##fileformat=VCFv4.1 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/apply_recalibrator/d2cd22743d3eea79f59dd21ebb84a0d7/SM.recal.snps.vcf.log help=false input=[(RodBinding name=input source=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.raw.vcf)] recal_file=(RodBinding name=recal_file source=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.VarRecal.recal) tranches_file=/tmp/generate_APPLY_RECALIBRATOR.py/d2cd22743d3eea79f59dd21ebb84a0d7/ISDB11122.snps.VarRecal.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=99.0 ignore_filter=null mode=SNP filter_mismatching_base_and_quals=false" ##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/combine_variants/00e90c599e331929a09028693bed91f7/ISDB11122.SNPrecal.IndelFiltered.vcf.log help=false variant=[(RodBinding name=variant source=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/ISDB11122.indel.filtered.vcf), (RodBinding name=variant2 source=/tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/SM.recal.snps.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false" ##FILTER= 200.0"> ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##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= ##SelectVariants="analysis_type=SelectVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_SELECTEDVARIANTS.py/3aed2f246e8c0249ff8a031bd209dc10/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/tmp/generate_SELECTEDVARIANTS.py/3aed2f246e8c0249ff8a031bd209dc10/ISDB11122.variants.raw.vcf) discordance=(RodBinding name= source=UNBOUND) concordance=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sample_name=[] sample_expressions=null sample_file=null exclude_sample_name=[] exclude_sample_file=[] select_expressions=[] excludeNonVariants=false excludeFiltered=false regenotype=false restrictAllelesTo=ALL keepOriginalAC=false mendelianViolation=false mendelianViolationQualThreshold=0.0 select_random_number=0 select_random_fraction=0.0 remove_fraction_genotypes=0.0 selectTypeToInclude=[SNP] keepIDs=null fullyDecode=false forceGenotypesDecode=false justRead=false filter_mismatching_base_and_quals=false" ##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322016/printreads/880ddadd1566253466a7e6761e854445/ISDBM322016.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322018/printreads/c3a712cdc76c431297effdb013de7bd2/ISDBM322018.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322017/printreads/b43e7abc909888a6a066fc3da4c305e7/ISDBM322017.recal.bam, /storage/gluster/insilico/data/GenomicsData/ISDBM32/ISDBM322015/printreads/8eb77fc396f7325f7da846402d1a6df9/ISDBM322015.recal.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_UNIFIEDGENOTYPER.py/dbe01e32e5f0143c1e3d62bfa4a46bd0/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=6 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 generateShadowBCF=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT pcr_error_rate=1.0E-4 noSLOD=false annotateNDA=false min_base_quality_score=17 max_deletion_fraction=0.05 cap_max_alternate_alleles_for_indels=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.0010 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=/tmp/generate_UNIFIEDGENOTYPER.py/dbe01e32e5f0143c1e3d62bfa4a46bd0/dbsnp_135.b37.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[AlleleBalance, DepthOfCoverage, FisherStrand] excludeAnnotation=[] filter_mismatching_base_and_quals=false" ##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/tmp/generate_VARIANT_FILTRATION.py/af94a8015760f0c3d105ae21bdcee583/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 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 generateShadowBCF=false logging_level=INFO log_to_file=/storage/gluster/insilico/data/GenomicsData/Series//ISDB11122GPL11154/variant_filtration/af94a8015760f0c3d105ae21bdcee583/ISDB11122.indel.filtered.vcf.log help=false variant=(RodBinding name=variant source=/tmp/generate_VARIANT_FILTRATION.py/af94a8015760f0c3d105ae21bdcee583/ISDB11122.indels.raw.vcf) mask=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub filterExpression=[QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0] filterName=[GATKStandard] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskExtension=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=true invalidatePreviousFilters=false 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:///tmp/generate_COMBINE_VARIANTS.py/00e90c599e331929a09028693bed91f7/human_g1k_v37.fasta ##source=SelectVariants ##SnpEffVersion="3.3c (build 2013-06-28), by Pablo Cingolani" ##SnpEffCmd="SnpEff -t hg19 /tmp/generate_SNPEFF.py/98b17a7321fce5a67e5dcd5a1c24a311/ISDB11122.SNPrecal.IndelFiltered.vcf " ##INFO= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2 Sample3 2 9614523 rs13411809 G A 221.4 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=37.00;MQ0=0;QD=31.63;SB=-6.727e+01;VQSLOD=20.5768;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||684|CPSF3||CODING|NM_016207.3||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||||248|IAH1||CODING|NM_001039613.1||1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:73,6,0 1/1:0,2:2:6:75,6,0 2 9631340 rs10495562 T C 1193.56 PASS ABHet=0.429;ABHom=1.00;AC=7;AF=0.875;AN=8;BaseQRankSum=0.515;DB;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=37.00;MQ0=0;MQRankSum=1.030;QD=33.15;ReadPosRankSum=-1.259;SB=-1.150e+02;VQSLOD=21.4141;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||248|IAH1||CODING|NM_001039613.1||1),INTRON(MODIFIER||||824|ADAM17||CODING|NM_003183.4|17|1) GT:AD:DP:GQ:PL 1/1:0,10:10:30:362,30,0 1/1:0,8:8:24:314,24,0 0/1:3,4:7:98:138,0,98 2 9632975 rs73913116 G A 153.43 PASS ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-0.953;DB;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.260;QD=30.69;ReadPosRankSum=0.606;SB=8.184e-03;VQSLOD=21.4354;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||248|IAH1||CODING|NM_001039613.1||1),INTRON(MODIFIER||||824|ADAM17||CODING|NM_003183.4|17|1) GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,116 0/0:7,0:7:21:0,21,259 1/1:0,5:5:15:199,15,0 2 9667751 rs17525468 T C 178.77 PASS ABHet=0.667;ABHom=1.00;AC=3;AF=0.375;AN=8;BaseQRankSum=1.532;DB;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=0.825;QD=22.35;ReadPosRankSum=-0.466;SB=-1.182e-02;VQSLOD=20.6268;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||824|ADAM17||CODING|NM_003183.4|5|1) GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,40 1/1:0,5:5:15:193,15,0 0/0:2,0:2:6:0,6,73 2 9667930 rs2230818 T C 443.99 PASS ABHet=0.528;ABHom=1.00;AC=1;AF=0.125;AN=8;BaseQRankSum=-4.482;DB;DP=144;Dels=0.00;FS=2.332;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.125;MQ=37.00;MQ0=0;MQRankSum=0.087;QD=12.33;ReadPosRankSum=-1.189;SB=-1.620e+02;VQSLOD=14.1781;culprit=MQ;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aga/Gga|R202G|824|ADAM17||CODING|NM_003183.4|5|1) GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,156,2016 0/0:29,0:29:87:0,87,1151 0/1:19,17:36:99:480,0,633 2 9727657 rs41308184 C T 581.55 PASS ABHet=0.400;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-4.834;DB;DP=84;Dels=0.00;FS=1.713;HaplotypeScore=0.4661;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.547;QD=16.62;ReadPosRankSum=1.209;SB=-4.001e+01;VQSLOD=13.4379;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||245|YWHAQ||CODING|NM_006826.2|4|1) GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,742 0/1:7,10:17:99:282,0,232 0/0:30,0:30:87:0,87,1120 2 9770050 rs13417081 A G 33.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=16.51;SB=-1.182e-02;VQSLOD=20.3578;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||245|YWHAQ||CODING|NM_006826.2|2|1) GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:34,3,0 ./. 2 21232195 rs693 G A 2881.56 PASS ABHet=0.350;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=-2.447;DB;DP=135;Dels=0.00;FS=14.868;HaplotypeScore=0.4333;MLEAC=4;MLEAF=0.500;MQ=36.79;MQ0=1;MQRankSum=0.765;QD=27.18;ReadPosRankSum=-0.825;SB=-1.388e+03;VQSLOD=2.6460;culprit=FS;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T2515|4563|APOB||CODING|NM_000384.2|26|1) GT:AD:DP:GQ:PL 0/1:14,21:35:99:710,0,407 0/0:29,0:29:87:0,87,1124 1/1:0,41:41:99:1539,120,0 2 29110068 . T C 47.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.88;SB=-3.776e+01;VQSLOD=19.3897;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:79,6,0 ./. 2 40342600 rs148215685 G T 1046.81 PASS ABHet=0.461;ABHom=1.00;AC=3;AF=0.375;AN=8;BaseQRankSum=0.270;DB;DP=68;Dels=0.00;FS=3.309;HaplotypeScore=0.6947;MLEAC=3;MLEAF=0.375;MQ=37.00;MQ0=0;MQRankSum=0.319;QD=17.45;ReadPosRankSum=-1.252;SB=-4.647e+02;VQSLOD=13.3835;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER|||||SLC8A1-AS1||NON_CODING|NR_038441.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G869|937|SLC8A1||CODING|NM_001112802.1|8|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G892|960|SLC8A1||CODING|NM_001112801.1|8|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G897|965|SLC8A1||CODING|NM_001252624.1|9|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G900|968|SLC8A1||CODING|NM_001112800.1|9|1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggA|G905|973|SLC8A1||CODING|NM_021097.2|10|1) GT:AD:DP:GQ:PL 0/1:15,19:34:99:643,0,427 0/1:7,5:12:99:149,0,222 0/1:5,9:14:99:298,0,142 2 40345471 rs13005439 T C 47.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.50;SB=-1.182e-02;VQSLOD=21.1570;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||937|SLC8A1||CODING|NM_001112802.1|7|1),INTRON(MODIFIER||||960|SLC8A1||CODING|NM_001112801.1|7|1),INTRON(MODIFIER||||965|SLC8A1||CODING|NM_001252624.1|8|1),INTRON(MODIFIER||||968|SLC8A1||CODING|NM_001112800.1|8|1),INTRON(MODIFIER||||973|SLC8A1||CODING|NM_021097.2|9|1),INTRON(MODIFIER|||||SLC8A1-AS1||NON_CODING|NR_038441.1|3|1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 ./. 2 50148972 . G T 47.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.50;SB=-1.182e-02;VQSLOD=21.1570;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||937|SLC8A1||CODING|NM_001112802.1|7|1),INTRON(MODIFIER||||960|SLC8A1||CODING|NM_001112801.1|7|1),INTRON(MODIFIER||||965|SLC8A1||CODING|NM_001252624.1|8|1),INTRON(MODIFIER||||968|SLC8A1||CODING|NM_001112800.1|8|1),INTRON(MODIFIER||||973|SLC8A1||CODING|NM_021097.2|9|1),INTRON(MODIFIER|||||SLC8A1-AS1||NON_CODING|NR_038441.1|3|1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 ./. 2 71012734 rs7566476 C G 10020.01 PASS ABHet=0.502;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=0.528;DB;DP=594;Dels=0.00;FS=9.258;HaplotypeScore=2.8284;MLEAC=4;MLEAF=0.500;MQ=36.98;MQ0=0;MQRankSum=0.249;OND=1.316e-03;QD=22.57;ReadPosRankSum=0.462;SB=-4.322e+03;VQSLOD=3.3483;culprit=HaplotypeScore;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGt/aCt|S141T|219|FIGLA||CODING|NM_001004311.3|3|1) GT:AD:DP:GQ:PL 0/1:105,84:190:99:2623,0,3377 1/1:0,129:129:99:5056,388,0 0/0:150,0:150:99:0,445,5781 2 71705909 rs60945667 C T 41.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.88;SB=-1.182e-02;VQSLOD=20.4883;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|1|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|1|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|1|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|1|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|1|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|1|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|1|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|1|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|1|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|1|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|1|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|1|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|1|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|1|1) GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:73,6,0 2 71708918 rs35628632 C T 238.77 PASS ABHet=0.550;ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-1.670;DB;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=37.00;MQ0=0;MQRankSum=1.381;QD=18.37;ReadPosRankSum=0.533;SB=-1.182e-02;VQSLOD=20.5138;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|2|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|2|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|2|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|2|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|2|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|2|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|2|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|2|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|2|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|2|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|2|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|2|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|2|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|2|1) GT:AD:DP:GQ:PL ./. 