##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\12030_S5.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\Sample617 -i D:\Illumina\MiSeqAnalysis\181130_M05705_0031_000000000-C5R45\Alignment_3\20181203_130703\Temp_03-VariantCalling\interval\12030_S5.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=<ID=<M>,Description="There is an overlapping other allele that has been called in a separate VCF record">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##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=<ID=AF1000G,Number=A,Type=Float,Description="The allele frequency from all populations of 1000 genomes data">
##INFO=<ID=AA,Number=A,Type=String,Description="The inferred allele ancestral (if determined) to the chimpanzee/human lineage.">
##INFO=<ID=GMAF,Number=A,Type=String,Description="Global minor allele frequency (GMAF); technically, the frequency of the second most frequent allele.  Format: GlobalMinorAllele|AlleleFreqGlobalMinor">
##INFO=<ID=cosmic,Number=.,Type=String,Description="The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. Format: GenotypeIndex|Significance">
##INFO=<ID=clinvar,Number=.,Type=String,Description="Clinical significance. Format: GenotypeIndex|Significance">
##INFO=<ID=EVS,Number=A,Type=String,Description="Allele frequency, coverage and sample count taken from the Exome Variant Server (EVS). Format: AlleleFreqEVS|EVSCoverage|EVSSamples.">
##INFO=<ID=RefMinor,Number=0,Type=Flag,Description="Denotes positions where the reference base is a minor allele and is annotated as though it were a variant">
##INFO=<ID=phyloP,Number=A,Type=Float,Description="PhyloP conservation score. Denotes how conserved the reference sequence is between species throughout evolution">
##INFO=<ID=CSQT,Number=.,Type=String,Description="Consequence type as predicted by Nirvana. Format: GenotypeIndex|HGNC|TranscriptID|Consequence">
##INFO=<ID=CSQR,Number=.,Type=String,Description="Predicted regulatory consequence type. Format: GenotypeIndex|RegulatoryID|Consequence">
##FILTER=<ID=q30,Description="Quality score less than 30">
##FILTER=<ID=LowDP,Description="Low coverage (DP tag), therefore no genotype called">
##FILTER=<ID=SB,Description="Variant strand bias too high">
##FILTER=<ID=LowVariantFreq,Description="Variant frequency less than 0.200">
##FILTER=<ID=MultiAllelicSite,Description="Variant does not conform to diploid model">
##FILTER=<ID=R5x9,Description="Repeats of part or all of the variant allele (max repeat length 5) in the reference greater than or equal to 9">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth Used For Variant Calling">
##FORMAT=<ID=VF,Number=.,Type=Float,Description="Variant Frequency">
##FORMAT=<ID=NL,Number=1,Type=Integer,Description="Applied BaseCall Noise Level">
##FORMAT=<ID=SB,Number=1,Type=Float,Description="StrandBias Score">
##FORMAT=<ID=NC,Number=1,Type=Float,Description="Fraction of bases which were uncalled or with basecall quality below the minimum threshold">
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	12030_S5.bam
chr1	11181327	rs11121691	C	T	100	PASS	DP=24;cosmic=1|COSM3996743;EVS=0.302091|72|6503;GMAF=T|0.2206;AA=C;AF1000G=0.220647;phyloP=0.56;CSQT=1|MTOR|NM_004958.3|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:28:10,14:24:0.583:20:-100.0000:0.0000
