18;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379370;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:2,140:134:99:0:5080,393,0
1	982941	rs3128102	T	C	6374.77	.	ABHom=1.000;AC=2;AF=1.00;AN=2;BaseCounts=0,175,0,0;DB;DP=175;Dels=0.00;FS=0.000;GC=63.37;GQ_MEAN=499.00;HRun=3;HaplotypeScore=2.0321;LowMQ=0.0000,0.0000,175;MLEAC=2;MLEAF=1.00;MQ=59.58;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=31.06;SNPEFF_CODON_CHANGE=968;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000492947;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,175:166:99:0:6403,499,0
1	982960	.	A	G	2853.77	.	ABHet=0.525;AC=1;AF=0.500;AN=2;BaseCounts=100,0,93,0;BaseQRankSum=6.399;ClippingRankSum=-4.400e-01;DP=193;Dels=0.00;FS=1.150;GC=60.40;GQ_MEAN=2882.00;HRun=1;HaplotypeScore=0.8667;LowMQ=0.0000,0.0000,193;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.317;NCC=0;PercentNBaseSolid=0.0000;QD=15.59;ReadPosRankSum=0.068;SNPEFF_AMINO_ACID_CHANGE=D1175G;SNPEFF_CODON_CHANGE=gAc/gGc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=21;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379370;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.520:100,93:183:99:0:2882,0,3043
1	982994	rs10267	T	C	8179.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,220,0,0;DB;DP=220;Dels=0.00;FS=0.000;GC=61.39;GQ_MEAN=623.00;HRun=1;HaplotypeScore=2.9645;LowMQ=0.0000,0.0000,220;MLEAC=2;MLEAF=1.00;MQ=59.66;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.33;SNPEFF_AMINO_ACID_CHANGE=F1186;SNPEFF_CODON_CHANGE=ttT/ttC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=21;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379370;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,220:207:99:0:8208,623,0
1	984302	rs9442391	T	C	2188.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,60,0,0;DB;DP=60;Dels=0.00;FS=0.000;GC=72.28;GQ_MEAN=172.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,60;MLEAC=2;MLEAF=1.00;MQ=56.85;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=28.59;SNPEFF_AMINO_ACID_CHANGE=T1387;SNPEFF_CODON_CHANGE=acT/acC;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=24;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379370;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,60:57:99:0:2217,172,0
1	985266	rs2275813	C	T	4970.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,0,130;DB;DP=130;Dels=0.00;FS=0.000;GC=67.33;GQ_MEAN=379.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,130;MLEAC=2;MLEAF=1.00;MQ=59.14;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=27.32;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,130:126:99:0:4999,379,0
1	986443	rs2710887	C	T	3903.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,0,104;DB;DP=104;Dels=0.00;FS=0.000;GC=63.37;GQ_MEAN=301.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,104;MLEAC=2;MLEAF=1.00;MQ=59.60;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=25.51;SNPEFF_CODON_CHANGE=923;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000461111;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,104:100:99:0:3932,301,0
1	987200	rs9803031	C	T	5935.77	.	ABHom=1.000;AC=2;AF=1.00;AN=2;BaseCounts=0,0,0,162;DB;DP=162;Dels=0.00;FS=0.000;GC=62.38;GQ_MEAN=466.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,162;MLEAC=2;MLEAF=1.00;MQ=58.27;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=28.34;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,162:155:99:0:5964,466,0
1	988932	rs2710871	G	C	1062.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,31,0,0;DB;DP=31;Dels=0.00;FS=0.000;GC=65.35;GQ_MEAN=84.00;HRun=3;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,31;MLEAC=2;MLEAF=1.00;MQ=58.49;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.95;SNPEFF_CODON_CHANGE=1481;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=sense_intronic;SNPEFF_GENE_NAME=RP11-54O7.14;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000418300;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,31:28:84:0:1091,84,0
1	990280	rs4275402	C	T	527.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,0,0,15;DB;DP=15;Dels=0.00;FS=0.000;GC=69.31;GQ_MEAN=42.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,15;MLEAC=2;MLEAF=1.00;MQ=58.45;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=30.98;SNPEFF_AMINO_ACID_CHANGE=D2019;SNPEFF_CODON_CHANGE=gaC/gaT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=36;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=AGRN;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000379370;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,15:14:42:0:556,42,0