0/1:2,2:4:65:65,0,68 0/1:3,2:5:64:64,0,101 2 71709120 rs12470028 G A 212.09 PASS ABHet=0.784;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=-3.247;DB;DP=28;Dels=0.00;FS=0.000;HaplotypeScore=0.4261;MLEAC=4;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=-0.098;QD=9.64;ReadPosRankSum=-0.344;SB=-2.975e+01;VQSLOD=20.0716;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|3|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|3|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|3|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|3|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|3|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|3|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|3|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|3|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|3|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|3|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|3|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|3|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|3|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|3|1) GT:AD:DP:GQ:PL 0/0:6,0:6:15:0,15,193 0/1:10,2:12:5:5,0,366 0/1:3,1:4:24:24,0,108 2 71740897 rs34999029 C A 330.21 PASS ABHet=0.375;ABHom=0.893;AC=3;AF=0.375;AN=8;BaseQRankSum=1.215;DB;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.4096;MLEAC=3;MLEAF=0.375;MQ=36.75;MQ0=0;MQRankSum=1.098;OND=0.083;QD=15.01;ReadPosRankSum=-0.512;SB=-1.615e+02;VQSLOD=4.1125;culprit=FS;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A170E|2066|DYSF||CODING|NM_001130976.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A170E|2080|DYSF||CODING|NM_003494.3|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A170E|2087|DYSF||CODING|NM_001130977.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A170E|2101|DYSF||CODING|NM_001130978.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A171E|2067|DYSF||CODING|NM_001130986.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A171E|2081|DYSF||CODING|NM_001130455.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A171E|2088|DYSF||CODING|NM_001130984.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A171E|2102|DYSF||CODING|NM_001130983.1|6|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A201E|2097|DYSF||CODING|NM_001130980.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A201E|2111|DYSF||CODING|NM_001130979.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A201E|2118|DYSF||CODING|NM_001130981.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A202E|2098|DYSF||CODING|NM_001130985.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A202E|2112|DYSF||CODING|NM_001130982.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCg/gAg|A202E|2119|DYSF||CODING|NM_001130987.1|7|1) GT:AD:DP:GQ:PL 0/1:6,10:16:99:231,0,153 0/0:9,0:9:27:0,27,295 1/1:2,4:6:12:147,12,0 2 71747235 rs11675897 A G 867.55 PASS ABHet=0.438;ABHom=1.000;AC=2;AF=0.250;AN=8;BaseQRankSum=-4.345;DB;DP=108;Dels=0.00;FS=10.501;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=0.744;QD=16.07;ReadPosRankSum=-1.197;SB=-2.180e+02;VQSLOD=12.9995;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|9|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|9|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|9|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|9|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|9|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|9|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|10|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|10|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|9|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|9|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|10|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|10|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|10|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|10|1) GT:AD:DP:GQ:PL 0/1:15,16:31:99:496,0,502 0/1:9,14:23:99:413,0,276 0/0:28,0:28:84:0,84,1069 2 71747432 rs75190231 G T 603.55 PASS ABHet=0.441;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-3.411;DB;DP=72;Dels=0.00;FS=0.000;HaplotypeScore=0.2333;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-1.750;QD=17.75;ReadPosRankSum=0.102;SB=-1.182e-02;VQSLOD=20.2872;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|10|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|10|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|10|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|10|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|10|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|10|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|11|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|11|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|10|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|10|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|11|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|11|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|11|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|11|1) GT:AD:DP:GQ:PL 0/1:8,10:18:99:339,0,264 0/1:7,9:16:99:306,0,227 0/0:19,0:19:57:0,57,745 2 71747568 rs12997658 G T 40.36 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.000;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=1.026;QD=20.18;ReadPosRankSum=1.026;SB=0.889;VQSLOD=20.6034;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|10|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|10|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|10|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|10|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|10|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|10|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|11|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|11|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|10|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|10|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|11|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|11|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|11|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|11|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:76,6,0 ./. 2 71747723 rs12713754 C G 62.02 PASS ABHet=0.417;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.895;DB;DP=10;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.546;QD=12.40;ReadPosRankSum=0.895;SB=-1.182e-02;VQSLOD=20.0621;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|10|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|10|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|10|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|10|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|10|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|10|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|11|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|11|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|10|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|10|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|11|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|11|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|11|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|11|1) GT:AD:DP:GQ:PL 0/1:1,1:2:34:34,0,34 0/1:1,2:3:31:68,0,31 0/0:1,0:1:3:0,3,39 2 71747851 rs12713755 T C 702.55 PASS ABHet=0.450;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=5.406;DB;DP=75;Dels=0.00;FS=0.000;HaplotypeScore=0.6968;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.155;QD=16.73;ReadPosRankSum=-1.982;SB=-1.164e-02;VQSLOD=17.3424;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|10|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|10|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|10|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|10|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|10|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|10|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|11|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|11|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|10|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|10|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|11|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|11|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|11|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|11|1) GT:AD:DP:GQ:PL 0/1:8,11:19:99:343,0,237 0/1:11,12:23:99:401,0,300 0/0:17,0:17:48:0,48,547 2 71747899 rs12713756 G A 1251.55 PASS ABHet=0.501;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-0.264;DB;DP=136;Dels=0.00;FS=1.654;HaplotypeScore=0.1835;MLEAC=2;MLEAF=0.250;MQ=36.93;MQ0=0;MQRankSum=1.803;OND=7.813e-03;QD=15.45;ReadPosRankSum=0.318;SB=-4.370e+02;VQSLOD=4.0277;culprit=MQRankSum;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|10|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|10|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|10|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|10|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|10|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|10|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|11|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|11|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|10|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|10|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|11|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|11|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|11|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|11|1) GT:AD:DP:GQ:PL 0/1:27,22:49:99:717,0,781 0/1:14,17:32:99:576,0,423 0/0:24,0:24:69:0,69,904 2 71754259 rs72900813 T A 41.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.88;SB=-3.176e+01;VQSLOD=21.0192;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|12|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|12|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|12|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|12|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|12|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|12|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|13|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|13|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|12|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|12|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|13|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|13|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|13|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|13|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:73,6,0 ./. ./. 2 71755380 rs4852800 A G 260.91 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.375;AN=8;BaseQRankSum=3.098;DB;DP=16;Dels=0.00;FS=3.310;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=37.00;MQ0=0;MQRankSum=-0.473;QD=28.99;ReadPosRankSum=0.053;SB=-7.550e+01;VQSLOD=14.2830;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|12|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|12|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|12|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|12|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|12|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|12|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|13|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|13|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|12|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|12|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|13|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|13|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|13|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|13|1) GT:AD:DP:GQ:PL 1/1:0,7:7:21:275,21,0 0/0:3,0:3:9:0,9,105 0/1:1,1:2:29:34,0,29 2 71757860 rs13404803 A G 38.77 VQSRTrancheSNP99.00to99.90 ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=31.58;MQ0=0;QD=19.38;SB=-2.876e+01;VQSLOD=1.5631;culprit=MQ;set=FilteredInAll;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|13|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|13|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|13|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|13|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|13|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|13|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|14|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|14|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|13|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|13|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|14|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|14|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|14|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|14|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:70,6,0 ./. ./. 