##fileformat=VCFv4.1 ##fileDate=20181203 ##source=Pisces 5.2.3.6 ##Pisces_cmdline="-BamPaths D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\stitchedBams\4450_S11.bam -GenomePaths C:\Illumina\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta -gVCF True -OutFolder D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03.04-VariantCalling.VariantCalling\Sample623 -i D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\interval\4450_S11.intervals.picard -CallMNVs True -MaxMNVLength 3 -MaxGapBetweenMNV 1 -MinimumFrequency 0.01 -MinBaseCallQuality 20 -MaxVariantQScore 100 -MinVariantQScore 20 -CrushVcf True -MinDP 10 -ReportNoCalls True -Ploidy diploid -EnableSingleStrandFilter False -MinDPFilter 10 -MaxAcceptableStrandBiasFilter 0.5 -VariantQualityFilter 30 -MinVariantFrequencyFilter 0.2 -RMxNFilter 5,9,0.35 -MaxNumThreads 2" ##reference=C:\Illumina\Genomes\Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFasta ##ALT=,Description="There is an overlapping other allele that has been called in a separate VCF record"> ##INFO= ##annotator=Illumina Annotation Engine 1.6.2.0 ##annotatorDataVersion=84.24.38 ##annotatorTranscriptSource=RefSeq ##dataSource=ClinVar,version:20170227,release date:2017-02-27 ##dataSource=COSMIC,version:80,release date:2017-02-13 ##dataSource=dbSNP,version:149,release date:2016-11-21 ##dataSource=ExAC,version:0.3.1,release date:2016-03-16 ##dataSource=EVS,version:2,release date:2013-11-13 ##dataSource=1000 Genomes Project,version:Phase 3 v5a,release date:2013-05-27 ##dataSource=phyloP,version:hg19,release date:2009-11-10 ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4450_S11.bam chr1 11205058 rs1057079 C T 100 PASS DP=13;cosmic=1|COSM4142146;EVS=0.545902|115|6503;GMAF=C|0.4525;AA=C;AF1000G=0.547524;phyloP=0.078;CSQT=1|MTOR|NM_004958.3|synonymous_variant,1|MTOR-AS1|NR_046600.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:47:0,13:13:1.000:20:-100.0000:0.0000 chr1 11288758 rs1064261 G A 100 PASS DP=28;cosmic=1|COSM4142152;EVS=0.617561|95|6503;GMAF=G|0.2995;AA=A;AF1000G=0.700479;phyloP=-0.406;CSQT=1|MTOR|NM_004958.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,28:28:1.000:20:-100.0000:0.0000 chr1 11297762 rs7524202 T C 100 PASS DP=19;GMAF=T|0.2991;AA=C;AF1000G=0.700879;phyloP=-0.016;CSQT=1|MTOR|NM_004958.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr1 11301714 rs1135172 A G 100 PASS DP=34;cosmic=1|COSM4142157;EVS=0.585345|98|6503;GMAF=A|0.3604;AA=G;AF1000G=0.639577;phyloP=0.008;CSQT=1|MTOR|NM_004958.3|synonymous_variant;CSQR=1|ENSR00001577764|regulatory_region_variant,1|ENSR00001577765|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr1 36563797 rs35495320 C T 100 PASS DP=13;cosmic=1|COSM5452443;EVS=0.022429|2|4882;GMAF=T|0.1815;AA=C;AF1000G=0.18151;phyloP=-0.349;CSQT=1|ADPRHL2|NM_017825.2|downstream_gene_variant,1|COL8A2|NM_005202.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:47:0,13:13:1.000:20:-100.0000:0.0000 chr1 36565584 rs274753 C G 100 PASS DP=53;GMAF=C|0.07827;AA=G;AF1000G=0.921725;phyloP=-0.461;CSQT=1|COL8A2|NM_005202.2|intron_variant;CSQR=1|ENSR00001581937|regulatory_region_variant,1|ENSR00000076318|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,53:53:1.000:20:-100.0000:0.0000 chr1 36565739 rs57985157 C T 100 PASS