chr1	11190646	rs2275527	G	A	100	PASS	DP=35;cosmic=1|COSM3996746;EVS=0.305936|95|6503;GMAF=A|0.2286;AA=G;AF1000G=0.228634;phyloP=-0.401;CSQT=1|MTOR|NM_004958.3|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:34:14,21:35:0.600:20:-100.0000:0.0000
chr1	11193089	rs145092514	C	T	100	PASS	DP=64;cosmic=1|COSN17141962;EVS=0.004459|96|6503;GMAF=T|0.003395;AA=c;AF1000G=0.003395;phyloP=-0.669;CSQT=1|MTOR|NM_004958.3|intron_variant;CSQR=1|ENSR00001577754|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:36,28:64:0.438:20:-100.0000:0.0000
chr1	36563158	rs3738360	C	A	100	PASS	DP=59;EVS=0.783869|40|6503;GMAF=C|0.3437;AA=C;AF1000G=0.65635;phyloP=0.367;CSQT=1|ADPRHL2|NM_017825.2|downstream_gene_variant,1|COL8A2|NM_005202.2|3_prime_UTR_variant;CSQR=1|ENSR00001581936|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:28,31:59:0.525:20:-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	36565617	rs274754	G	A	100	PASS	DP=53;EVS=0.652929|44|6503;GMAF=A|0.4826;AA=G;AF1000G=0.482628;phyloP=-1.5;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	47882497	rs34082359	C	T	88	PASS	DP=19;clinvar=1|benign;cosmic=1|COSM3751263;EVS=0.313176|9|6383;GMAF=T|0.2786;AA=c;AF1000G=0.278554;phyloP=-0.391;CSQT=1|FOXE3|NM_012186.2|synonymous_variant;CSQR=1|ENSR00001583800|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:21:12,7:19:0.368:20:-100.0000:0.0000
chr1	47883019	rs6666370	T	C	100	PASS	DP=69;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	0/1:100:34,35:69:0.507:20:-100.0000:0.0143
chr1	47883024	rs2820969	A	G	100	PASS	DP=70;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	1/1:100:0,70:70:1.000:20:-100.0000:0.0000
chr1	59042181	rs14008	G	T	100	PASS	DP=71;clinvar=1|likely_benign;EVS=0.149207|16|6491;GMAF=T|0.1571;AA=G;AF1000G=0.157149;phyloP=-0.115;CSQT=1|TACSTD2|NM_002353.2|missense_variant;CSQR=1|ENSR00000537412|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:40,31:71:0.437:20:-89.8384:0.0000
chr1	59042254	rs761334700	G	A	100	PASS	DP=34;phyloP=0.485;CSQT=1|TACSTD2|NM_002353.2|missense_variant;CSQR=1|ENSR00000537412|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:72:17,17:34:0.500:20:-100.0000:0.0000
chr1	59042882	rs232835	T	G	25	LowDP;q30	DP=8;clinvar=1|likely_benign;GMAF=G|0.1569;AA=G;AF1000G=0.156949;phyloP=-0.489;CSQT=1|TACSTD2|NM_002353.2|5_prime_UTR_variant;CSQR=1|ENSR00000537412|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	./.:0:6,2:8:0.250:20:-100.0000:0.0000
chr1	94463396	rs1800699	G	A	100	PASS	DP=62;clinvar=1|not_provided,1|likely_benign;EVS=0.010534|75|6503;GMAF=A|0.01398;AA=G;AF1000G=0.013978;phyloP=-0.246;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:31,31:62:0.500:20:-100.0000:0.0000
chr1	94466659	rs1801555	A	G	100	PASS	DP=38;clinvar=1|not_provided,1|benign,1|benign,1|benign,1|benign,1|benign;cosmic=1|COSM3751459,1|COSM5828042;EVS=0.298862|48|6503;GMAF=G|0.3011;AA=G;AF1000G=0.301118;phyloP=1.481;CSQT=1|ABCA4|NM_000350.2|splice_region_variant&synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,38:38:1.000:20:-100.0000:0.0000
chr1	94467407	rs17110761	C	T	100	PASS	DP=61;clinvar=1|likely_benign,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;EVS=0.145933|51|6503;GMAF=T|0.134;AA=C;AF1000G=0.133986;phyloP=-0.001;CSQT=1|ABCA4|NM_000350.2|splice_region_variant&intron_variant;CSQR=1|ENSR00001587944|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:28,33:61:0.541:20:-100.0000:0.0000