2 71761197 rs74484032 G A 67.24 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;BaseQRankSum=0.406;DB;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=0.406;QD=13.45;ReadPosRankSum=0.406;SB=-2.901e+01;VQSLOD=20.7133;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|13|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|13|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|13|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|13|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|13|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|13|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|14|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|14|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|13|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|13|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|14|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|14|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|14|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|14|1) GT:AD:DP:GQ:PL 0/1:2,2:4:64:66,0,64 0/0:1,0:1:3:0,3,40 1/1:0,1:1:3:39,3,0 2 71762092 rs184773309 G A 295.61 PASS ABHet=0.597;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=2.476;DB;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.5844;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.329;OND=0.019;QD=9.54;ReadPosRankSum=-1.403;SB=-3.996e+01;VQSLOD=11.8563;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|13|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|13|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|13|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|13|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|13|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|13|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|14|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|14|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|13|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|13|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|14|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|14|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|14|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|14|1) GT:AD:DP:GQ:PL 0/1:11,7:18:99:219,0,311 0/0:10,0:10:24:0,24,245 0/1:7,5:13:99:118,0,174 2 71762232 rs4852801 C T 418.55 PASS ABHet=0.562;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-4.478;DB;DP=86;Dels=0.00;FS=5.746;HaplotypeScore=0.9383;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.816;QD=10.46;ReadPosRankSum=0.405;SB=-1.210e+02;VQSLOD=13.6122;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|14|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|14|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|14|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|14|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|14|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|14|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|15|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|15|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|14|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|14|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|15|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|15|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|15|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|15|1) GT:AD:DP:GQ:PL 0/1:18,6:24:99:150,0,606 0/1:6,10:16:99:310,0,185 0/0:26,0:26:78:0,78,988 2 71762310 rs4852802 A G 725.56 PASS ABHet=0.610;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=-3.684;DB;DP=64;Dels=0.00;FS=3.636;HaplotypeScore=0.1835;MLEAC=4;MLEAF=0.500;MQ=36.84;MQ0=0;MQRankSum=0.718;QD=16.12;ReadPosRankSum=1.073;SB=-1.840e+02;VQSLOD=4.5364;culprit=FS;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|14|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|14|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|14|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|14|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|14|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|14|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|15|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|15|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|14|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|14|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|15|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|15|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|15|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|15|1) GT:AD:DP:GQ:PL 1/1:0,14:14:42:494,42,0 0/1:8,7:15:99:170,0,252 0/1:11,5:16:99:110,0,377 2 71766499 rs10174042 C G 38.28 PASS ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.720;DB;DP=6;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.720;QD=19.14;ReadPosRankSum=-0.720;SB=-1.182e-02;VQSLOD=19.9623;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|16|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|16|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|16|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|16|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|16|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|16|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|17|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|17|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|16|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|16|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|17|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|17|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|17|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|17|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 0/0:1,0:1:3:0,3,33 0/0:1,0:1:3:0,3,37 2 71770667 rs75205546 C T 37.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=18.89;SB=-3.076e+01;VQSLOD=20.0312;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|16|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|16|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|16|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|16|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|16|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|16|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|17|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|17|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|16|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|16|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|17|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|17|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|17|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|17|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:69,6,0 ./. ./. 2 71772774 rs75392876 A C 85.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=28.41;SB=-3.922e+01;VQSLOD=20.9828;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|16|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|16|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|16|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|16|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|16|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|16|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|17|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|17|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|16|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|16|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|17|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|17|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|17|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|17|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 ./. 1/1:0,1:1:3:39,3,0 2 71776346 rs934061 A G 99.45 PASS ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=-1.300;DB;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=37.00;MQ0=0;MQRankSum=0.550;QD=24.86;ReadPosRankSum=0.550;SB=-1.182e-02;VQSLOD=20.2881;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|16|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|16|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|16|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|16|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|16|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|16|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|17|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|17|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|16|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|16|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|17|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|17|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|17|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|17|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:75,6,0 ./. 1/1:0,2:2:6:67,6,0 2 71779756 rs7599385 T G 44.26 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.736;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.736;QD=22.13;ReadPosRankSum=-0.736;SB=-3.525e+01;VQSLOD=20.6354;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|18|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|18|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|19|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|19|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|18|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|18|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|19|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|19|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|19|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|19|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|20|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|20|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|19|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|19|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 0/0:1,0:1:3:0,3,37 ./. 2 71781161 rs74340297 GAC G 243.13 PASS AC=1;AF=0.125;AN=8;BaseQRankSum=0.637;DB;DP=30;FS=10.837;HaplotypeScore=1.1821;MLEAC=1;MLEAF=0.125;MQ=37.31;MQ0=0;MQRankSum=-0.690;QD=17.37;RPA=3,2;RU=AC;ReadPosRankSum=-0.053;SB=-1.319e+02;STR;set=variant;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|20|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|20|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|21|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|21|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|20|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|20|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|21|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|21|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|21|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|21|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|22|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|22|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|21|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|21|1) GT:AD:DP:GQ:PL 0/1:7,7:14:99:288,0,344 0/0:6,0:6:18:0,18,334 0/0:4,0:5:12:0,12,216 2 71782067 rs7566581 A G 100.05 PASS ABHet=0.667;ABHom=1.00;AC=3;AF=0.375;AN=8;BaseQRankSum=1.368;DB;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.2492;MLEAC=4;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=1.368;QD=16.68;ReadPosRankSum=0.421;SB=-2.140e+01;VQSLOD=19.9803;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|20|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|20|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|21|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|21|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|20|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|20|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|21|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|21|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|21|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|21|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|22|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|22|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|21|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|21|1) GT:AD:DP:GQ:PL 0/1:2,1:3:23:23,0,67 0/0:1,0:1:3:0,3,39 1/1:0,3:3:9:120,9,0 2 71784787 rs75663047 G A 34.26 PASS ABHet=0.333;ABHom=1.00;AC=1;AF=0.250;AN=4;BaseQRankSum=-1.026;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=1.026;QD=11.42;ReadPosRankSum=1.026;SB=-3.325e+01;VQSLOD=19.7209;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|21|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|21|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|22|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|22|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|21|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|21|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|22|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|22|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|22|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|22|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|23|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|23|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|22|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|22|1) GT:AD:DP:GQ:PL 0/1:1,2:3:31:66,0,31 0/0:1,0:1:3:0,3,40 ./. 2 71795152 rs2288355 A T 1648.58 PASS ABHet=0.556;AC=4;AF=0.500;AN=8;BaseQRankSum=-0.870;DB;DP=127;Dels=0.00;FS=3.258;HaplotypeScore=0.4339;MLEAC=4;MLEAF=0.500;MQ=36.92;MQ0=0;MQRankSum=-1.153;QD=12.98;ReadPosRankSum=0.861;SB=-7.910e+02;VQSLOD=4.2010;culprit=FS;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S847|2066|DYSF||CODING|NM_001130976.1|24|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S847|2087|DYSF||CODING|NM_001130977.1|24|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S848|2067|DYSF||CODING|NM_001130986.1|24|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S848|2088|DYSF||CODING|NM_001130984.1|24|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S861|2080|DYSF||CODING|NM_003494.3|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S861|2101|DYSF||CODING|NM_001130978.