DP=25;EVS=0.011533|30|6503;GMAF=T|0.09665;AA=T;AF1000G=0.096645;phyloP=-0.138;CSQT=1|COL8A2|NM_005202.2|synonymous_variant;CSQR=1|ENSR00001581937|regulatory_region_variant,1|ENSR00000076318|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:91:0,25:25:1.000:20:-100.0000:0.0000 chr1 47881974 rs181190356 G A 100 PASS DP=22;clinvar=1|benign;GMAF=A|0.08866;AA=G;AF1000G=0.088658;phyloP=1.618;CSQT=1|FOXE3|NM_012186.2|5_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:39:12,10:22:0.455:20:-100.0000:0.0833 chr1 47882058 . C T 84 PASS DP=12;phyloP=2.969;CSQT=1|FOXE3|NM_012186.2|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:25:6,6:12:0.500:20:-100.0000:0.0769 chr1 47882102 . C A 82 PASS DP=13;phyloP=1.079;CSQT=1|FOXE3|NM_012186.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:23:7,6:13:0.462:20:-44.6323:0.0000 chr1 47883019 rs6666370 T C 100 PASS DP=31;GMAF=T|0.2031;AA=C;AF1000G=0.796925;phyloP=-0.792;CSQT=1|FOXE3|NM_012186.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,31:31:1.000:20:-100.0000:0.0000 chr1 47883024 rs2820969 A G 100 PASS DP=29;GMAF=A|0.005192;AA=G;AF1000G=0.994808;phyloP=0.19;CSQT=1|FOXE3|NM_012186.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,29:29:1.000:20:-100.0000:0.0645 chr1 94471075 rs1762114 A G 100 PASS DP=17;clinvar=1|benign,1|benign,1|benign,1|benign,1|benign;cosmic=1|COSM3997712;EVS=0.775719|112|6503;GMAF=A|0.23;AA=G;AF1000G=0.769968;phyloP=-3.057;CSQT=1|ABCA4|NM_000350.2|synonymous_variant;CSQR=1|ENSR00001522544|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:62:0,17:17:1.000:20:-100.0000:0.0000 chr1 94476555 rs537831 G A 100 PASS DP=53;clinvar=1|not_provided;cosmic=1|COSN8862524;GMAF=G|0.3085;AA=A;AF1000G=0.691494;phyloP=-4.216;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,53:53:1.000:20:-100.0000:0.0000 chr1 94481239 . AC A 34 LowDP DP=3;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541012|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:1,2:3:0.667:20:-100.0000:0.0000 chr1 94487285 rs55860151;rs3831251 AAC A 39 LowDP DP=9;clinvar=1|benign,1|benign,1|benign,1|benign,1|benign;EVS=0.149089|38|6258;AF1000G=0.224042;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522546|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:6,3:9:0.333:20:-100.0000:0.0000 chr1 94495930 rs547806 T C 100 PASS DP=13;GMAF=T|0.01178;AA=C;AF1000G=0.988219;phyloP=-1.706;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:47:0,13:13:1.000:20:-100.0000:0.0000 chr1 94496729 . C T 100 PASS DP=64;phyloP=0.257;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:57:25,39:64:0.609:20:-100.0000:0.0000 chr1 94497662 . AT A 78 R5x9 DP=27;cosmic=1|COSN1110290;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:6:20,7:27:0.259:20:-33.8535:0.0000 chr1 94526044 rs56197337 A G 100 PASS DP=36;clinvar=1|benign;EVS=0.052591|42|6503;GMAF=G|0.05431;AA=G;AF1000G=0.054313;phyloP=0.231;CSQT=1|ABCA4|NM_000350.2|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:76:18,18:36:0.500:20:-100.0000:0.0000 chr1 94528363 rs4147833 C T 100 PASS DP=39;clinvar=1|not_provided;GMAF=T|0.3736;AA=C;AF1000G=0.373602;phyloP=-0.036;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587959|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,39:39:1.000:20:-100.0000:0.0000 chr1 94544233 rs4147831 G A 56 LowDP