chr1	94467447	rs1801359	G	A	100	PASS	DP=62;clinvar=1|not_provided,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM3751460,1|COSM5828043;EVS=0.146010|71|6503;GMAF=A|0.134;AA=G;AF1000G=0.133986;phyloP=-0.492;CSQT=1|ABCA4|NM_000350.2|synonymous_variant;CSQR=1|ENSR00001587944|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:98:28,34:62:0.548:20:-100.0000:0.0000
chr1	94471075	rs1762114	A	G	100	PASS	DP=21;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	0/1:39:10,11:21:0.524:20:-71.1533:0.0000
chr1	94473845	rs2275029	T	C	100	PASS	DP=27;clinvar=1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM146561;EVS=0.199677|72|6503;GMAF=C|0.1671;AA=T;AF1000G=0.167133;phyloP=-0.281;CSQT=1|ABCA4|NM_000350.2|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:0:8,19:27:0.704:20:-100.0000:0.0000
chr1	94473864	rs1800739	C	T	100	PASS	DP=27;clinvar=1|not_provided,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSN163160,1|COSN6473501;EVS=0.208365|68|6503;GMAF=T|0.1833;AA=C;AF1000G=0.183307;phyloP=0.176;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:0:8,19:27:0.704:20:-100.0000:0.0000
chr1	94473896	rs2275031	G	T	100	PASS	DP=27;clinvar=1|benign;cosmic=1|COSN15662434,1|COSN163161,1|COSN6473502;EVS=0.201138|51|6503;GMAF=T|0.1781;AA=T;AF1000G=0.178115;phyloP=-0.5;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:0:8,19:27:0.704:20:-100.0000:0.0000
chr1	94474328	rs4147857	T	C	100	PASS	DP=67;clinvar=1|not_provided,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM146562;EVS=0.206905|221|6503;GMAF=C|0.1875;AA=T;AF1000G=0.1875;phyloP=-0.181;CSQT=1|ABCA4|NM_000350.2|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:36,31:67:0.463:20:-100.0000:0.0147
chr1	94474452	rs4147856	T	G	100	PASS	DP=66;clinvar=1|not_provided,1|benign;cosmic=1|COSN163162;EVS=0.206981|77|6503;GMAF=G|0.1877;AA=T;AF1000G=0.1877;phyloP=-1.483;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:35,31:66:0.470:20:-100.0000:0.0294
chr1	94476388	rs1801574	C	G	100	PASS	DP=20;clinvar=1|not_provided,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM146563;EVS=0.249270|162|6503;GMAF=G|0.2007;AA=G;AF1000G=0.200679;phyloP=-0.332;CSQT=1|ABCA4|NM_000350.2|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:34:11,9:20:0.450:20:-54.1490:0.0000
chr1	94476555	rs537831	G	A	100	PASS	DP=67;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	0/1:100:35,32:67:0.478:20:-100.0000:0.0000
chr1	94476695	rs2065711	C	T	100	PASS	DP=15;cosmic=1|COSN6473505;GMAF=T|0.2003;AA=C;AF1000G=0.20028;phyloP=0.88;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:26:7,8:15:0.533:20:-100.0000:0.0000
chr1	94476991	rs4147899	CT	C	100	PASS	DP=31;EVS=0.248642|37|6260;GMAF=C|0.0009984;AF1000G=0.198882;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:54:17,14:31:0.452:20:-93.3432:0.0000
chr1	94480037	rs2275033	C	T	100	PASS	DP=34;GMAF=T|0.3271;AA=T;AF1000G=0.327077;phyloP=-0.648;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541012|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:56:19,15:34:0.441:20:-93.3432:0.0000
chr1	94481271	.	T	C	20	LowDP;q30	DP=1;phyloP=0.114;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541012|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	./.:0:0,1:1:1.000:20:-100.0000:0.0000