1	1007432	rs4333796	G	A	2522.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=60,0,0,0;DB;DP=60;Dels=0.00;FS=0.000;GC=78.22;GQ_MEAN=184.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,60;MLEAC=2;MLEAF=1.00;MQ=59.62;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.62;SNPEFF_AMINO_ACID_CHANGE=A172V;SNPEFF_CODON_CHANGE=gCg/gTg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=2;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=RNF223;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000453464;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,60:60:99:0:2551,184,0
1	1007433	rs185263154	C	T	1190.77	.	ABHet=0.417;AC=1;AF=0.500;AN=2;BaseCounts=0,25,0,35;BaseQRankSum=3.134;ClippingRankSum=-2.249e+00;DB;DP=60;Dels=0.00;FS=0.000;GC=78.22;GQ_MEAN=725.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,60;MLEAC=1;MLEAF=0.500;MQ=59.62;MQ0=0;MQRankSum=1.005;NCC=0;PercentNBaseSolid=0.0000;QD=19.85;ReadPosRankSum=1.484;SNPEFF_AMINO_ACID_CHANGE=A172T;SNPEFF_CODON_CHANGE=Gcg/Acg;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=2;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=RNF223;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000453464;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.420:25,35:60:99:0:1219,0,725
1	1018136	.	G	A	573.77	.	ABHet=0.526;AC=1;AF=0.500;AN=2;BaseCounts=18,0,22,0;BaseQRankSum=2.207;ClippingRankSum=0.921;DP=40;Dels=0.00;FS=4.887;GC=76.24;GQ_MEAN=602.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,40;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.102;NCC=0;PercentNBaseSolid=0.0000;QD=15.10;ReadPosRankSum=-0.424;SNPEFF_CODON_CHANGE=137;SNPEFF_EFFECT=UTR_3_PRIME;SNPEFF_EXON_ID=10;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf159;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000294576;VariantType=SNP	GT:AB:AD:DP:GQ:MQ0:PL	0/1:0.550:22,18:38:99:0:602,0,624
1	1018144	rs9442395	T	C	1501.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=0,39,0,0;DB;DP=39;Dels=0.00;FS=0.000;GC=74.26;GQ_MEAN=111.00;HRun=1;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,39;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=27.35;SNPEFF_CODON_CHANGE=129;SNPEFF_EFFECT=UTR_3_PRIME;SNPEFF_EXON_ID=10;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf159;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000294576;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,39:37:99:0:1530,111,0
1	1026707	rs4074137	C	A	2039.77	.	ABHom=0.982;AC=2;AF=1.00;AN=2;BaseCounts=56,1,0,0;BaseQRankSum=1.672;ClippingRankSum=0.213;DB;DP=57;Dels=0.00;FS=0.000;GC=68.32;GQ_MEAN=161.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,57;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-1.003;NCC=0;OND=0.018;PercentNBaseSolid=0.0000;QD=28.71;ReadPosRankSum=-1.064;SNPEFF_AMINO_ACID_CHANGE=G40;SNPEFF_CODON_CHANGE=ggG/ggT;SNPEFF_EFFECT=SYNONYMOUS_CODING;SNPEFF_EXON_ID=4;SNPEFF_FUNCTIONAL_CLASS=SILENT;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=C1orf159;SNPEFF_IMPACT=LOW;SNPEFF_TRANSCRIPT_ID=ENST00000427787;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:1,56:57:99:0:2068,161,0
1	1026801	rs4562563	T	A	1655.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=45,0,0,0;DB;DP=45;Dels=0.00;FS=0.000;GC=64.36;GQ_MEAN=132.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,45;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=32.35;SNPEFF_CODON_CHANGE=3785;SNPEFF_EFFECT=UPSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=retained_intron;SNPEFF_GENE_NAME=C1orf159;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000487177;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,45:44:99:0:1684,132,0
1	1132938	rs2274791	G	A	1552.77	.	ABHom=1.00;AC=2;AF=1.00;AN=2;BaseCounts=50,0,0,0;DB;DP=50;Dels=0.00;FS=0.000;GC=76.24;GQ_MEAN=137.00;HRun=0;HaplotypeScore=0.0000;LowMQ=0.0000,0.0000,50;MLEAC=2;MLEAF=1.00;MQ=57.66;MQ0=0;NCC=0;PercentNBaseSolid=0.0000;QD=33.76;SNPEFF_AMINO_ACID_CHANGE=G578D;SNPEFF_CODON_CHANGE=gGc/gAc;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=16;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=TTLL10;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379289;VariantType=SNP	GT:AD:DP:GQ:MQ0:PL	1/1:0,50:46:99:0:1581,137,0