DP=9;clinvar=1|not_provided,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM146564,1|COSM3997713;EVS=0.094572|190|6503;GMAF=A|0.1146;AA=G;AF1000G=0.114617;phyloP=-1.09;CSQT=1|ABCA4|NM_000350.2|synonymous_variant;CSQR=1|ENSR00001522555|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:5,4:9:0.444:20:-100.0000:0.0000 chr1 94544276 rs4147830 G A 100 LowDP DP=9;clinvar=1|not_provided,1|benign,1|benign,1|benign,1|benign,1|benign;EVS=0.465477|128|6503;GMAF=G|0.4852;AA=G;AF1000G=0.514776;phyloP=1.577;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522555|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,9:9:1.000:20:-100.0000:0.0000 chr1 94576893 rs2297635 G A 100 PASS DP=14;GMAF=A|0.2212;AA=G;AF1000G=0.221246;phyloP=-0.75;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587977|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:1:4,10:14:0.714:20:-78.7900:0.0000 chr1 94576968 rs2297634 T C 100 PASS DP=14;clinvar=1|not_provided,1|benign;cosmic=1|COSN15654490;EVS=0.473089|46|6503;GMAF=T|0.4531;AA=C;AF1000G=0.546925;phyloP=-3.871;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001587977|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:51:0,14:14:1.000:20:-100.0000:0.0000 chr1 94578548 rs4847281 T C 100 LowDP DP=9;clinvar=1|benign;EVS=0.987698|111|6503;GMAF=T|0.01298;AA=C;AF1000G=0.987021;phyloP=-2.955;CSQT=1|ABCA4|NM_000350.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,9:9:1.000:20:-69.8586:0.0000 chr1 206941945 rs5743628 A G 100 PASS DP=29;EVS=0.002537|67|6503;GMAF=G|0.002196;AA=A;AF1000G=0.002196;phyloP=0.189;CSQT=1|IL10|NM_000572.2|3_prime_UTR_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:67:14,15:29:0.517:20:-100.0000:0.0333 chr1 206943204 rs771681458 G C 100 PASS DP=68;phyloP=-3.32;CSQT=1|IL10|NM_000572.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:35,33:68:0.485:20:-100.0000:0.0000 chr1 228112121 rs4653889 A G 100 PASS DP=29;EVS=0.570198|36|6503;GMAF=A|0.4838;AA=G;AF1000G=0.516174;phyloP=0.263;CSQT=1|WNT9A|NM_003395.2|intron_variant;CSQR=1|ENSR00001599361|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:57:15,14:29:0.483:20:-97.3268:0.0000 chr1 228112131 rs141239747 C T 100 PASS DP=29;EVS=0.000231|33|6502;GMAF=T|0.01038;AA=C;AF1000G=0.010383;phyloP=-0.03;CSQT=1|WNT9A|NM_003395.2|intron_variant;CSQR=1|ENSR00001599361|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:57:15,14:29:0.483:20:-97.3268:0.0000 chr1 228113163 rs3795768 A G 100 PASS DP=32;cosmic=1|COSM425495;EVS=0.753507|7|6345;GMAF=A|0.3123;AA=G;AF1000G=0.6877;phyloP=-4.017;CSQT=1|WNT9A|NM_003395.2|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:10,22:32:0.688:20:-20.0000:0.0588 chr2 1642537 rs386642327 TGC CGT 100 PASS DP=44;GMAF=T|0.1218;CSQT=1|PXDN|NM_012293.1|intron_variant;CSQR=1|ENSR00001696178|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:1,43:44:0.977:20:-100.0000:0.0000 chr2 1642545 rs6742039 C G 100 PASS DP=44;cosmic=1|COSN6678655;GMAF=C|0.1218;AA=C;AF1000G=0.878195;phyloP=0.175;CSQT=1|PXDN|NM_012293.1|intron_variant;CSQR=1|ENSR00001696178|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,44:44:1.000:20:-100.0000:0.0000 chr2 1647171 rs6730800 T C 100 PASS DP=34;clinvar=1|benign;EVS=0.863442|70|6327;GMAF=T|0.09225;AA=C;AF1000G=0.907748;phyloP=-0.045;CSQT=1|PXDN|NM_012293.1|synonymous_variant;CSQR=1|ENSR00001696179|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr2 1652822 rs1863135 T G 100 PASS