chr1	94487308	rs551303378	AT	A	34	R5x9	DP=14;AF1000G=0.000599;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522546|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:0:11,3:14:0.214:20:-100.0000:0.0000
chr1	94487354	rs472908	G	A	100	PASS	DP=55;clinvar=1|not_provided,1|benign;cosmic=1|COSN15324643,1|COSN8862525;EVS=0.630231|41|6500;GMAF=G|0.4111;AA=A;AF1000G=0.588858;phyloP=0.368;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522546|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,55:55:1.000:20:-100.0000:0.0179
chr1	94495930	rs547806	T	C	100	PASS	DP=19;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	1/1:69:0,19:19:1.000:20:-100.0000:0.0000
chr1	94495952	rs75424561	T	C	73	PASS	DP=19;EVS=0.050900|55|6503;GMAF=C|0.04852;AA=T;AF1000G=0.048522;phyloP=-0.151;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:13:13,6:19:0.316:20:-38.1069:0.0000
chr1	94496446	rs56253197	T	C	100	PASS	DP=30;GMAF=C|0.09485;AA=T;AF1000G=0.094848;phyloP=-0.753;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:48:17,13:30:0.433:20:-100.0000:0.0000
chr1	94506734	rs115209782	G	T	100	PASS	DP=76;EVS=0.012840|53|6503;GMAF=T|0.01498;AA=G;AF1000G=0.014976;phyloP=-0.069;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:39,37:76:0.487:20:-100.0000:0.0130
chr1	94508791	rs79871431	C	T	100	PASS	DP=63;GMAF=T|0.03275;AA=C;AF1000G=0.032748;phyloP=-0.321;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522551|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:31,32:63:0.508:20:-100.0000:0.0000
chr1	94514560	rs386633545	AC	GG	100	PASS	DP=82;GMAF=G|0.05092;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00000541026|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:41,41:82:0.500:20:-100.0000:0.0000
chr1	94544109	.	TCCTCC	T	20	LowDP;q30	DP=1;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	./.:0:0,1:1:1.000:20:-100.0000:0.0000
chr1	94544234	rs3112831	T	C	100	PASS	DP=21;clinvar=1|likely_benign,1|benign,1|likely_benign,1|likely_benign,1|likely_benign,1|likely_benign;cosmic=1|COSM3735986,1|COSM3735987;EVS=0.260649|188|6503;GMAF=C|0.2208;AA=C;AF1000G=0.220847;phyloP=4.076;CSQT=1|ABCA4|NM_000350.2|missense_variant;CSQR=1|ENSR00001522555|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:40:11,10:21:0.476:20:-100.0000:0.0000
chr1	94544276	rs4147830	G	A	100	PASS	DP=21;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	0/1:39:10,11:21:0.524:20:-100.0000:0.0000
chr1	94544812	rs200943894	C	T	100	PASS	DP=15;GMAF=T|0.009385;AA=C;AF1000G=0.009385;phyloP=0.034;CSQT=1|ABCA4|NM_000350.2|intron_variant;CSQR=1|ENSR00001522555|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:16:3,12:15:0.800:20:-98.1279:0.3478
chr1	94549029	rs526016	A	G	100	PASS	DP=30;clinvar=1|not_provided,1|benign;cosmic=1|COSN19623402,1|COSN20281454;EVS=0.244881|57|6495;GMAF=G|0.1977;AA=A;AF1000G=0.197684;phyloP=-0.264;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:63:15,15:30:0.500:20:-100.0000:0.0000
chr1	94564500	rs61748536	G	A	100	PASS	DP=36;EVS=0.003229|43|6503;GMAF=A|0.004193;AA=G;AF1000G=0.004193;phyloP=-0.068;CSQT=1|ABCA4|NM_000350.2|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:8:12,24:36:0.667:20:-100.0000:0.0000
chr1	94568491	rs4847278	A	G	100	PASS	DP=54;GMAF=G|0.3405;AA=A;AF1000G=0.340455;phyloP=-0.522;CSQT=1|ABCA4|NM_000350.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:27,27:54:0.500:20:-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	0/1:7:5,9:14:0.643:20:-60.2411:0.0000