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S862|2081|DYSF||CODING|NM_001130455.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S862|2102|DYSF||CODING|NM_001130983.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S878|2097|DYSF||CODING|NM_001130980.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S878|2118|DYSF||CODING|NM_001130981.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S879|2098|DYSF||CODING|NM_001130985.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S879|2119|DYSF||CODING|NM_001130987.1|25|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S892|2111|DYSF||CODING|NM_001130979.1|26|1),SYNONYMOUS_CODING(LOW|SILENT|tcA/tcT|S893|2112|DYSF||CODING|NM_001130982.1|26|1) GT:AD:DP:GQ:PL 0/1:32,21:53:99:654,0,1098 0/1:20,13:33:99:406,0,657 0/1:13,11:24:99:342,0,434 2 71795712 rs111459768 G C 43.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=21.88;SB=-1.182e-02;VQSLOD=20.0164;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|25|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|25|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|26|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|26|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|25|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|25|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|26|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|26|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|26|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|26|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|27|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|27|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|26|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|26|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:75,6,0 ./. 2 71796865 rs10205023 C G 547.01 PASS ABHet=0.667;ABHom=1.00;AC=7;AF=0.875;AN=8;BaseQRankSum=0.313;DB;DP=21;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=7;MLEAF=0.875;MQ=37.00;MQ0=0;MQRankSum=-0.313;QD=26.05;ReadPosRankSum=0.582;SB=-1.182e-02;VQSLOD=20.8798;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|25|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|25|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|26|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|26|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|25|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|25|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|26|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|26|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|26|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|26|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|27|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|27|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|26|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|26|1) GT:AD:DP:GQ:PL 1/1:0,5:5:15:186,15,0 1/1:0,7:7:21:263,21,0 1/1:0,3:3:9:117,9,0 2 71797712 rs3764971 G A 121.26 PASS ABHet=0.459;ABHom=1.000;AC=2;AF=0.333;AN=6;BaseQRankSum=1.379;DB;DP=23;Dels=0.00;FS=2.634;HaplotypeScore=0.3332;MLEAC=2;MLEAF=0.333;MQ=37.00;MQ0=0;MQRankSum=0.112;QD=12.13;ReadPosRankSum=-0.186;SB=-4.250e+00;VQSLOD=14.4044;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2066|DYSF||CODING|NM_001130976.1|27|1),INTRON(MODIFIER||||2067|DYSF||CODING|NM_001130986.1|27|1),INTRON(MODIFIER||||2080|DYSF||CODING|NM_003494.3|28|1),INTRON(MODIFIER||||2081|DYSF||CODING|NM_001130455.1|28|1),INTRON(MODIFIER||||2087|DYSF||CODING|NM_001130977.1|27|1),INTRON(MODIFIER||||2088|DYSF||CODING|NM_001130984.1|27|1),INTRON(MODIFIER||||2097|DYSF||CODING|NM_001130980.1|28|1),INTRON(MODIFIER||||2098|DYSF||CODING|NM_001130985.1|28|1),INTRON(MODIFIER||||2101|DYSF||CODING|NM_001130978.1|28|1),INTRON(MODIFIER||||2102|DYSF||CODING|NM_001130983.1|28|1),INTRON(MODIFIER||||2111|DYSF||CODING|NM_001130979.1|29|1),INTRON(MODIFIER||||2112|DYSF||CODING|NM_001130982.1|29|1),INTRON(MODIFIER||||2118|DYSF||CODING|NM_001130981.1|28|1),INTRON(MODIFIER||||2119|DYSF||CODING|NM_001130987.1|28|1) GT:AD:DP:GQ:PL 0/0:13,0:13:36:0,36,438 ./. 0/1:1,3:4:27:101,0,27 2 71797754 rs143475751 C T 238.76 PASS ABHet=0.589;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-0.272;DB;DP=30;Dels=0.00;FS=0.000;HaplotypeScore=0.2235;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.136;QD=13.26;ReadPosRankSum=-1.086;SB=-1.098e+02;VQSLOD=19.6665;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1005|2066|DYSF||CODING|NM_001130976.1|28|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1005|2087|DYSF||CODING|NM_001130977.1|28|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1006|2067|DYSF||CODING|NM_001130986.1|28|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1006|2088|DYSF||CODING|NM_001130984.1|28|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1019|2080|DYSF||CODING|NM_003494.3|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1019|2101|DYSF||CODING|NM_001130978.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1020|2081|DYSF||CODING|NM_001130455.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1020|2102|DYSF||CODING|NM_001130983.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1036|2097|DYSF||CODING|NM_001130980.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1036|2118|DYSF||CODING|NM_001130981.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1037|2098|DYSF||CODING|NM_001130985.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1037|2119|DYSF||CODING|NM_001130987.1|29|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1050|2111|DYSF||CODING|NM_001130979.1|30|1),SYNONYMOUS_CODING(LOW|SILENT|ccC/ccT|P1051|2112|DYSF||CODING|NM_001130982.1|30|1) GT:AD:DP:GQ:PL 0/1:6,8:14:99:252,0,198 0/1:3,1:4:28:28,0,106 0/0:4,0:4:12:0,12,143 2 92296844 rs62149077 A G 535.4 VQSRTrancheSNP99.90to100.00 ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=20;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=25.12;MQ0=1;QD=26.77;SB=-2.465e+02;VQSLOD=-5.9577;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,4:4:12:118,12,0 1/1:0,5:5:15:148,15,0 1/1:0,11:11:30:307,30,0 2 96610811 . G A 99.24 VQSRTrancheSNP99.90to100.00 ABHet=0.750;ABHom=0.924;AC=1;AF=0.167;AN=6;BaseQRankSum=-3.160;DP=98;Dels=0.00;FS=31.030;HaplotypeScore=0.9950;MLEAC=1;MLEAF=0.167;MQ=35.63;MQ0=2;MQRankSum=-3.208;OND=0.051;QD=3.54;ReadPosRankSum=-3.640;SB=-6.909e+01;VQSLOD=-16.6138;culprit=ReadPosRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:21,7:28:99:134,0,742 0/0:26,3:29:35:0,35,967 2 96610836 rs11893977 T C 1525.26 VQSRTrancheSNP99.90to100.00 ABHet=0.484;AC=3;AF=0.500;AN=6;BaseQRankSum=8.339;DB;DP=237;Dels=0.00;FS=25.415;HaplotypeScore=0.6200;MLEAC=3;MLEAF=0.500;MQ=29.07;MQ0=44;MQRankSum=-11.162;QD=6.44;ReadPosRankSum=-1.887;SB=-6.880e+02;VQSLOD=-32.5847;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:31,51:82:99:802,0,982 0/1:34,36:70:99:490,0,1059 2 96610899 rs62154593 T C 9177.01 VQSRTrancheSNP99.90to100.00 ABHet=0.254;AC=3;AF=0.500;AN=6;BaseQRankSum=-5.028;DB;DP=524;Dels=0.00;FS=13.215;HaplotypeScore=1.2245;MLEAC=3;MLEAF=0.500;MQ=30.98;MQ0=57;MQRankSum=-7.033;QD=17.51;ReadPosRankSum=-0.905;SB=-3.757e+03;VQSLOD=-7.6117;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:46,143:189:99:3500,0,1289 0/1:44,128:172:99:3051,0,1251 2 96610921 rs62154594 T G 10486.01 VQSRTrancheSNP99.90to100.00 ABHet=0.246;AC=3;AF=0.500;AN=6;BaseQRankSum=11.125;DB;DP=466;Dels=0.00;FS=11.140;HaplotypeScore=41.9519;MLEAC=3;MLEAF=0.500;MQ=33.62;MQ0=25;MQRankSum=0.239;OND=2.151e-03;QD=22.50;ReadPosRankSum=3.358;SB=-2.937e+03;VQSLOD=-154.9558;culprit=HaplotypeScore;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:38,126:164:99:3868,0,1028 0/1:39,115:155:99:3406,0,1076 2 96610923 rs75080810 C G 2925.26 VQSRTrancheSNP99.90to100.00 ABHet=0.708;AC=3;AF=0.500;AN=6;BaseQRankSum=-2.420;DB;DP=463;Dels=0.00;FS=19.553;HaplotypeScore=37.4395;MLEAC=3;MLEAF=0.500;MQ=33.82;MQ0=20;MQRankSum=-3.167;QD=6.32;ReadPosRankSum=0.847;SB=-4.990e+02;VQSLOD=-138.5010;culprit=HaplotypeScore;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:142,20:162:99:175,0,4755 0/1:83,71:154:99:1829,0,2623 2 96610952 rs62154595 T C 7643.01 VQSRTrancheSNP99.90to100.00 ABHet=0.220;AC=3;AF=0.500;AN=6;BaseQRankSum=9.447;DB;DP=333;Dels=0.00;FS=1.517;HaplotypeScore=11.2789;MLEAC=3;MLEAF=0.500;MQ=32.19;MQ0=33;MQRankSum=-3.305;QD=22.95;ReadPosRankSum=-0.247;SB=-1.450e+03;VQSLOD=-95.3881;culprit=HaplotypeScore;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:24,92:116:99:2895,0,459 0/1:25,90:115:99:2439,0,482 2 96610958 rs79852024 G T 335.24 VQSRTrancheSNP99.90to100.00 ABHet=0.769;ABHom=0.924;AC=1;AF=0.167;AN=6;BaseQRankSum=-7.711;DB;DP=305;Dels=0.00;FS=3.611;HaplotypeScore=11.5769;MLEAC=1;MLEAF=0.167;MQ=31.32;MQ0=44;MQRankSum=-3.385;OND=0.051;QD=3.10;ReadPosRankSum=-0.713;SB=-1.801e+01;VQSLOD=-100.3547;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/0:95,7:102:83:0,83,2985 0/1:83,25:108:99:370,0,2250 2 96611018 rs62154596 G A 124.3 VQSRTrancheSNP99.90to100.00 ABHet=0.343;ABHom=0.619;AC=5;AF=0.833;AN=6;BaseQRankSum=0.736;DB;DP=112;Dels=0.00;FS=0.000;HaplotypeScore=0.3328;MLEAC=5;MLEAF=0.833;MQ=8.11;MQ0=106;MQRankSum=-0.736;OND=0.259;QD=1.11;ReadPosRankSum=0.736;SB=-1.182e-02;VQSLOD=-21.6074;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:12,23:35:24:56,0,24 1/1:13,24:37:6:70,6,0 2 96611078 rs62154597 T G 187.26 VQSRTrancheSNP99.90to100.00 ABHom=0.670;AC=6;AF=1.00;AN=6;DB;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=7.98;MQ0=61;OND=0.328;QD=2.71;SB=-1.182e-02;VQSLOD=-21.1490;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 1/1:8,14:22:6:57,6,0 1/1:5,14:19:6:57,6,0 2 96611088 rs62154598 G A 221.08 VQSRTrancheSNP99.90to100.00 ABHet=0.323;ABHom=0.684;AC=4;AF=0.667;AN=6;BaseQRankSum=2.451;DB;DP=65;Dels=0.00;FS=0.000;HaplotypeScore=0.3277;MLEAC=4;MLEAF=0.667;MQ=12.65;MQ0=52;MQRankSum=-2.113;OND=0.105;QD=3.40;ReadPosRankSum=1.944;SB=-1.182e-02;VQSLOD=-14.8839;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:6,14:20:30:48,0,30 1/1:6,13:19:6:57,6,0 2 96611145 . C A 31.9 VQSRTrancheSNP99.00to99.90 ABHet=0.853;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=1.739;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.3282;MLEAC=2;MLEAF=0.333;MQ=28.26;MQ0=9;MQRankSum=-1.007;QD=1.23;ReadPosRankSum=0.336;SB=-1.182e-02;VQSLOD=-3.3263;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/0:13,0:13:30:0,30,329 0/1:7,1:8:12:12,0,155 2 96611146 rs149738552 A G 584.26 VQSRTrancheSNP99.00to99.90 ABHet=0.353;AC=3;AF=0.500;AN=6;BaseQRankSum=-1.035;DB;DP=39;Dels=0.00;FS=0.000;HaplotypeScore=1.3282;MLEAC=3;MLEAF=0.500;MQ=28.88;MQ0=8;MQRankSum=-1.331;QD=14.98;ReadPosRankSum=-0.866;SB=-1.182e-02;VQSLOD=-0.6526;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:6,7:13:99:185,0,105 0/1:3,5:8:62:115,0,62 2 96614212 rs4907288 A G 328.24 VQSRTrancheSNP99.00to99.90 ABHet=0.313;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=4.912;DB;DP=62;Dels=0.00;FS=4.109;HaplotypeScore=0.5239;MLEAC=1;MLEAF=0.167;MQ=30.82;MQ0=11;MQRankSum=0.492;QD=20.52;ReadPosRankSum=-0.607;SB=-4.001e+01;VQSLOD=0.9683;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:5,11:16:26:363,0,26 0/0:26,0:26:63:0,63,698 2 96614407 rs77346146 G A 65.9 VQSRTrancheSNP99.00to99.90 ABHet=0.787;AC=3;AF=0.500;AN=6;BaseQRankSum=-3.043;DB;DP=61;Dels=0.00;FS=0.000;HaplotypeScore=0.9484;MLEAC=3;MLEAF=0.500;MQ=33.73;MQ0=6;MQRankSum=0.795;QD=1.08;ReadPosRankSum=-0.694;SB=-1.182e-02;VQSLOD=-0.3939;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:23,5:28:33:33,0,808 0/1:10,2:12:8:8,0,309 2 96614424 rs148880632 G T 82.9 VQSRTrancheSNP99.00to99.90 ABHet=0.807;AC=3;AF=0.500;AN=6;BaseQRankSum=-1.957;DB;DP=53;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=34.36;MQ0=3;MQRankSum=1.398;QD=1.56;ReadPosRankSum=2.237;SB=-1.182e-02;VQSLOD=-0.4324;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:21,4:25:43:43,0,720 0/1:9,2:11:8:8,0,297 2 96614438 rs113916465 C A 250.4 VQSRTrancheSNP99.00to99.90 ABHet=0.776;AC=3;AF=0.500;AN=6;BaseQRankSum=-2.625;DB;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=34.86;MQ0=1;MQRankSum=0.859;QD=5.11;ReadPosRankSum=0.515;SB=-1.182e-02;VQSLOD=0.6556;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:17,5:22:99:130,0,561 0/1:7,1:8:15:15,0,240 2 96614520 rs112706144 A G 127.02 PASS ABHet=0.583;ABHom=1.00;AC=4;AF=0.667;AN=6;BaseQRankSum=0.729;DB;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.667;MQ=36.57;MQ0=0;MQRankSum=-0.361;QD=14.11;ReadPosRankSum=-2.219;SB=-1.182e-02;VQSLOD=1.8880;culprit=ReadPosRankSum;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:68,6,0 0/1:2,1:3:31:31,0,67 2 96615669 rs77357028 T A 120.67 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=37.00;MQ0=0;QD=30.17;SB=-3.643e+01;VQSLOD=20.5801;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:76,6,0 2 96615681 rs80305494 A G 122.67 