DP=44;clinvar=1|benign;EVS=0.899146|32|6207;GMAF=T|0.0645;AA=G;AF1000G=0.935503;phyloP=-0.143;CSQT=1|PXDN|NM_012293.1|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,44:44:1.000:20:-100.0000:0.0000 chr2 1664654 rs17841813 A G 100 PASS DP=35;clinvar=1|benign;EVS=0.713489|87|6279;GMAF=A|0.1891;AA=G;AF1000G=0.810903;phyloP=-0.535;CSQT=1|PXDN|NM_012293.1|splice_region_variant&synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 1683889 rs796323306;rs368301056 A AGATGGTGTGTGTGTG 100 PASS DP=42;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:27:29,13:42:0.310:20:-100.0000:0.0000 chr2 1683923 rs72763569 G T 100 PASS DP=43;cosmic=1|COSN19648512;EVS=0.112945|29|6180;GMAF=T|0.1012;AA=g;AF1000G=0.101238;phyloP=1.597;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:48:27,16:43:0.372:20:-100.0000:0.0000 chr2 1687263 rs138434519 TC T 100 PASS DP=32;AA=C;AF1000G=0.188099;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:45:14,18:32:0.563:20:-100.0000:0.0000 chr2 1687266 rs115883224 T A 100 PASS DP=32;cosmic=1|COSN20344924;GMAF=A|0.1881;AA=T;AF1000G=0.188099;phyloP=-0.18;CSQT=1|PXDN|NM_012293.1|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:45:14,18:32:0.563:20:-100.0000:0.0000 chr2 113877495 rs928940 G T 100 PASS DP=37;GMAF=G|0.2909;AA=T;AF1000G=0.709065;phyloP=-0.241;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00001706991|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,37:37:1.000:20:-100.0000:0.0000 chr2 113887335 rs2232354 T G 100 PASS DP=31;GMAF=G|0.1166;AA=T;AF1000G=0.116613;phyloP=0.864;CSQT=1|IL1RN|NM_173841.2|intron_variant;CSQR=1|ENSR00000677374|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,31:31:1.000:20:-100.0000:0.0000 chr2 135745129 rs16831235 G A 100 PASS DP=21;cosmic=1|COSM4417452;EVS=0.130017|102|6503;GMAF=A|0.1324;AA=G;AF1000G=0.132388;phyloP=0.984;CSQT=1|MAP3K19|NM_025052.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:39:10,11:21:0.524:20:-100.0000:0.0000 chr2 189899541 rs4666770 T C 100 PASS DP=35;cosmic=1|COSN19619790;GMAF=T|0.1552;AA=C;AF1000G=0.844848;phyloP=-1.115;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 189899572 rs7420715 T C 100 PASS DP=35;GMAF=T|0.1552;AA=C;AF1000G=0.844848;phyloP=0.056;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,35:35:1.000:20:-100.0000:0.0000 chr2 189901295 rs12693526 G A 100 PASS DP=28;clinvar=1|benign;cosmic=1|COSN19615392;EVS=0.712782|14|6462;GMAF=G|0.3566;AA=G;AF1000G=0.643371;phyloP=-0.332;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,28:28:1.000:20:-100.0000:0.0000 chr2 189904156 rs558404005 G A 60 PASS DP=17;GMAF=A|0.0003994;AA=G;AF1000G=0.000399;phyloP=5.978;CSQT=1|COL5A2|NM_000393.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:8:12,5:17:0.294:20:-100.0000:0.0000 chr2 189907937 rs6434312 A G 100 PASS DP=57;cosmic=1|COSM4001449;EVS=0.971321|94|6503;GMAF=A|0.05911;AA=G;AF1000G=0.940895;phyloP=-0.085;CSQT=1|COL5A2|NM_000393.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,57:57:1.000:20:-100.0000:0.0000 chr2 189918787 rs6738371 C T 100 PASS DP=11;GMAF=C|0.3596;AA=C;AF1000G=0.640375;phyloP=0.41;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:40:0,11:11:1.000:20:-100.0000:0.0000 chr2 189923104 rs7556733 A G 100 PASS DP=40;EVS=0.962863|50|6503;GMAF=A|0.05691;AA=G;AF1000G=0.943091;phyloP=-1.181;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,40:40:1.000:20:-100.0000:0.0000 chr2 189923630 rs398090949;rs398080909;rs5837121;rs574915386 AT A 100 