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	0/1:7:5,9:14:0.643:20:-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	154938235	rs1131397	G	C	100	PASS	DP=21;cosmic=1|COSM3750397,1|COSM3750398,1|COSM3750399;EVS=0.175227|34|6503;GMAF=C|0.1583;AA=C;AF1000G=0.158347;phyloP=-0.875;CSQT=1|PYGO2|NM_138300.3|upstream_gene_variant,1|SHC1|NM_001130040.1|synonymous_variant;CSQR=1|ENSR00001592269|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:39:10,11:21:0.524:20:-100.0000:0.0000
chr1	206944233	rs1554286	A	G	100	PASS	DP=20;EVS=0.750884|106|6503;GMAF=A|0.4081;AA=G;AF1000G=0.591853;phyloP=1.334;CSQT=1|IL10|NM_000572.2|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:73:0,20:20:1.000:20:-100.0000:0.0000
chr1	206944645	rs1518111	T	C	100	PASS	DP=28;cosmic=1|COSN19767692,1|COSN8861895;EVS=0.732589|75|2283;GMAF=T|0.4269;AA=C;AF1000G=0.573083;phyloP=-1.494;CSQT=1|IL10|NM_000572.2|intron_variant;CSQR=1|ENSR00000551734|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,28:28:1.000:20:-100.0000:0.0000
chr1	228112121	rs4653889	A	G	100	PASS	DP=55;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	1/1:100:0,55:55:1.000:20:-100.0000:0.0000
chr1	228113134	rs201711724	C	T	100	PASS	DP=54;EVS=0.000310|12|6459;GMAF=T|0.0003994;AA=C;AF1000G=0.000399;phyloP=2.059;CSQT=1|WNT9A|NM_003395.2|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:83:31,23:54:0.426:20:-100.0000:0.0357
chr1	228113163	rs3795768	A	G	100	PASS	DP=60;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	1/1:100:0,60:60:1.000:20:-37.0476:0.0164
chr2	1642537	rs386642327	TGC	CGT	100	PASS	DP=72;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	1/1:100:0,72:72:1.000:20:-100.0000:0.0000
chr2	1642545	rs6742039	C	G	100	PASS	DP=72;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	1/1:100:0,72:72:1.000:20:-100.0000:0.0000
chr2	1647171	rs6730800	T	C	100	PASS	DP=51;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	1/1:100:0,51:51:1.000:20:-100.0000:0.0192
chr2	1648512	rs61731247	C	A	100	PASS	DP=68;EVS=0.008747|22|6002;GMAF=A|0.01018;AA=C;AF1000G=0.010184;phyloP=-2.369;CSQT=1|PXDN|NM_012293.1|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:99:30,38:68:0.559:20:-100.0000:0.0000
chr2	1651842	rs11685976	C	A	100	PASS	DP=17;cosmic=1|COSN15304688,1|COSN15323800,1|COSN8867748,1|COSN19673469;GMAF=A|0.2448;AA=C;AF1000G=0.244808;phyloP=-0.312;CSQT=1|PXDN|NM_012293.1|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:19:7,10:17:0.588:20:-100.0000:0.0556
chr2	1652660	rs3811613	G	A	100	PASS	DP=61;clinvar=1|benign;cosmic=1|COSM3757715;EVS=0.250239|16|6278;GMAF=A|0.2448;AA=G;AF1000G=0.244808;phyloP=0.047;CSQT=1|PXDN|NM_012293.1|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:33,28:61:0.459:20:-100.0000:0.0000
chr2	1652822	rs1863135	T	G	100	PASS	DP=86;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	1/1:100:0,86:86:1.000:20:-100.0000:0.0000
chr2	1664654	rs17841813	A	G	100	PASS	DP=50;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	1/1:100:0,50:50:1.000:20:-100.0000:0.0000
chr2	1687263	rs138434519	TC	T	100	PASS	DP=62;AA=C;AF1000G=0.188099;CSQT=1|PXDN|NM_012293.1|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:75:26,36:62:0.581:20:-100.0000:0.0000