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=37.00;MQ0=0;QD=30.67;SB=-3.943e+01;VQSLOD=20.4635;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:39,3,0 1/1:0,2:2:6:79,6,0 2 96616354 rs78161475 T C 54.35 VQSRTrancheSNP99.00to99.90 ABHet=0.667;ABHom=0.972;AC=1;AF=0.167;AN=6;BaseQRankSum=3.502;DB;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.2217;MLEAC=1;MLEAF=0.167;MQ=36.19;MQ0=0;MQRankSum=-0.052;OND=0.020;QD=4.53;ReadPosRankSum=-2.674;SB=-1.182e-02;VQSLOD=-0.1925;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:8,4:12:89:89,0,236 0/0:16,1:17:12:0,12,518 2 96616378 rs62154611 C T 310.3 VQSRTrancheSNP99.00to99.90 ABHet=0.680;AC=3;AF=0.500;AN=6;BaseQRankSum=-4.324;DB;DP=74;Dels=0.00;FS=0.000;HaplotypeScore=0.3332;MLEAC=3;MLEAF=0.500;MQ=33.47;MQ0=2;MQRankSum=-3.841;QD=4.19;ReadPosRankSum=-2.812;SB=-1.182e-02;VQSLOD=-2.1720;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:11,11:22:99:249,0,369 0/1:20,7:27:79:79,0,704 2 96616442 rs74960926 C A 1111.26 VQSRTrancheSNP99.90to100.00 ABHet=0.562;AC=3;AF=0.500;AN=6;BaseQRankSum=-7.018;DB;DP=143;Dels=0.00;FS=29.215;HaplotypeScore=0.5999;MLEAC=3;MLEAF=0.500;MQ=28.67;MQ0=2;MQRankSum=-8.054;QD=7.77;ReadPosRankSum=4.430;SB=-1.182e-02;VQSLOD=-38.0784;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:26,27:53:99:587,0,756 0/1:31,19:50:99:297,0,879 2 96616448 rs76503749 G T 1008.26 VQSRTrancheSNP99.90to100.00 ABHet=0.596;AC=3;AF=0.500;AN=6;BaseQRankSum=8.344;DB;DP=148;Dels=0.00;FS=45.553;HaplotypeScore=0.6221;MLEAC=3;MLEAF=0.500;MQ=27.68;MQ0=2;MQRankSum=-8.477;QD=6.81;ReadPosRankSum=4.454;SB=-1.182e-02;VQSLOD=-86.2849;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:28,24:52:99:485,0,687 0/1:32,19:51:99:305,0,696 2 96616485 rs78218362 C G 343.26 VQSRTrancheSNP99.90to100.00 ABHet=0.821;AC=3;AF=0.500;AN=6;BaseQRankSum=-2.583;DB;DP=153;Dels=0.00;FS=28.899;HaplotypeScore=0.3245;MLEAC=3;MLEAF=0.500;MQ=21.96;MQ0=58;MQRankSum=-6.031;QD=2.24;ReadPosRankSum=-5.438;SB=-1.182e-02;VQSLOD=-38.2841;culprit=ReadPosRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:36,10:46:99:162,0,685 0/1:43,9:52:99:140,0,644 2 96616667 rs77249402 A C 54.83 VQSRTrancheSNP99.90to100.00 ABHet=0.776;AC=3;AF=0.500;AN=6;BaseQRankSum=-0.690;DB;DP=31;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=17.88;MQ0=13;MQRankSum=2.169;QD=1.77;ReadPosRankSum=0.591;SB=-1.182e-02;VQSLOD=-9.9478;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:7,2:9:10:10,0,120 0/1:9,3:12:68:68,0,90 2 96616690 rs111409549 T C 75.46 VQSRTrancheSNP99.90to100.00 ABHet=0.759;AC=3;AF=0.500;AN=6;BaseQRankSum=1.545;DB;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.3111;MLEAC=3;MLEAF=0.500;MQ=17.39;MQ0=11;MQRankSum=1.855;QD=3.14;ReadPosRankSum=0.271;SB=-1.182e-02;VQSLOD=-9.9602;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:5,2:7:16:16,0,71 0/1:8,3:11:16:77,0,16 2 96616693 rs112782601 C A 69.51 VQSRTrancheSNP99.90to100.00 ABHet=0.738;AC=3;AF=0.500;AN=6;BaseQRankSum=0.400;DB;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.3111;MLEAC=3;MLEAF=0.500;MQ=19.81;MQ0=8;MQRankSum=1.733;QD=3.16;ReadPosRankSum=0.533;SB=-1.182e-02;VQSLOD=-7.7034;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:5,2:7:13:13,0,93 0/1:7,3:10:40:74,0,40 2 96616749 rs76572760 G T 111.66 VQSRTrancheSNP99.00to99.90 ABHet=0.550;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=0.933;DB;DP=14;Dels=0.00;FS=2.963;HaplotypeScore=0.7463;MLEAC=4;MLEAF=0.500;MQ=32.90;MQ0=0;MQRankSum=0.533;QD=12.41;ReadPosRankSum=-0.800;SB=-7.442e+01;VQSLOD=1.1134;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 0/1:3,2:5:53:53,0,99 0/0:5,0:5:12:0,12,135 2 96616758 rs79038786 T C 136.83 VQSRTrancheSNP99.00to99.90 ABHet=0.625;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=0.935;DB;DP=13;Dels=0.00;FS=2.522;HaplotypeScore=0.7463;MLEAC=4;MLEAF=0.500;MQ=34.39;MQ0=0;MQRankSum=0.935;QD=11.40;ReadPosRankSum=1.791;SB=-7.855e+01;VQSLOD=0.9819;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 0/1:3,3:6:78:78,0,94 0/1:3,1:4:23:23,0,58 2 96617194 rs75924615 A G 71.35 VQSRTrancheSNP99.00to99.90 ABHet=0.860;AC=3;AF=0.500;AN=6;BaseQRankSum=-3.490;DB;DP=79;Dels=0.00;FS=0.000;HaplotypeScore=0.9412;MLEAC=3;MLEAF=0.500;MQ=33.19;MQ0=7;MQRankSum=-4.570;QD=0.90;ReadPosRankSum=0.517;SB=-5.442e-02;VQSLOD=-2.0819;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:29,5:34:55:55,0,921 0/1:23,3:26:17:17,0,737 2 96617209 rs74343816 G T 89.43 VQSRTrancheSNP99.00to99.90 ABHet=0.835;AC=3;AF=0.500;AN=6;BaseQRankSum=-2.898;DB;DP=76;Dels=0.00;FS=0.000;HaplotypeScore=1.1971;MLEAC=3;MLEAF=0.500;MQ=34.63;MQ0=1;MQRankSum=-4.993;QD=1.18;ReadPosRankSum=0.181;SB=-9.556e-02;VQSLOD=-2.5442;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:27,5:32:52:52,0,958 0/1:23,3:26:14:14,0,756 2 96617231 rs2443879 G A 691.26 VQSRTrancheSNP99.00to99.90 ABHet=0.437;AC=3;AF=0.500;AN=6;BaseQRankSum=-4.653;DB;DP=46;Dels=0.00;FS=0.000;HaplotypeScore=0.6639;MLEAC=3;MLEAF=0.500;MQ=35.44;MQ0=1;MQRankSum=-1.217;QD=15.03;ReadPosRankSum=-0.466;SB=-1.182e-02;VQSLOD=1.6378;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:10,11:21:99:332,0,330 0/1:8,8:16:99:204,0,258 2 96617256 rs2438948 A G 246.26 VQSRTrancheSNP99.00to99.90 ABHet=0.511;AC=3;AF=0.500;AN=6;BaseQRankSum=2.878;DB;DP=22;Dels=0.00;FS=0.000;HaplotypeScore=0.2629;MLEAC=3;MLEAF=0.500;MQ=34.53;MQ0=1;MQRankSum=-1.386;QD=11.19;ReadPosRankSum=-0.320;SB=-1.182e-02;VQSLOD=1.5544;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:7,3:10:90:90,0,216 0/1:3,3:6:61:67,0,61 2 96619449 rs2918874 C T 105.53 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;BaseQRankSum=-1.754;DB;DP=7;Dels=0.00;FS=3.680;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=0.000;QD=21.11;ReadPosRankSum=0.550;SB=0.237;VQSLOD=13.7224;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:115,9,0 0/1:1,1:2:32:32,0,34 2 96619688 rs74946480 T G 1159.26 VQSRTrancheSNP99.90to100.00 ABHet=0.554;AC=3;AF=0.500;AN=6;BaseQRankSum=-3.384;DB;DP=176;Dels=0.00;FS=15.042;HaplotypeScore=8.6619;MLEAC=3;MLEAF=0.500;MQ=21.31;MQ0=42;MQRankSum=0.842;QD=6.59;ReadPosRankSum=-1.354;SB=-5.580e+02;VQSLOD=-53.0155;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:31,33:64:99:535,0,469 0/1:34,23:57:99:328,0,664 2 96619734 rs62154618 C T 1612.26 VQSRTrancheSNP99.90to100.00 ABHet=0.388;AC=3;AF=0.500;AN=6;BaseQRankSum=-7.591;DB;DP=216;Dels=0.00;FS=1.411;HaplotypeScore=4.1822;MLEAC=3;MLEAF=0.500;MQ=22.11;MQ0=79;MQRankSum=-4.882;QD=7.46;ReadPosRankSum=-2.582;SB=-6.060e+02;VQSLOD=-15.0894;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:30,49:79:99:792,0,444 0/1:32,40:72:99:397,0,765 2 96619735 . A G 36.24 VQSRTrancheSNP99.90to100.00 ABHet=0.795;ABHom=0.964;AC=1;AF=0.167;AN=6;BaseQRankSum=0.165;DP=217;Dels=0.00;FS=6.870;HaplotypeScore=4.4933;MLEAC=1;MLEAF=0.167;MQ=22.20;MQ0=79;MQRankSum=-0.833;OND=0.024;QD=0.50;ReadPosRankSum=-2.390;SB=-3.067e-03;VQSLOD=-16.0016;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/0:77,2:79:99:0,126,1490 0/1:58,15:73:71:71,0,1120 2 96619774 rs77522461 G A 580.26 VQSRTrancheSNP99.90to100.00 ABHet=0.409;AC=3;AF=0.500;AN=6;BaseQRankSum=-6.923;DB;DP=120;Dels=0.00;FS=10.691;HaplotypeScore=2.2406;MLEAC=3;MLEAF=0.500;MQ=27.56;MQ0=42;MQRankSum=-4.574;OND=7.092e-03;QD=4.84;ReadPosRankSum=5.535;SB=-1.182e-02;VQSLOD=-10.3675;culprit=ReadPosRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:13,25:38:99:352,0,435 0/1:25,21:47:99:108,0,836 2 96619799 rs145806545 A C 662.26 VQSRTrancheSNP99.00to99.90 ABHet=0.431;AC=3;AF=0.500;AN=6;BaseQRankSum=3.492;DB;DP=77;Dels=0.00;FS=0.000;HaplotypeScore=1.2951;MLEAC=3;MLEAF=0.500;MQ=29.08;MQ0=18;MQRankSum=-2.092;QD=8.60;ReadPosRankSum=0.814;SB=-1.182e-02;VQSLOD=-1.6141;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:11,18:29:99:374,0,338 0/1:13,15:28:99:152,0,441 2 96619831 rs76870447 T C 66.26 VQSRTrancheSNP99.00to99.90 ABHet=0.768;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=-0.993;DB;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=1.9927;MLEAC=2;MLEAF=0.333;MQ=33.82;MQ0=1;MQRankSum=-3.095;QD=2.55;ReadPosRankSum=-1.849;SB=-1.182e-02;VQSLOD=-3.0066;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:11,3:14:50:50,0,303 0/0:14,0:14:42:0,42,507 2 96622072 . T A 36.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=18.39;SB=-2.676e+01;VQSLOD=18.1852;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:68,6,0 ./. ./. 2 96622390 . G A 69.63 VQSRTrancheSNP99.90to100.00 ABHet=0.641;ABHom=0.908;AC=2;AF=0.250;AN=8;BaseQRankSum=-1.284;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.2467;MLEAC=2;MLEAF=0.250;MQ=22.68;MQ0=4;MQRankSum=-1.414;OND=0.038;QD=3.16;ReadPosRankSum=-2.024;SB=-1.182e-02;VQSLOD=-6.8584;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 0/0:11,2:13:6:0,6,298 0/1:8,5:13:83:83,0,164 2 96622402 rs80151265 T C 121.13 VQSRTrancheSNP99.90to100.00 ABHet=0.656;ABHom=1.00;AC=3;AF=0.375;AN=8;BaseQRankSum=3.883;DB;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.375;MQ=24.44;MQ0=4;MQRankSum=-2.256;QD=3.46;ReadPosRankSum=0.427;SB=-1.182e-02;VQSLOD=-6.1140;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,25 0/1:7,6:13:99:125,0,171 0/1:10,3:13:13:13,0,263 2 96626030 rs7566050 T C 33.72 PASS ABHet=0.500;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=2.003;DB;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.167;MQ=37.00;MQ0=0;MQRankSum=0.589;QD=8.43;ReadPosRankSum=1.296;SB=-1.182e-02;VQSLOD=19.0635;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:2,2:4:57:68,0,57 0/0:5,0:5:15:0,15,177 2 96627942 rs78301520 T C 253.34 VQSRTrancheSNP99.00to99.90 ABHet=0.604;ABHom=1.00;AC=5;AF=0.625;AN=8;BaseQRankSum=3.973;DB;DP=47;Dels=0.00;FS=0.000;HaplotypeScore=0.2290;MLEAC=5;MLEAF=0.625;MQ=31.19;MQ0=6;MQRankSum=-5.210;QD=5.39;ReadPosRankSum=1.526;SB=-1.182e-02;VQSLOD=-2.8448;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,3:3:6:59,6,0 0/1:9,6:15:79:79,0,271 0/1:12,4:16:44:44,0,356 2 96627949 rs116292556 G A 223.34 VQSRTrancheSNP99.00to99.90 ABHet=0.619;ABHom=1.00;AC=5;AF=0.625;AN=8;BaseQRankSum=3.936;DB;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=0.2290;MLEAC=5;MLEAF=0.625;MQ=31.32;MQ0=6;MQRankSum=-5.243;QD=4.65;ReadPosRankSum=2.628;SB=-1.182e-02;VQSLOD=-3.7286;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,3:3:6:59,6,0 0/1:10,6:16:76:76,0,293 0/1:11,4:15:47:47,0,313 2 96627959 rs117426905 A G 217.59 VQSRTrancheSNP99.90to100.00 ABHet=0.540;AC=4;AF=0.500;AN=8;BaseQRankSum=-4.431;DB;DP=54;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=31.60;MQ0=7;MQRankSum=-5.385;QD=4.03;ReadPosRankSum=4.524;SB=-1.182e-02;VQSLOD=-6.1629;culprit=ReadPosRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 0/1:1,3:4:24:50,0,24 0/1:11,7:18:68:68,0,370 0/1:13,4:17:38:38,0,439 2 96627980 rs75281835 A G 197.34 VQSRTrancheSNP99.00to99.90 ABHet=0.725;ABHom=0.750;AC=5;AF=0.625;AN=8;BaseQRankSum=3.976;DB;DP=66;Dels=0.00;FS=0.000;HaplotypeScore=0.4832;MLEAC=5;MLEAF=0.625;MQ=32.97;MQ0=6;MQRankSum=-5.637;OND=0.063;QD=2.99;ReadPosRankSum=0.987;SB=-1.182e-02;VQSLOD=-2.8976;culprit=MQRankSum;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:1,3:4:6:59,6,0 0/1:15,7:22:61:61,0,495 0/1:17,4:21:29:29,0,562 2 96628443 rs79028115 C T 1157.55 VQSRTrancheSNP99.90to100.00 ABHet=0.400;ABHom=0.500;AC=5;AF=0.625;AN=8;BaseQRankSum=-7.084;DB;DP=203;Dels=0.00;FS=3.596;HaplotypeScore=0.2489;MLEAC=5;MLEAF=0.625;MQ=17.60;MQ0=100;MQRankSum=-3.228;OND=0.125;QD=5.70;ReadPosRankSum=2.862;SB=-1.182e-02;VQSLOD=-10.0131;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:4,4:8:9:83,9,0 0/1:27,42:69:99:368,0,437 0/1:24,38:62:99:325,0,329 2 96628454 rs80053599 T C 1183.55 VQSRTrancheSNP99.90to100.00 ABHet=0.438;ABHom=0.750;AC=5;AF=0.625;AN=8;BaseQRankSum=4.134;DB;DP=173;Dels=0.00;FS=3.491;HaplotypeScore=0.2489;MLEAC=5;MLEAF=0.625;MQ=19.48;MQ0=68;MQRankSum=-3.825;OND=0.063;QD=6.84;ReadPosRankSum=1.911;SB=-1.182e-02;VQSLOD=-7.7946;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:1,3:4:9:83,9,0 0/1:27,35:62:99:373,0,432 0/1:23,31:54:99:341,0,349 2 96628490 rs76756953 A T 532.26 VQSRTrancheSNP99.90to100.00 ABHet=0.580;AC=3;AF=0.500;AN=6;BaseQRankSum=-5.697;DB;DP=94;Dels=0.00;FS=0.000;HaplotypeScore=0.5758;MLEAC=3;MLEAF=0.500;MQ=22.96;MQ0=21;MQRankSum=-4.659;QD=5.66;ReadPosRankSum=-2.662;SB=-1.182e-02;VQSLOD=-6.0718;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:19,14:33:99:201,0,383 0/1:14,13:27:99:211,0,233 2 96628512 rs74500800 T C 33.73 VQSRTrancheSNP99.90to100.00 ABHet=0.825;AC=3;AF=0.500;AN=6;BaseQRankSum=-3.817;DB;DP=50;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=24.96;MQ0=16;MQRankSum=-0.294;QD=0.67;ReadPosRankSum=-3.682;SB=-1.957e-02;VQSLOD=-7.1477;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:11,3:14:4:4,0,211 0/1:14,2:16:26:26,0,257 2 96628809 rs72935861 G C 40.69 VQSRTrancheSNP99.90to100.00 ABHet=0.720;AC=3;AF=0.500;AN=6;BaseQRankSum=0.727;DB;DP=38;Dels=0.00;FS=2.133;HaplotypeScore=1.6018;MLEAC=3;MLEAF=0.500;MQ=22.82;MQ0=9;MQRankSum=0.242;QD=1.07;ReadPosRankSum=1.481;SB=-4.048e+01;VQSLOD=-5.6579;culprit=MQ;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:8,4:12:10:10,0,114 0/1:8,2:10:25:25,0,228 2 96647856 rs4144055 G T 57.24 VQSRTrancheSNP99.00to99.90 ABHet=0.500;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=-3.106;DB;DP=48;Dels=0.00;FS=0.000;HaplotypeScore=1.2486;MLEAC=1;MLEAF=0.167;MQ=34.20;MQ0=4;MQRankSum=-2.441;QD=3.18;ReadPosRankSum=-1.664;SB=-1.182e-02;VQSLOD=-1.3732;culprit=QD;set=FilteredInAll;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. 