PASS DP=33;clinvar=1|benign;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:0:10,23:33:0.697:20:-100.0000:0.0000 chr2 189925548 rs6414122 T A 100 PASS DP=36;clinvar=1|benign;EVS=0.962325|31|6503;GMAF=T|0.05751;AA=A;AF1000G=0.942492;phyloP=-0.376;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,36:36:1.000:20:-100.0000:0.0000 chr2 189927506 rs7424947 C G 100 PASS DP=19;GMAF=C|0.1705;AA=G;AF1000G=0.829473;phyloP=-0.215;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr2 189932831 rs2229495 T C 100 PASS DP=21;EVS=0.962633|77|6503;GMAF=T|0.05711;AA=C;AF1000G=0.942891;phyloP=-2.844;CSQT=1|COL5A2|NM_000393.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:76:0,21:21:1.000:20:-100.0000:0.0000 chr2 189953285 rs5837124;rs397758641;rs746250131 A AAATG 100 PASS DP=38;cosmic=1|COSN19656478;AF1000G=0.798323;CSQT=1|COL5A2|NM_000393.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,38:38:1.000:20:-100.0000:0.0000 chr2 189974958 rs4128539 G T 100 PASS DP=34;EVS=0.939951|72|6503;GMAF=G|0.1114;AA=T;AF1000G=0.888578;phyloP=-0.223;CSQT=1|COL5A2|NM_000393.3|synonymous_variant;CSQR=1|ENSR00001712810|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,34:34:1.000:20:-100.0000:0.0000 chr2 209166830 rs10497897 T G 100 PASS DP=20;GMAF=G|0.09964;AA=T;AF1000G=0.099641;phyloP=0.229;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:19:8,12:20:0.600:20:-100.0000:0.0000 chr2 209168853 rs893256 C T 100 PASS DP=19;EVS=0.921113|48|6503;GMAF=C|0.08926;AA=C;AF1000G=0.910743;phyloP=0.565;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr2 209182480 rs10174541 A G 100 PASS DP=21;GMAF=G|0.116;AA=A;AF1000G=0.116014;phyloP=1.057;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:40:11,10:21:0.476:20:-71.1533:0.0000 chr2 209182499 rs113250005;rs67838836;rs779551370 T TA 100 PASS DP=21;GMAF=T|0.001997;AA=aAAAAAAA;AF1000G=0.116414;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:40:11,10:21:0.476:20:-69.1198:0.0000 chr2 209182548 rs10497898 A G 100 PASS DP=21;EVS=0.141396|123|6503;GMAF=G|0.09984;AA=A;AF1000G=0.09984;phyloP=-0.088;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:40:11,10:21:0.476:20:-100.0000:0.0000 chr2 209184980 rs10932258 G A 100 PASS DP=19;clinvar=1|benign;cosmic=1|COSM4133415;EVS=0.992151|90|6498;GMAF=G|0.008187;AA=A;AF1000G=0.991813;phyloP=3.604;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr2 209184999 rs10932259 C T 100 PASS DP=19;clinvar=1|benign;cosmic=1|COSM4133416;EVS=0.922135|100|6492;GMAF=C|0.08846;AA=C;AF1000G=0.911542;phyloP=1.019;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:69:0,19:19:1.000:20:-100.0000:0.0000 chr2 209190330 rs2363468 T C 100 PASS DP=26;clinvar=1|benign;EVS=0.922420|63|6503;GMAF=T|0.08826;AA=C;AF1000G=0.911741;phyloP=0.579;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:81:1,25:26:0.962:20:-100.0000:0.0000 chr2 209190519 rs893254 A T 100 PASS DP=23;clinvar=1|benign;EVS=0.922344|65|6503;GMAF=A|0.08846;AA=A;AF1000G=0.911542;phyloP=1.35;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:84:0,23:23:1.000:20:-100.0000:0.0000 chr2 209190528 rs893253 C G 100 PASS DP=22;clinvar=1|benign;EVS=0.923112|68|6503;GMAF=C|0.08786;AA=G;AF1000G=0.912141;phyloP=-0.255;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr2 209190632 rs999890 T G 100 PASS