chr2	1687266	rs115883224	T	A	100	PASS	DP=63;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	0/1:83:27,36:63:0.571:20:-100.0000:0.0000
chr2	113532885	rs3783550	G	T	87	PASS	DP=20;EVS=0.725896|55|6503;GMAF=G|0.3796;AA=T;AF1000G=0.620407;phyloP=-1.505;CSQT=1|IL1A|NM_000575.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:19:13,7:20:0.350:20:-100.0000:0.0000
chr2	113536925	rs147376170	G	GT	100	PASS	DP=30;AA=T;AF1000G=0.016573;CSQT=1|IL1A|NM_000575.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:48:17,13:30:0.433:20:-100.0000:0.0000
chr2	113537223	rs17561	C	A	100	PASS	DP=30;cosmic=1|COSM3757583;EVS=0.261648|106|6503;GMAF=A|0.2175;AA=C;AF1000G=0.217452;phyloP=2.738;CSQT=1|IL1A|NM_000575.3|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:29:12,18:30:0.600:20:-100.0000:0.0000
chr2	113539291	.	C	T	100	PASS	DP=71;phyloP=0.088;CSQT=1|IL1A|NM_000575.3|missense_variant;CSQR=1|ENSR00000596855|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:38,33:71:0.465:20:-100.0000:0.0000
chr2	113877495	rs928940	G	T	100	PASS	DP=66;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	1/1:100:0,66:66:1.000:20:-100.0000:0.0149
chr2	113890304	rs315952	T	C	100	PASS	DP=55;clinvar=1|benign;EVS=0.333154|94|6503;GMAF=C|0.35;AA=C;AF1000G=0.35004;phyloP=-2.655;CSQT=1|IL1RN|NM_173841.2|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:77:24,31:55:0.564:20:-100.0000:0.0000
chr2	113890586	rs315951	C	G	100	PASS	DP=28;clinvar=1|benign;GMAF=G|0.355;AA=c;AF1000G=0.355032;phyloP=0.648;CSQT=1|IL1RN|NM_173841.2|3_prime_UTR_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:25:11,17:28:0.607:20:-100.0000:0.0000
chr2	189899541	rs4666770	T	C	100	PASS	DP=61;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	0/1:48:41,20:61:0.328:20:-100.0000:0.0161
chr2	189899572	rs7420715	T	C	100	PASS	DP=62;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	0/1:46:42,20:62:0.323:20:-100.0000:0.0000
chr2	189901295	rs12693526	G	A	100	PASS	DP=76;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	0/1:100:35,41:76:0.539:20:-100.0000:0.0000
chr2	189907937	rs6434312	A	G	100	PASS	DP=77;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	0/1:45:28,49:77:0.636:20:-100.0000:0.0000
chr2	189918787	rs6738371	C	T	100	PASS	DP=18;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	0/1:38:9,9:18:0.500:20:-100.0000:0.0000
chr2	189923104	rs7556733	A	G	100	PASS	DP=68;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	0/1:88:29,39:68:0.574:20:-100.0000:0.0145
chr2	189923630	rs398090949;rs398080909;rs5837121;rs574915386	AT	A	100	PASS	DP=29;clinvar=1|benign;CSQT=1|COL5A2|NM_000393.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:34:18,11:29:0.379:20:-62.5291:0.0000
chr2	189925548	rs6414122	T	A	100	PASS	DP=64;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	0/1:57:25,39:64:0.609:20:-100.0000:0.0000
chr2	189927506	rs7424947	C	G	100	PASS	DP=23;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	0/1:9:8,15:23:0.652:20:-100.0000:0.0417
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	0/1:25:13,8:21:0.381:20:-100.0000:0.0455
chr2	189953285	rs5837124;rs397758641;rs746250131	A	AAATG	100	PASS	DP=66;cosmic=1|COSN19656478;AF1000G=0.798323;CSQT=1|COL5A2|NM_000393.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:95:29,37:66:0.561:20:-100.0000:0.0000
chr2	189974958	rs4128539	G	T	100	PASS	DP=55;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	0/1:88:25,30:55:0.545:20:-100.0000:0.0000