0/1:9,9:18:92:92,0,315 0/0:18,0:18:51:0,51,651 2 96679384 rs2579517 C T 185.09 PASS ABHet=0.587;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=2.996;DB;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.4894;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.696;QD=10.28;ReadPosRankSum=0.393;SB=-1.182e-02;VQSLOD=18.6267;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/1:3,5:8:96:176,0,96 0/1:8,2:10:50:50,0,284 0/0:3,0:3:9:0,9,118 2 96679740 rs2438978 G C 120.07 PASS ABHet=0.286;ABHom=1.00;AC=1;AF=0.125;AN=8;BaseQRankSum=0.284;DB;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.1835;MLEAC=1;MLEAF=0.125;MQ=35.55;MQ0=0;MQRankSum=0.640;QD=17.15;ReadPosRankSum=-0.426;SB=7.963e-03;VQSLOD=2.1206;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/0:6,0:6:18:0,18,200 0/1:2,5:7:49:156,0,49 0/0:6,0:6:18:0,18,188 2 96684876 rs2579516 A G 448.86 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=37.00;MQ0=0;QD=32.06;SB=-1.467e+02;VQSLOD=21.4891;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 1/1:0,6:6:18:218,18,0 1/1:0,3:3:9:106,9,0 1/1:0,4:4:12:130,12,0 2 96685021 rs2969475 A G 81.02 VQSRTrancheSNP99.00to99.90 ABHet=0.309;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-2.163;DB;DP=15;Dels=0.00;FS=9.792;HaplotypeScore=0.6212;MLEAC=2;MLEAF=0.250;MQ=32.01;MQ0=2;MQRankSum=-1.381;QD=8.10;ReadPosRankSum=0.000;SB=-1.016e+00;VQSLOD=-1.7303;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/1:2,5:7:65:73,0,65 0/1:1,2:3:25:48,0,25 0/0:4,0:4:12:0,12,152 2 96685052 . T G 106.12 VQSRTrancheSNP99.00to99.90 ABHet=0.400;ABHom=1.00;AC=1;AF=0.125;AN=8;BaseQRankSum=3.110;DP=18;Dels=0.00;FS=6.117;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.125;MQ=32.63;MQ0=1;MQRankSum=-0.685;QD=10.61;ReadPosRankSum=-0.685;SB=1.88;VQSLOD=-0.9425;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/1:4,6:10:79:141,0,79 0/0:4,0:4:9:0,9,98 0/0:3,0:3:6:0,6,70 2 96685085 rs62155521 G A 161.8 VQSRTrancheSNP99.00to99.90 ABHet=0.563;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=1.427;DB;DP=21;Dels=0.00;FS=1.871;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=33.11;MQ0=1;MQRankSum=-1.659;QD=9.52;ReadPosRankSum=0.656;SB=-6.026e+01;VQSLOD=0.7982;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/1:5,8:13:99:188,0,154 0/1:3,1:4:13:13,0,95 0/0:3,0:3:9:0,9,110 2 96685092 rs62155522 A G 183.23 VQSRTrancheSNP99.00to99.90 ABHet=0.549;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.735;DB;DP=23;Dels=0.00;FS=3.821;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=31.78;MQ0=1;MQRankSum=-1.402;QD=10.18;ReadPosRankSum=0.534;SB=-5.758e+01;VQSLOD=0.3670;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL 0/1:5,9:14:99:210,0,160 0/1:3,1:4:13:13,0,87 0/0:3,0:3:9:0,9,115 2 96686723 rs2579515 A G 76.25 PASS ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=-0.550;DB;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.333;MQ=37.00;MQ0=0;MQRankSum=0.000;QD=25.42;ReadPosRankSum=-0.937;SB=-1.182e-02;VQSLOD=20.4634;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||795|GPAT2||CODING|NM_207328.2||1),INTRON(MODIFIER|||||FAHD2CP||NON_CODING|NR_003698.1|1|1) GT:AD:DP:GQ:PL ./. 1/1:0,3:3:9:116,9,0 0/0:2,0:2:6:0,6,80 2 96697699 . G A 46.7 VQSRTrancheSNP99.90to100.00 ABHet=0.500;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-1.774;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=23.00;MQ0=0;MQRankSum=-0.540;QD=5.84;ReadPosRankSum=-0.386;SB=-1.182e-02;VQSLOD=-7.6172;culprit=MQ;set=FilteredInAll;EFF=INTRON(MODIFIER||||795|GPAT2||CODING|NM_207328.2|3|1) GT:AD:DP:GQ:PL 0/1:3,3:6:65:65,0,65 0/0:2,0:2:6:0,6,55 0/1:1,1:2:22:22,0,22 2 96698185 . G A 71.23 VQSRTrancheSNP99.90to100.00 ABHom=0.813;AC=4;AF=0.667;AN=6;BaseQRankSum=0.731;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=17.14;MQ0=4;MQRankSum=0.731;OND=0.133;QD=11.87;ReadPosRankSum=0.731;SB=-2.722e+01;VQSLOD=-9.8312;culprit=MQ;set=FilteredInAll;EFF=INTRON(MODIFIER||||795|GPAT2||CODING|NM_207328.2|1|1) GT:AD:DP:GQ:PL 1/1:2,3:5:9:83,9,0 ./. 1/1:0,1:1:3:28,3,0 2 96738585 rs2579551 G C 47.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.88;SB=-3.776e+01;VQSLOD=21.4638;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 ./. ./. 2 96852842 . GA G 147.22 PASS AC=3;AF=0.500;AN=6;BaseQRankSum=0.775;DP=32;FS=0.000;HaplotypeScore=7.7984;MLEAC=3;MLEAF=0.500;MQ=36.68;MQ0=0;MQRankSum=0.217;QD=4.60;RPA=14,13;RU=A;ReadPosRankSum=-0.031;SB=-2.200e+01;STR;set=variant;EFF=INTRON(MODIFIER||||370|STARD7||CODING|NM_020151.3|7|1) GT:AD:DP:GQ:PL ./. 0/1:7,2:11:42:42,0,112 0/1:7,3:10:61:61,0,130 2 96888164 rs62153022 T C 127.9 PASS ABHet=0.286;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=0.529;DB;DP=12;Dels=0.00;FS=0.000;HaplotypeScore=0.2217;MLEAC=1;MLEAF=0.167;MQ=37.00;MQ0=0;MQRankSum=0.380;QD=18.27;ReadPosRankSum=-1.788;SB=-3.236e+01;VQSLOD=19.9910;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER|||||LOC285033||NON_CODING|NR_046322.1|1|1) GT:AD:DP:GQ:PL ./. 0/1:2,5:7:54:162,0,54 0/0:2,0:2:6:0,6,76 2 97011362 rs4907311 C T 33.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=16.89;SB=-3.076e+01;VQSLOD=20.7570;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||741|NCAPH||CODING|NM_015341.3|6|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:65,6,0 ./. ./. 2 97016334 rs17633463 G A 81.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=27.07;SB=-3.522e+01;VQSLOD=21.1384;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||741|NCAPH||CODING|NM_015341.3|6|1) GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:75,6,0 2 97026576 rs62153915 C T 983.78 PASS ABHet=0.533;ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=-2.604;DB;DP=35;Dels=0.00;FS=0.000;HaplotypeScore=0.2433;MLEAC=6;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.678;QD=28.11;ReadPosRankSum=-0.853;SB=-1.182e-02;VQSLOD=20.3425;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||741|NCAPH||CODING|NM_015341.3|12|1) GT:AD:DP:GQ:PL 0/1:2,3:5:65:94,0,65 0/1:4,2:6:58:58,0,131 1/1:0,13:13:39:468,39,0 2 97058660 rs56027554 T C 82.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=27.41;SB=-3.622e+01;VQSLOD=20.8047;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 ./. 1/1:0,1:1:3:39,3,0 2 97075826 rs582014 A G 84.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=28.07;SB=-3.722e+01;VQSLOD=20.6538;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:78,6,0 1/1:0,1:1:3:40,3,0 ./. 2 97094536 rs609765 C G 48.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=24.38;SB=-3.876e+01;VQSLOD=20.0638;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 ./. ./. 2 97198800 rs2579502 T C 33.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=16.89;SB=-2.976e+01;VQSLOD=20.6904;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||||594|ARID5A||CODING|NM_212481.1||1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:65,6,0 ./. 2 97199694 rs2438709 A G 39.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=19.51;SB=-2.901e+01;VQSLOD=20.6865;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||||594|ARID5A||CODING|NM_212481.1||1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 ./. 1/1:0,1:1:3:32,3,0 2 97212755 rs1011040 T C 125.51 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=31.38;SB=-1.182e-02;VQSLOD=20.8751;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||594|ARID5A||CODING|NM_212481.1|1|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 ./. 1/1:0,2:2:6:80,6,0 2 97243305 rs12469420 G A 45.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=22.88;SB=-3.776e+01;VQSLOD=20.6884;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 ./. ./. 2 97249103 rs11678174 T C 40.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.38;SB=-3.276e+01;VQSLOD=20.4612;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:72,6,0 2 97262493 . C T 41.26 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.736;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.736;QD=20.63;ReadPosRankSum=0.736;SB=-3.325e+01;VQSLOD=19.0418;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||878|KANSL3||CODING|NM_001115016.2|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047653.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047654.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047655.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047656.1|19|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047657.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047658.1|19|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:76,6,0 ./. ./. 2 97267260 rs6759099 G C 451.04 PASS ABHet=0.750;ABHom=1.00;AC=7;AF=0.875;AN=8;BaseQRankSum=1.883;DB;DP=16;Dels=0.00;FS=0.000;HaplotypeScore=0.2433;MLEAC=7;MLEAF=0.875;MQ=37.00;MQ0=0;MQRankSum=0.673;QD=28.19;ReadPosRankSum=-1.614;SB=-1.182e-02;VQSLOD=20.1602;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||878|KANSL3||CODING|NM_001115016.2|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047653.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047654.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047655.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047656.1|19|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047657.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047658.1|19|1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:37,3,0 0/1:3,1:4:28:28,0,92 1/1:0,4:4:12:159,12,0 2 97267293 rs6749159 T C 703.87 PASS ABHet=0.732;ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=2.611;DB;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=-0.512;QD=24.27;ReadPosRankSum=1.830;SB=-6.293e+01;VQSLOD=20.3540;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||878|KANSL3||CODING|NM_001115016.2|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047653.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047654.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047655.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047656.1|19|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047657.1|20|1),INTRON(MODIFIER|||||KANSL3||CODING|NR_047658.1|19|1) GT:AD:DP:GQ:PL 0/1:3,1:4:28:28,0,98 0/1:5,2:7:22:22,0,177 1/1:0,6:6:18:230,18,0 2 97366303 rs2280355 A G 117.73 PASS ABHet=0.607;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=-2.571;DB;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.2499;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=1.155;QD=9.06;ReadPosRankSum=0.335;SB=-1.182e-02;VQSLOD=20.2311;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||2093|FER1L5||CODING|NM_001113382.1|44|1) GT:AD:DP:GQ:PL 0/0:5,0:5:15:0,15,200 0/1:3,3:6:99:101,0,102 0/0:5,0:5:15:0,15,199 2 97373817 rs56351161 G A 37.68 PASS ABHet=0.333;ABHom=1.00;AC=1;AF=0.250;AN=4;BaseQRankSum=-1.231;DB;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=1.231;QD=12.56;ReadPosRankSum=1.231;SB=-1.182e-02;VQSLOD=19.7309;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||2093|FER1L5||CODING|NM_001113382.1||1),INTRON(MODIFIER||||348|LMAN2L||CODING|NM_030805.3|6|1),INTRON(MODIFIER||||359|LMAN2L||CODING|NM_001142292.1|7|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024518.1|6|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024519.1|6|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024520.1|5|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024521.1|4|1) GT:AD:DP:GQ:PL ./. 0/1:1,2:3:31:70,0,31 0/0:2,0:2:6:0,6,80 2 97400324 rs6727384 A G 93.55 PASS ABHet=0.701;ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=0.890;DB;DP=43;Dels=0.00;FS=0.000;HaplotypeScore=0.2499;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-1.345;QD=5.50;ReadPosRankSum=-0.474;SB=-9.298e-03;VQSLOD=19.4554;culprit=QD;set=variant2;EFF=INTRON(MODIFIER||||348|LMAN2L||CODING|NM_030805.3|2|1),INTRON(MODIFIER||||359|LMAN2L||CODING|NM_001142292.1|2|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024518.1|2|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024519.1|1|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024520.1|1|1),INTRON(MODIFIER|||||LMAN2L||CODING|NR_024521.1|1|1) GT:AD:DP:GQ:PL 0/0:12,0:12:36:0,36,440 0/1:7,2:9:46:46,0,226 0/0:14,0:14:42:0,42,491 2 97496022 rs11682764 A G 113.76 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=28.44;SB=-6.676e+01;VQSLOD=20.8621;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||659|CNNM3||CODING|NM_199078.2|6|1),INTRON(MODIFIER||||707|CNNM3||CODING|NM_017623.4|7|1) GT:AD:DP:GQ:PL 1/1:0,3:3:9:108,9,0 ./. 1/1:0,1:1:3:40,3,0 2 97543936 rs12473528 T C 104.86 PASS ABHet=0.500;ABHom=1.00;AC=5;AF=0.625;AN=8;BaseQRankSum=0.421;DB;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.625;MQ=37.00;MQ0=0;MQRankSum=0.421;QD=20.97;ReadPosRankSum=0.922;SB=-3.585e+01;VQSLOD=20.7680;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||119|FAM178B||CODING|NM_016490.4|3|1),INTRON(MODIFIER||||138|FAM178B||CODING|NM_001172667.1|3|1),INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|15|1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,2:2:6:77,6,0 0/0:3,0:3:9:0,9,117 2 97544089 rs6750988 G C 304.65 PASS ABHet=0.650;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=4.070;DB;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=-0.322;QD=16.03;ReadPosRankSum=1.376;SB=-3.902e+01;VQSLOD=19.9199;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||119|FAM178B||CODING|NM_016490.4|3|1),INTRON(MODIFIER||||138|FAM178B||CODING|NM_001172667.1|3|1),INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|15|1) GT:AD:DP:GQ:PL 0/1:5,5:10:99:169,0,133 1/1:0,4:4:12:158,12,0 0/0:5,0:5:15:0,15,154 2 97553747 rs12613171 G A 45.