DP=24;clinvar=1|benign;cosmic=1|COSM3736239;EVS=0.141166|100|6503;GMAF=G|0.09904;AA=T;AF1000G=0.099042;phyloP=0.701;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:27:15,9:24:0.375:20:-100.0000:0.0400 chr2 209190649 rs999891 A G 100 PASS DP=25;clinvar=1|benign;cosmic=1|COSM3757922;EVS=0.140781|98|6503;GMAF=G|0.09904;AA=A;AF1000G=0.099042;phyloP=-0.648;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:33:15,10:25:0.400:20:-67.2664:0.0000 chr2 209191082 rs1529979 C A 100 PASS DP=24;clinvar=1|benign;EVS=0.922344|98|6503;GMAF=C|0.08846;AA=A;AF1000G=0.911542;phyloP=2.372;CSQT=1|PIKFYVE|NM_015040.3|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:87:0,24:24:1.000:20:-100.0000:0.0000 chr2 209191099 rs1529978 T C 100 PASS DP=24;clinvar=1|benign;EVS=0.994618|103|6503;GMAF=T|0.003994;AA=C;AF1000G=0.996006;phyloP=-0.071;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:87:0,24:24:1.000:20:-100.0000:0.0000 chr2 209194696 rs1437414 G C 100 PASS DP=22;EVS=0.928477|72|2279;GMAF=G|0.08786;AA=C;AF1000G=0.912141;phyloP=-0.68;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:80:0,22:22:1.000:20:-100.0000:0.0000 chr2 209200394 rs6718402 A C 100 PASS DP=37;GMAF=A|0.08826;AA=A;AF1000G=0.911741;phyloP=0.18;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,36:37:0.973:20:-100.0000:0.0000 chr2 209201739 rs7596571 T C 100 PASS DP=25;GMAF=T|0.01697;AA=C;AF1000G=0.983027;phyloP=-1.077;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:91:0,25:25:1.000:20:-100.0000:0.0000 chr2 209204319 rs17699838 A G 100 PASS DP=64;EVS=0.106105|30|6503;GMAF=G|0.07169;AA=A;AF1000G=0.071685;phyloP=-0.791;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:81:39,25:64:0.391:20:-100.0000:0.0000 chr2 209204714 rs2289171 G A 54 PASS DP=10;cosmic=1|COSN166391,1|COSN18890388,1|COSN20282112,1|COSN19624383;EVS=0.307136|44|6502;GMAF=A|0.3123;AA=G;AF1000G=0.3123;phyloP=-0.322;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:13:6,4:10:0.400:20:-100.0000:0.0000 chr2 209209827 rs2304544 G A 100 PASS DP=18;clinvar=1|benign;EVS=0.921652|54|6503;GMAF=G|0.08906;AA=A;AF1000G=0.910942;phyloP=-1.449;CSQT=1|PIKFYVE|NM_015040.3|splice_region_variant&intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:65:0,18:18:1.000:20:-100.0000:0.0526 chr2 209209997 rs2043718 C T 100 PASS DP=26;GMAF=C|0.008187;AA=T;AF1000G=0.991813;phyloP=0.163;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:94:0,26:26:1.000:20:-100.0000:0.0000 chr2 209210975 rs200295076 ACTACTTATGAT A 100 PASS DP=23;AF1000G=0.015375;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:32:10,13:23:0.565:20:-100.0000:0.0000 chr2 209212707 rs2304545 G A 92 PASS DP=17;clinvar=1|benign;EVS=0.683069|111|6503;GMAF=G|0.2839;AA=G;AF1000G=0.716054;phyloP=0.162;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:24:10,7:17:0.412:20:-100.0000:0.0000 chr2 209214770 rs2118297 A G 100 PASS DP=30;clinvar=1|benign;EVS=0.921793|116|6502;GMAF=A|0.08886;AA=A;AF1000G=0.911142;phyloP=0.473;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,30:30:1.000:20:-100.0000:0.0000 chr2 209215448 rs994696 A G 100 PASS DP=17;EVS=0.922178|44|6502;GMAF=A|0.08886;AA=A;AF1000G=0.911142;phyloP=-0.562;CSQT=1|PIKFYVE|NM_015040.3|intron_variant;CSQR=1|ENSR00001714460|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:62:0,17:17:1.000:20:-100.0000:0.0000 chr2 209215586 rs994697 A G 100 PASS DP=51;clinvar=1|benign;EVS=0.921882|129|6503;GMAF=A|0.08886;AA=G;AF1000G=0.911142;phyloP=-0.301;CSQT=1|PIKFYVE|NM_015040.3|synonymous_variant;CSQR=1|ENSR00001714460|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,51:51:1.000:20:-100.0000:0.0000 chr2 209219049 rs6435452 T A 70 LowDP DP=4;GMAF=T|0.08886;AA=T;AF1000G=0.911142;phyloP=0.257;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,4:4:1.000:20:-100.0000:0.0000 chr2 209219190 rs6435453 A G 100 PASS DP=27;GMAF=A|0.08826;AA=A;AF1000G=0.911741;phyloP=-0.43;CSQT=1|PIKFYVE|NM_015040.3|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:98:0,27:27:1.000:20:-100.0000:0.0000 chr2 227927189 rs35717623;rs398081120;rs796278870 GT G 61 R5x9 DP=16;AF1000G=0.558307;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:10:11,5:16:0.313:20:-100.0000:0.0000 chr2 227954599 rs2229814 G A 100 PASS DP=30;clinvar=1|benign,1|benign;cosmic=1|COSM3757996;EVS=0.509039|111|5974;GMAF=G|0.4515;AA=A;AF1000G=0.548522;phyloP=-0.088;CSQT=1|COL4A4|NM_000092.4|missense_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:48:17,13:30:0.433:20:-78.5655:0.0000 chr2 227966148 rs16823202 C T 100 PASS DP=28;cosmic=1|COSN18720449,1|COSN19634668;EVS=0.656236|18|2269;GMAF=C|0.4163;AA=T;AF1000G=0.583666;phyloP=-0.103;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:25:11,17:28:0.607:20:-100.0000:0.0000 chr2 227966298 rs59443812;rs397724904 T TA 100 PASS DP=28;AF1000G=0.535343;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:44:16,12:28:0.429:20:-100.0000:0.0000 chr2 227967601 rs11274738;rs150877371 ACAATATTTCAGCAATAGGGAAAG A 70 LowDP DP=4;EVS=0.560269|98|5575;AF1000G=0.604832;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC ./.:0:0,4:4:1.000:20:-100.0000:0.0000 chr2 227967830 rs398081123;rs573969560;rs796369993;rs10707643 GA G 100 PASS DP=28;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:89:1,27:28:0.964:20:-100.0000:0.0000 chr2 227973193 rs10174459 G A 100 PASS DP=13;cosmic=1|COSN8867965;GMAF=A|0.1851;AA=G;AF1000G=0.185104;phyloP=2.93;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:10:5,8:13:0.615:20:-100.0000:0.0000 chr2 227973410 rs55741079 C A 66 PASS DP=13;GMAF=A|0.3391;AA=C;AF1000G=0.339058;phyloP=-0.34;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:16:8,5:13:0.385:20:-100.0000:0.0000 chr2 227973623 rs12475686 A G 100 PASS DP=30;EVS=0.622897|30|5944;GMAF=A|0.3996;AA=A;AF1000G=0.600439;phyloP=0.246;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,30:30:1.000:20:-100.0000:0.0000 chr2 227973873 rs58363082 T C 100 PASS DP=26;cosmic=1|COSN8867966;EVS=0.195243|149|5150;GMAF=C|0.2867;AA=C;AF1000G=0.286741;phyloP=-0.556;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:47:14,12:26:0.462:20:-100.0000:0.0000 chr2 227973878 rs59938187 C T 100 PASS DP=26;cosmic=1|COSN8867967;EVS=0.191942|151|5150;GMAF=T|0.2845;AA=C;AF1000G=0.284545;phyloP=0.048;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:47:14,12:26:0.462:20:-100.0000:0.0000 chr2 227973892 rs73082223 T C 100 PASS DP=26;cosmic=1|COSN8867968;EVS=0.262746|137|6002;GMAF=C|0.3522;AA=T;AF1000G=0.352236;phyloP=-1.218;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:47:14,12:26:0.462:20:-100.0000:0.0000 chr2 227979533 rs12465531 A C 100 PASS DP=20;GMAF=A|0.3578;AA=C;AF1000G=0.642173;phyloP=-2.486;CSQT=1|COL4A4|NM_000092.4|intron_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:8:7,13:20:0.650:20:-100.0000:0.0000 chr2 228102680 rs148393022 C T 100 PASS