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=22.50;SB=-1.182e-02;VQSLOD=21.0881;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||119|FAM178B||CODING|NM_016490.4|2|1),INTRON(MODIFIER||||138|FAM178B||CODING|NM_001172667.1|2|1),INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|14|1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:38,3,0 ./. 2 97570081 rs4260285 A G 35.25 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.500;AN=6;BaseQRankSum=1.026;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.500;MQ=37.00;MQ0=0;MQRankSum=-1.026;QD=11.75;ReadPosRankSum=1.026;SB=-1.182e-02;VQSLOD=19.6296;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|12|1) GT:AD:DP:GQ:PL ./. 0/0:1,0:1:3:0,3,36 0/1:1,1:2:27:33,0,27 2 97570759 rs58984980 T A 38.25 PASS ABHet=0.500;ABHom=1.00;AC=3;AF=0.750;AN=4;BaseQRankSum=0.736;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.736;QD=12.75;ReadPosRankSum=0.736;SB=-1.182e-02;VQSLOD=19.8977;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|12|1) GT:AD:DP:GQ:PL ./. ./. 0/1:1,1:2:33:33,0,33 2 97577495 rs17119655 T C 47.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.88;SB=-3.776e+01;VQSLOD=20.8406;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|12|1) GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:79,6,0 2 97587049 rs34895357 T C 47.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.88;SB=-1.182e-02;VQSLOD=20.9633;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|11|1) GT:AD:DP:GQ:PL ./. ./. ./. 2 97589191 . G A 96.53 PASS ABHet=0.417;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=2.520;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.333;MQ=37.00;MQ0=0;MQRankSum=-1.034;QD=13.79;ReadPosRankSum=-1.398;SB=-1.182e-02;VQSLOD=18.8173;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|10|1) GT:AD:DP:GQ:PL ./. 0/0:4,0:4:12:0,12,136 0/1:1,2:3:23:68,0,23 2 97605748 rs7594227 A G 42.56 PASS ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=1.231;DB;DP=5;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.333;MQ=37.00;MQ0=0;MQRankSum=-1.231;QD=21.28;ReadPosRankSum=0.358;SB=-3.556e+01;VQSLOD=21.1048;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|8|1) GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,72 ./. 0/0:1,0:1:3:0,3,35 2 97612214 rs6707255 G C 48.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=24.38;SB=-3.876e+01;VQSLOD=21.2346;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|8|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:80,6,0 ./. 2 97613616 rs1624844 T C 519.4 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=0.1446;MLEAC=8;MLEAF=1.00;MQ=37.00;MQ0=0;QD=28.86;SB=-2.372e+02;VQSLOD=21.5694;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acA/acG|T339|679|FAM178B||CODING|NM_001122646.2|8|1) GT:AD:DP:GQ:PL 1/1:0,3:3:9:110,9,0 1/1:0,7:7:18:204,18,0 1/1:0,4:4:12:129,12,0 2 97613748 rs1623881 C A 119.67 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=37.00;MQ0=0;QD=29.92;SB=-1.182e-02;VQSLOD=21.0473;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|7|1) GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:39,3,0 1/1:0,1:1:3:39,3,0 2 97615367 . G T 41.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.88;SB=-3.476e+01;VQSLOD=18.8371;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|7|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:73,6,0 ./. 2 97617140 rs1257019 T C 72.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=24.07;SB=-3.246e+01;VQSLOD=21.4362;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V323|679|FAM178B||CODING|NM_001122646.2|7|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:71,6,0 1/1:0,1:1:3:35,3,0 2 97619682 rs1730129 G C 47.01 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=23.50;SB=-3.700e+01;VQSLOD=20.4212;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|6|1) GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:40,3,0 2 97619913 rs1730128 T C 61.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.41;SB=-1.182e-02;VQSLOD=20.1786;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|6|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:60,6,0 ./. 2 97631982 rs1257013 T C 44.26 PASS ABHom=1.00;AC=2;AF=0.500;AN=4;BaseQRankSum=0.736;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=3;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.736;QD=22.13;ReadPosRankSum=0.736;SB=-3.425e+01;VQSLOD=20.5936;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|5|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:79,6,0 ./. ./. 2 97634434 rs60283912 G A 39.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=19.88;SB=-3.076e+01;VQSLOD=20.4581;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|4|1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:71,6,0 ./. ./. 2 97637516 rs6714860 T C 41.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=20.88;SB=-3.176e+01;VQSLOD=20.4232;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||679|FAM178B||CODING|NM_001122646.2|3|1) GT:AD:DP:GQ:PL ./. ./. ./. 2 97637905 rs6715329 T C 84.25 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=37.00;MQ0=0;QD=28.08;SB=-1.182e-02;VQSLOD=21.2864;culprit=MQ;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|atA/atG|I99M|679|FAM178B||CODING|NM_001122646.2|3|1) GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:40,3,0 1/1:0,1:1:3:39,3,0 2 103300756 . G A 2226.55 PASS ABHet=0.557;ABHom=0.992;AC=2;AF=0.250;AN=8;BaseQRankSum=4.833;DP=309;Dels=0.00;FS=0.000;HaplotypeScore=2.8709;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=0.753;OND=3.906e-03;QD=13.83;ReadPosRankSum=0.066;SB=-1.100e+03;VQSLOD=7.4915;culprit=HaplotypeScore;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|acG/acA|T462|812|SLC9A2||CODING|NM_003048.3|5|1) GT:AD:DP:GQ:PL 0/1:51,35:86:99:1094,0,1650 0/1:39,36:75:99:1174,0,1145 0/0:63,0:64:99:0,189,2220 2 103322817 . A T 31.02 VQSRTrancheSNP99.00to99.90 ABHom=1.00;AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=31.58;MQ0=0;QD=15.51;SB=-1.182e-02;VQSLOD=0.1573;culprit=MQ;set=FilteredInAll;EFF=INTRON(MODIFIER||||812|SLC9A2||CODING|NM_003048.3|11|1) GT:AD:DP:GQ:PL ./. 1/1:0,1:1:3:34,3,0 ./. 2 111873932 rs4849402 G A 77.22 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=25.74;SB=-1.182e-02;VQSLOD=20.8031;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||580|ACOXL||CODING|NM_001142807.1|17|1),UPSTREAM(MODIFIER||||108|BCL2L11||CODING|NM_001204106.1||1),UPSTREAM(MODIFIER||||109|BCL2L11||CODING|NM_138623.3||1),UPSTREAM(MODIFIER||||112|BCL2L11||CODING|NM_207002.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138624.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138626.3||1),UPSTREAM(MODIFIER||||138|BCL2L11||CODING|NM_006538.4||1),UPSTREAM(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1||1),UPSTREAM(MODIFIER||||169|BCL2L11||CODING|NM_138622.3||1),UPSTREAM(MODIFIER||||172|BCL2L11||CODING|NM_001204108.1||1),UPSTREAM(MODIFIER||||198|BCL2L11||CODING|NM_138621.4||1),UPSTREAM(MODIFIER||||45|BCL2L11||CODING|NM_138627.3||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_138625.3||1),UPSTREAM(MODIFIER||||79|BCL2L11||CODING|NM_207003.2||1),UPSTREAM(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1||1),UPSTREAM(MODIFIER||||82|BCL2L11||CODING|NM_001204110.1||1),UPSTREAM(MODIFIER||||85|BCL2L11||CODING|NM_001204107.1||1),UPSTREAM(MODIFIER||||98|BCL2L11||CODING|NM_001204113.1||1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:38,3,0 ./. 1/1:0,2:2:6:73,6,0 2 111874037 rs4849403 T C 48.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=24.38;SB=-1.182e-02;VQSLOD=20.0137;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||580|ACOXL||CODING|NM_001142807.1|17|1),UPSTREAM(MODIFIER||||108|BCL2L11||CODING|NM_001204106.1||1),UPSTREAM(MODIFIER||||109|BCL2L11||CODING|NM_138623.3||1),UPSTREAM(MODIFIER||||112|BCL2L11||CODING|NM_207002.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138624.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138626.3||1),UPSTREAM(MODIFIER||||138|BCL2L11||CODING|NM_006538.4||1),UPSTREAM(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1||1),UPSTREAM(MODIFIER||||169|BCL2L11||CODING|NM_138622.3||1),UPSTREAM(MODIFIER||||172|BCL2L11||CODING|NM_001204108.1||1),UPSTREAM(MODIFIER||||198|BCL2L11||CODING|NM_138621.4||1),UPSTREAM(MODIFIER||||45|BCL2L11||CODING|NM_138627.3||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_138625.3||1),UPSTREAM(MODIFIER||||79|BCL2L11||CODING|NM_207003.2||1),UPSTREAM(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1||1),UPSTREAM(MODIFIER||||82|BCL2L11||CODING|NM_001204110.1||1),UPSTREAM(MODIFIER||||85|BCL2L11||CODING|NM_001204107.1||1),UPSTREAM(MODIFIER||||98|BCL2L11||CODING|NM_001204113.1||1) GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:80,6,0 2 111875388 rs193151657 C T 34.66 VQSRTrancheSNP99.00to99.90 ABHet=0.200;ABHom=1.00;AC=1;AF=0.125;AN=8;BaseQRankSum=-0.361;DB;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.125;MQ=35.87;MQ0=0;MQRankSum=-0.876;QD=6.93;ReadPosRankSum=-2.219;SB=-1.182e-02;VQSLOD=0.2896;culprit=MQ;set=FilteredInAll;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L580F|580|ACOXL||CODING|NM_001142807.1|18|1),UPSTREAM(MODIFIER||||108|BCL2L11||CODING|NM_001204106.1||1),UPSTREAM(MODIFIER||||109|BCL2L11||CODING|NM_138623.3||1),UPSTREAM(MODIFIER||||112|BCL2L11||CODING|NM_207002.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138624.3||1),UPSTREAM(MODIFIER||||135|BCL2L11||CODING|NM_138626.3||1),UPSTREAM(MODIFIER||||138|BCL2L11||CODING|NM_006538.4||1),UPSTREAM(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1||1),UPSTREAM(MODIFIER||||169|BCL2L11||CODING|NM_138622.3||1),UPSTREAM(MODIFIER||||172|BCL2L11||CODING|NM_001204108.1||1),UPSTREAM(MODIFIER||||198|BCL2L11||CODING|NM_138621.4||1),UPSTREAM(MODIFIER||||45|BCL2L11||CODING|NM_138627.3||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1||1),UPSTREAM(MODIFIER||||75|BCL2L11||CODING|NM_138625.3||1),UPSTREAM(MODIFIER||||79|BCL2L11||CODING|NM_207003.2||1),UPSTREAM(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1||1),UPSTREAM(MODIFIER||||82|BCL2L11||CODING|NM_001204110.1||1),UPSTREAM(MODIFIER||||85|BCL2L11||CODING|NM_001204107.1||1),UPSTREAM(MODIFIER||||98|BCL2L11||CODING|NM_001204113.1||1) GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,34 0/1:1,4:5:31:69,0,31 0/0:1,0:1:3:0,3,27 2 111902124 rs114702002 G A 492.26 PASS ABHet=0.483;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=1.089;DB;DP=45;Dels=0.00;FS=7.459;HaplotypeScore=0.2980;MLEAC=2;MLEAF=0.333;MQ=37.00;MQ0=0;MQRankSum=0.667;QD=14.92;ReadPosRankSum=0.152;SB=-1.040e+02;VQSLOD=13.2237;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||108|BCL2L11||CODING|NM_001204106.1|2|1),INTRON(MODIFIER||||109|BCL2L11||CODING|NM_138623.3|3|1),INTRON(MODIFIER||||135|BCL2L11||CODING|NM_138624.3|3|1),INTRON(MODIFIER||||135|BCL2L11||CODING|NM_138626.3|2|1),INTRON(MODIFIER||||138|BCL2L11||CODING|NM_006538.4|3|1),INTRON(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1|2|1),INTRON(MODIFIER||||169|BCL2L11||CODING|NM_138622.3|2|1),INTRON(MODIFIER||||172|BCL2L11||CODING|NM_001204108.1|2|1),INTRON(MODIFIER||||198|BCL2L11||CODING|NM_138621.4|2|1),INTRON(MODIFIER||||45|BCL2L11||CODING|NM_138627.3|2|1),INTRON(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1|3|1),INTRON(MODIFIER||||75|BCL2L11||CODING|NM_138625.3|3|1),INTRON(MODIFIER||||79|BCL2L11||CODING|NM_207003.2|2|1),INTRON(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1|3|1),INTRON(MODIFIER||||82|BCL2L11||CODING|NM_001204110.1|2|1),INTRON(MODIFIER||||85|BCL2L11||CODING|NM_001204107.1|2|1),INTRON(MODIFIER||||98|BCL2L11||CODING|NM_001204113.1|5|1) GT:AD:DP:GQ:PL ./. 0/0:12,0:12:33:0,33,426 0/1:7,8:15:99:231,0,236 2 111907691 rs724710 T C 2411.99 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=73;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=37.00;MQ0=0;QD=33.04;SB=-5.390e+02;VQSLOD=21.7494;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||98|BCL2L11||CODING|NM_001204113.1||1),INTRON(MODIFIER||||135|BCL2L11||CODING|NM_138626.3|2|1),INTRON(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1|2|1),INTRON(MODIFIER||||45|BCL2L11||CODING|NM_138627.3|2|1),INTRON(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1|3|1),INTRON(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I155|169|BCL2L11||CODING|NM_138622.3|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I155|172|BCL2L11||CODING|NM_001204108.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I155|198|BCL2L11||CODING|NM_138621.4|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I65|108|BCL2L11||CODING|NM_001204106.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I65|79|BCL2L11||CODING|NM_207003.2|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I65|82|BCL2L11||CODING|NM_001204110.