DP=23;clinvar=1|benign,1|likely_benign;EVS=0.001436|182|5919;GMAF=T|0.01538;AA=C;AF1000G=0.015375;phyloP=0.56;CSQT=1|COL4A3|NM_000091.4|splice_region_variant&intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:43:11,12:23:0.522:20:-84.2687:0.0000 chr2 228102752 rs1882435 C A 100 PASS DP=23;clinvar=1|benign,1|benign;cosmic=1|COSN166420,1|COSN19624384,1|COSN20282113,1|COSN19674657;EVS=0.284798|137|5927;GMAF=A|0.3051;AA=A;AF1000G=0.305112;phyloP=-1.334;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:84:0,23:23:1.000:20:-100.0000:0.0000 chr2 228109626 rs113428834 T TG 100 PASS DP=23;EVS=0.766122|68|5629;GMAF=G|0.009585;AF1000G=0.749201;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:21:5,18:23:0.783:20:-100.0000:0.0000 chr2 228109784 rs6750210 C T 100 PASS DP=23;EVS=0.738043|25|2279;GMAF=C|0.252;AA=C;AF1000G=0.748003;phyloP=0.006;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:84:0,23:23:1.000:20:-100.0000:0.0000 chr2 228111435 rs10178458 T C 100 PASS DP=20;clinvar=1|benign,1|benign;EVS=0.770425|65|5924;GMAF=T|0.2033;AA=t;AF1000G=0.796725;phyloP=1.132;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:73:0,20:20:1.000:20:-100.0000:0.0000 chr2 228113175 rs6436669 A G 100 PASS DP=72;clinvar=1|benign,1|benign;EVS=0.770131|57|5899;GMAF=A|0.2037;AA=G;AF1000G=0.796326;phyloP=-0.094;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:0,72:72:1.000:20:-100.0000:0.0137 chr2 228118403 rs12621551 T G 100 PASS DP=14;EVS=0.772528|168|6159;GMAF=T|0.2131;AA=T;AF1000G=0.786941;phyloP=-0.184;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:18:6,8:14:0.571:20:-100.0000:0.0667 chr2 228121101 rs55703767 G T 80 PASS DP=14;clinvar=1|benign,1|likely_benign;cosmic=1|COSM3757999,1|COSM3758000;EVS=0.165770|117|5951;GMAF=T|0.1158;AA=G;AF1000G=0.115815;phyloP=0.606;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:22:8,6:14:0.429:20:-42.6564:0.0000 chr2 228128540 rs10205042 C T 100 PASS DP=58;clinvar=1|benign,1|benign;EVS=0.718037|31|5921;GMAF=C|0.2324;AA=T;AF1000G=0.767572;phyloP=-0.091;CSQT=1|COL4A3|NM_000091.4|synonymous_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:100:1,57:58:0.983:20:-100.0000:0.0169 chr2 228135426 rs73993878 G A 98 PASS DP=23;cosmic=1|COSN19664724;GMAF=A|0.1034;AA=G;AF1000G=0.103435;phyloP=1.179;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:21:15,8:23:0.348:20:-100.0000:0.0000 chr2 228135631 rs28381984 C T 100 PASS DP=96;clinvar=1|benign,1|benign;cosmic=1|COSM3758001,1|COSM3758002;EVS=0.389010|56|5951;GMAF=T|0.4;AA=C;AF1000G=0.39996;phyloP=3.691;CSQT=1|COL4A3|NM_000091.4|missense_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant;CSQR=1|ENSR00001716076|regulatory_region_variant GT:GQ:AD:DP:VF:NL:SB:NC 0/1:100:46,50:96:0.521:20:-100.0000:0.0000 chr2 228142038 rs775545588 GAAA GA,G 69 R5x9 DP=22;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant,2|COL4A3|NM_000091.4|intron_variant,2|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/2:7:14,6:22:0.909:20:-100.0000:0.0000 chr2 228149107 rs6436672 A G 100 PASS DP=11;EVS=0.878707|28|6002;GMAF=A|0.1851;AA=G;AF1000G=0.814896;phyloP=-1.192;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:NC 1/1:40:0,11:11:1.000:20:-100.0000:0.0000 chr2 228153667 . G GT 79 PASS DP=15;CSQT=1|COL4A3|NM_000091.4|intron_variant,1|LOC654841|NR_102371.1|intron_variant&non_coding_transcript_variant GT:GQ:AD:DP:VF:NL:SB:N