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I65|85|BCL2L11||CODING|NM_001204107.1|3|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I95|109|BCL2L11||CODING|NM_138623.3|4|1),SYNONYMOUS_CODING(LOW|SILENT|atT/atC|I95|138|BCL2L11||CODING|NM_006538.4|4|1),UTR_3_PRIME(MODIFIER||||135|BCL2L11||CODING|NM_138624.3|4|1),UTR_3_PRIME(MODIFIER||||75|BCL2L11||CODING|NM_138625.3|4|1) GT:AD:DP:GQ:PL 1/1:0,36:36:99:1227,102,0 1/1:0,18:18:54:604,54,0 1/1:0,8:8:24:264,24,0 2 111909247 rs3789068 A G 661.39 PASS ABHet=0.600;ABHom=1.00;AC=5;AF=0.833;AN=6;BaseQRankSum=1.506;DB;DP=23;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.833;MQ=37.00;MQ0=0;MQRankSum=0.320;QD=28.76;ReadPosRankSum=-0.137;SB=-4.001e+01;VQSLOD=21.7474;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||108|BCL2L11||CODING|NM_001204106.1|3|1),INTRON(MODIFIER||||109|BCL2L11||CODING|NM_138623.3|4|1),INTRON(MODIFIER||||135|BCL2L11||CODING|NM_138624.3|4|1),INTRON(MODIFIER||||135|BCL2L11||CODING|NM_138626.3|2|1),INTRON(MODIFIER||||138|BCL2L11||CODING|NM_006538.4|4|1),INTRON(MODIFIER||||140|BCL2L11||CODING|NM_001204109.1|2|1),INTRON(MODIFIER||||169|BCL2L11||CODING|NM_138622.3|3|1),INTRON(MODIFIER||||172|BCL2L11||CODING|NM_001204108.1|3|1),INTRON(MODIFIER||||198|BCL2L11||CODING|NM_138621.4|3|1),INTRON(MODIFIER||||45|BCL2L11||CODING|NM_138627.3|2|1),INTRON(MODIFIER||||75|BCL2L11||CODING|NM_001204111.1|3|1),INTRON(MODIFIER||||75|BCL2L11||CODING|NM_138625.3|4|1),INTRON(MODIFIER||||79|BCL2L11||CODING|NM_207003.2|3|1),INTRON(MODIFIER||||80|BCL2L11||CODING|NM_001204112.1|3|1),INTRON(MODIFIER||||82|BCL2L11||CODING|NM_001204110.1|3|1),INTRON(MODIFIER||||85|BCL2L11||CODING|NM_001204107.1|3|1) GT:AD:DP:GQ:PL ./. 0/1:3,2:5:59:59,0,92 1/1:0,12:12:36:448,36,0 2 122214035 . G A 30.17 PASS ABHet=0.500;ABHom=1.00;AC=1;AF=0.167;AN=6;BaseQRankSum=-1.179;DP=9;Dels=0.00;FS=3.802;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.167;MQ=37.00;MQ0=0;MQRankSum=1.179;QD=7.54;ReadPosRankSum=-1.179;SB=-2.617e+01;VQSLOD=11.5679;culprit=QD;set=variant2;EFF=INTRON(MODIFIER||||1471|CLASP1||CODING|NM_001142274.1|14|1),INTRON(MODIFIER||||1477|CLASP1||CODING|NM_001207051.1|14|1),INTRON(MODIFIER||||1479|CLASP1||CODING|NM_001142273.1|14|1),INTRON(MODIFIER||||1538|CLASP1||CODING|NM_015282.2|14|1) GT:AD:DP:GQ:PL 0/0:1,0:1:3:0,3,40 0/1:2,2:4:64:64,0,68 0/0:4,0:4:12:0,12,151 2 132292791 rs3101988 T C 119.03 VQSRTrancheSNP99.00to99.90 ABHet=0.389;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=0.583;DB;DP=13;Dels=0.00;FS=0.000;HaplotypeScore=0.3053;MLEAC=2;MLEAF=0.333;MQ=31.71;MQ0=1;MQRankSum=-1.813;QD=9.92;ReadPosRankSum=1.517;SB=-3.534e+01;VQSLOD=0.2011;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||272|CCDC74A||CODING|NM_001258305.1||1),DOWNSTREAM(MODIFIER||||312|CCDC74A||CODING|NM_001258306.1||1),DOWNSTREAM(MODIFIER||||375|CCDC74A||CODING|NM_001258304.1||1),DOWNSTREAM(MODIFIER||||378|CCDC74A||CODING|NM_138770.2||1),INTRON(MODIFIER|||||RNU6-81P||NON_CODING|NR_046946.1|2|1) GT:AD:DP:GQ:PL 0/1:4,5:9:99:110,0,123 ./. 0/1:1,2:3:30:46,0,30 2 132294248 rs13395008 C T 189.03 VQSRTrancheSNP99.00to99.90 ABHet=0.598;ABHom=1.00;AC=2;AF=0.333;AN=6;BaseQRankSum=2.357;DB;DP=25;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.333;MQ=29.98;MQ0=0;MQRankSum=-2.579;QD=8.22;ReadPosRankSum=0.305;SB=-6.191e+01;VQSLOD=-1.1832;culprit=MQ;set=FilteredInAll;EFF=DOWNSTREAM(MODIFIER||||272|CCDC74A||CODING|NM_001258305.1||1),DOWNSTREAM(MODIFIER||||312|CCDC74A||CODING|NM_001258306.1||1),DOWNSTREAM(MODIFIER||||375|CCDC74A||CODING|NM_001258304.1||1),DOWNSTREAM(MODIFIER||||378|CCDC74A||CODING|NM_138770.2||1),INTRON(MODIFIER|||||RNU6-81P||NON_CODING|NR_046946.1|2|1) GT:AD:DP:GQ:PL 0/1:9,8:17:99:189,0,190 0/1:4,2:6:37:37,0,102 ./. 2 166897864 rs6432860 A G 571.99 PASS ABHet=0.500;ABHom=1.00;AC=1;AF=0.125;AN=8;BaseQRankSum=-4.917;DB;DP=172;Dels=0.00;FS=17.049;HaplotypeScore=0.2496;MLEAC=1;MLEAF=0.125;MQ=37.00;MQ0=0;MQRankSum=-0.291;QD=13.00;ReadPosRankSum=0.470;SB=-1.300e+02;VQSLOD=10.5696;culprit=FS;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V736|1981|SCN1A||CODING|NM_001165964.1|13|1),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V753|1998|SCN1A||CODING|NM_006920.4|13|1),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V764|2009|SCN1A||CODING|NM_001165963.1|13|1),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V764|2009|SCN1A||CODING|NM_001202435.1|15|1) GT:AD:DP:GQ:PL 0/0:57,0:57:99:0,172,2230 0/0:37,0:37:99:0,108,1370 0/1:22,22:44:99:608,0,718 2 179444768 rs4145333 C G 13808.01 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=356;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=36.97;MQ0=0;QD=38.79;SB=-6.034e+03;VQSLOD=6.2013;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER|||||MIR548N||NON_CODING|NR_031666.1|3|1),INTRON(MODIFIER|||||TTN-AS1||NON_CODING|NR_038271.1|2|1),INTRON(MODIFIER|||||TTN-AS1||NON_CODING|NR_038272.1|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A13351P|26926|TTN||CODING|NM_003319.4|146|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A13476P|27051|TTN||CODING|NM_133432.3|147|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A13543P|27118|TTN||CODING|NM_133437.3|147|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A19848P|33423|TTN||CODING|NM_133378.4|267|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A20775P|34350|TTN||CODING|NM_001256850.1|268|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Cct|A22416P|35991|TTN||CODING|NM_001267550.1|318|1) GT:AD:DP:GQ:PL 1/1:0,74:74:99:2882,223,0 1/1:0,94:94:99:3698,283,0 1/1:0,94:94:99:3562,280,0 2 182521578 rs1473295 G A 509.41 PASS ABHet=0.592;ABHom=1.00;AC=4;AF=0.500;AN=8;BaseQRankSum=2.396;DB;DP=48;Dels=0.00;FS=1.126;HaplotypeScore=0.3526;MLEAC=4;MLEAF=0.500;MQ=36.58;MQ0=0;MQRankSum=0.884;QD=13.77;ReadPosRankSum=-0.032;SB=-2.288e+02;VQSLOD=3.0814;culprit=MQ;set=variant2;EFF=EXON(MODIFIER|||||CERKL||CODING|NR_027689.1|1|1),EXON(MODIFIER|||||CERKL||CODING|NR_027690.1|1|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F52|419|CERKL||CODING|NM_001030312.2|1|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F52|463|CERKL||CODING|NM_001030313.2|1|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F52|514|CERKL||CODING|NM_001160277.1|1|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F52|532|CERKL||CODING|NM_201548.4|1|1),SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F52|558|CERKL||CODING|NM_001030311.2|1|1) GT:AD:DP:GQ:PL 0/1:14,11:25:99:310,0,335 0/0:11,0:11:27:0,27,309 1/1:0,4:4:12:154,12,0 2 183988984 rs2705719 C G 142.23 PASS ABHet=0.500;ABHom=1.00;AC=5;AF=0.625;AN=8;BaseQRankSum=-0.922;DB;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=5;MLEAF=0.625;MQ=37.00;MQ0=0;MQRankSum=0.922;QD=23.71;ReadPosRankSum=0.198;SB=-1.182e-02;VQSLOD=20.6352;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||||326|NUP35||CODING|NM_138285.3||1) GT:AD:DP:GQ:PL 1/1:0,1:1:3:40,3,0 1/1:0,3:3:9:113,9,0 0/1:1,1:2:33:33,0,33 2 215593233 rs5020511 T A,C 47.28 PASS AC=1,3;AF=0.250,0.750;AN=4;DB;DP=3;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1,3;MLEAF=0.250,0.750;MQ=37.00;MQ0=0;QD=15.76;SB=-1.182e-02;VQSLOD=21.0000;culprit=MQ;set=variant2;EFF=DOWNSTREAM(MODIFIER||||777|BARD1||CODING|NM_000465.2||1),DOWNSTREAM(MODIFIER||||777|BARD1||CODING|NM_000465.2||2),INTERGENIC(MODIFIER||||||||||1),INTERGENIC(MODIFIER||||||||||2) GT:AD:DP:GQ:PL ./. ./. 2/2:0,0,1:1:3:36,36,36,3,3,0 2 215595765 rs6435849 C G 921.25 PASS ABHom=1.00;AC=6;AF=1.00;AN=6;DB;DP=26;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=6;MLEAF=1.00;MQ=36.61;MQ0=0;QD=35.43;SB=-1.182e-02;VQSLOD=6.2695;culprit=FS;set=variant2;EFF=INTRON(MODIFIER||||777|BARD1||CODING|NM_000465.2|9|1) GT:AD:DP:GQ:PL ./. 1/1:0,8:8:21:279,21,0 1/1:0,10:10:30:376,30,0 2 215632256 rs2070093 A G 2839.78 PASS ABHet=0.492;ABHom=1.000;AC=6;AF=0.750;AN=8;BaseQRankSum=0.138;DB;DP=114;Dels=0.00;FS=5.740;HaplotypeScore=0.4776;MLEAC=6;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=0.739;QD=24.91;ReadPosRankSum=-1.597;SB=-1.150e+03;VQSLOD=13.4923;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H506|777|BARD1||CODING|NM_000465.2|6|1) GT:AD:DP:GQ:PL 1/1:0,36:36:96:1220,96,0 0/1:21,14:35:99:376,0,696 0/1:5,8:13:99:199,0,157 2 215645464 rs2229571 C G 2726.58 PASS ABHet=0.429;AC=4;AF=0.500;AN=8;BaseQRankSum=-0.773;DB;DP=143;Dels=0.00;FS=2.129;HaplotypeScore=0.0000;MLEAC=4;MLEAF=0.500;MQ=36.93;MQ0=0;MQRankSum=0.920;QD=19.07;ReadPosRankSum=0.218;SB=-1.336e+03;VQSLOD=3.6260;culprit=HaplotypeScore;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agG/agC|R378S|777|BARD1||CODING|NM_000465.2|4|1) GT:AD:DP:GQ:PL 0/1:20,31:51:99:1057,0,629 0/1:16,16:32:99:529,0,530 0/1:10,17:27:99:570,0,300 2 215645662 . T G 42.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=21.38;SB=-3.276e+01;VQSLOD=20.2353;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||1235|HDLBP||CODING|NM_001243900.1|1|1),INTRON(MODIFIER||||1268|HDLBP||CODING|NM_005336.4|1|1),INTRON(MODIFIER||||1268|HDLBP||CODING|NM_203346.3|1|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:74,6,0 ./. 2 215674371 rs34732883 C T 110.51 PASS ABHom=1.00;AC=4;AF=1.00;AN=4;DB;DP=4;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=37.00;MQ0=0;QD=27.63;SB=-3.431e+01;VQSLOD=20.2259;culprit=MQ;set=variant2;EFF=UTR_5_PRIME(MODIFIER||||777|BARD1||CODING|NM_000465.2|1|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:72,6,0 ./. 2 219724196 rs75257157 T C 40.81 PASS ABHom=1.00;AC=2;AF=0.250;AN=8;BaseQRankSum=1.067;DB;DP=8;Dels=0.00;FS=3.332;HaplotypeScore=0.2080;MLEAC=2;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.572;QD=20.41;ReadPosRankSum=0.572;SB=0.970;VQSLOD=13.6421;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||||365|WNT6||CODING|NM_006522.3||1) GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,77 0/0:2,0:2:3:0,3,40 1/1:0,2:2:6:80,6,0 2 219736472 rs13417214 G A 178.25 PASS ABHet=0.400;ABHom=1.00;AC=1;AF=0.250;AN=4;BaseQRankSum=1.031;DB;DP=11;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.250;MQ=37.00;MQ0=0;MQRankSum=-0.825;QD=17.83;ReadPosRankSum=0.387;SB=-1.033e+02;VQSLOD=21.1202;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcG/gcA|A189|365|WNT6||CODING|NM_006522.3|3|1) GT:AD:DP:GQ:PL 0/1:4,6:10:90:210,0,90 0/0:1,0:1:3:0,3,32 ./. 2 234183368 rs2241880 A G 1819.78 PASS ABHet=0.764;ABHom=1.00;AC=6;AF=0.750;AN=8;BaseQRankSum=6.196;DB;DP=69;Dels=0.00;FS=0.000;HaplotypeScore=0.4125;MLEAC=6;MLEAF=0.750;MQ=37.00;MQ0=0;MQRankSum=-0.350;QD=26.37;ReadPosRankSum=1.223;SB=-6.748e+02;VQSLOD=20.5692;culprit=MQ;set=variant2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T137A|444|ATG16L1||CODING|NM_198890.2|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T184A|491|ATG16L1||CODING|NM_001190267.1|9|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T216A|523|ATG16L1||CODING|NM_001190266.1|9|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T281A|588|ATG16L1||CODING|NM_017974.3|8|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T300A|607|ATG16L1||CODING|NM_030803.6|9|1),UPSTREAM(MODIFIER|||||SCARNA5||NON_CODING|NR_003008.2||1) GT:AD:DP:GQ:PL 1/1:0,32:32:96:1269,96,0 0/1:8,3:11:85:85,0,253 0/1:12,3:15:73:73,0,387 2 235244488 rs74460055 C G 48.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=24.38;SB=-3.876e+01;VQSLOD=19.9299;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:80,6,0 ./. ./. 2 235244489 rs11687247 C T 45.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=22.88;SB=-3.576e+01;VQSLOD=19.9525;culprit=MQ;set=variant2;EFF=INTERGENIC(MODIFIER||||||||||1) GT:AD:DP:GQ:PL 1/1:0,2:2:6:77,6,0 ./. ./. 2 239016539 rs935415 C G 1089.45 PASS ABHom=1.00;AC=8;AF=1.00;AN=8;DB;DP=29;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=8;MLEAF=1.00;MQ=37.00;MQ0=0;QD=37.57;SB=-3.825e+02;VQSLOD=21.4355;culprit=MQ;set=variant2;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctG|L260|1005|ESPNL||CODING|NM_194312.2|4|1) GT:AD:DP:GQ:PL 1/1:0,19:19:57:737,57,0 1/1:0,4:4:12:160,12,0 1/1:0,2:2:6:77,6,0 2 239165633 rs2304671 C T 561.99 VQSRTrancheSNP99.00to99.90 ABHet=0.382;ABHom=0.958;AC=1;AF=0.125;AN=8;BaseQRankSum=3.093;DB;DP=155;Dels=0.00;FS=3.588;HaplotypeScore=8.1318;MLEAC=1;MLEAF=0.125;MQ=36.87;MQ0=0;MQRankSum=0.108;OND=0.047;QD=16.06;ReadPosRankSum=1.571;SB=-7.001e+01;VQSLOD=-0.2359;culprit=HaplotypeScore;set=FilteredInAll;EFF=SYNONYMOUS_CODING(LOW|SILENT|tcG/tcA|S665|1255|PER2||CODING|NM_022817.2|17|1) GT:AD:DP:GQ:PL 0/0:63,0:63:99:0,162,1853 0/0:21,0:25:57:0,57,586 0/1:13,21:35:99:598,0,206 2 241696840 rs71779512 ATCC A 474.0 PASS AC=5;AF=0.833;AN=6;BaseQRankSum=-0.467;DB;DP=20;FS=0.000;HaplotypeScore=3.5549;MLEAC=5;MLEAF=0.833;MQ=38.02;MQ0=0;MQRankSum=0.311;QD=23.70;RPA=11,10;RU=TCC;ReadPosRankSum=1.090;SB=-8.793e+01;STR;set=variant;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gaggat/gat|ED917D|1791|KIF1A||CODING|NM_001244008.1|27|1),INTRON(MODIFIER||||1690|KIF1A||CODING|NM_004321.6|24|1) GT:AD:DP:GQ:PL ./. 0/1:6,2:8:88:88,0,155 1/1:2,1:3:3:52,3,0 2 242210408 rs4675816 A G 42.77 PASS ABHom=1.00;AC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=37.00;MQ0=0;QD=21.38;SB=-3.276e+01;VQSLOD=20.2353;culprit=MQ;set=variant2;EFF=INTRON(MODIFIER||||1235|HDLBP||CODING|NM_001243900.1|1|1),INTRON(MODIFIER||||1268|HDLBP||CODING|NM_005336.4|1|1),INTRON(MODIFIER||||1268|HDLBP||CODING|NM_203346.3|1|1) GT:AD:DP:GQ:PL ./. 1/1:0,2:2:6:74,6,0 ./.