chr2	209168853	rs893256	C	T	100	PASS	DP=28;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	0/1:59:14,14:28:0.500:20:-100.0000:0.0000
chr2	209184980	rs10932258	G	A	100	PASS	DP=29;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	1/1:100:0,29:29:1.000:20:-100.0000:0.0000
chr2	209184999	rs10932259	C	T	100	PASS	DP=29;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	0/1:67:14,15:29:0.517:20:-97.3268:0.0000
chr2	209189972	rs144399707;rs377762628	TTC	T	100	PASS	DP=24;EVS=0.020850|23|6259;AF1000G=0.024561;CSQT=1|PIKFYVE|NM_015040.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:27:15,9:24:0.375:20:-100.0000:0.0000
chr2	209190330	rs2363468	T	C	100	PASS	DP=57;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	0/1:94:32,25:57:0.439:20:-100.0000:0.0000
chr2	209190519	rs893254	A	T	100	PASS	DP=27;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	0/1:45:15,12:27:0.444:20:-80.3261:0.0000
chr2	209190528	rs893253	C	G	100	PASS	DP=26;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	0/1:47:14,12:26:0.462:20:-100.0000:0.0370
chr2	209191082	rs1529979	C	A	100	PASS	DP=55;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	0/1:97:30,25:55:0.455:20:-100.0000:0.0000
chr2	209191099	rs1529978	T	C	100	PASS	DP=55;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	1/1:100:0,55:55:1.000:20:-100.0000:0.0000
chr2	209194696	rs1437414	G	C	100	PASS	DP=60;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	0/1:100:32,28:60:0.467:20:-100.0000:0.0164
chr2	209200394	rs6718402	A	C	100	PASS	DP=40;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	0/1:85:20,20:40:0.500:20:-100.0000:0.0000
chr2	209200733	rs73983751	A	G	100	PASS	DP=99;EVS=0.021913|61|6503;GMAF=G|0.02516;AA=A;AF1000G=0.02516;phyloP=-0.499;CSQT=1|PIKFYVE|NM_015040.3|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:45,54:99:0.545:20:-100.0000:0.0000
chr2	209201739	rs7596571	T	C	100	PASS	DP=24;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	1/1:87:0,24:24:1.000:20:-100.0000:0.0000
chr2	209209827	rs2304544	G	A	100	PASS	DP=56;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	0/1:100:29,27:56:0.482:20:-100.0000:0.0000
chr2	209209997	rs2043718	C	T	100	PASS	DP=35;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	1/1:100:0,35:35:1.000:20:-100.0000:0.0000
chr2	209214770	rs2118297	A	G	100	PASS	DP=40;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	0/1:28:15,25:40:0.625:20:-100.0000:0.0000
chr2	209215448	rs994696	A	G	100	PASS	DP=21;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	0/1:27:9,12:21:0.571:20:-88.9452:0.0000
chr2	209215586	rs994697	A	G	100	PASS	DP=66;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	0/1:100:38,28:66:0.424:20:-100.0000:0.0000
chr2	209219190	rs6435453	A	G	100	PASS	DP=40;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	0/1:39:16,24:40:0.600:20:-100.0000:0.0000
chr2	227872182	rs2228557	G	A	100	PASS	DP=71;clinvar=1|benign,1|benign;cosmic=1|COSM3757991;EVS=0.460410|193|6100;GMAF=G|0.4856;AA=A;AF1000G=0.514377;phyloP=0.537;CSQT=1|COL4A4|NM_000092.4|synonymous_variant;CSQR=1|ENSR00001716056|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,71:71:1.000:20:-100.0000:0.0000
chr2	227872995	rs2228555	T	C	100	PASS	DP=61;clinvar=1|benign,1|benign;cosmic=1|COSM3757992;EVS=0.585705|55|6324;GMAF=T|0.3594;AA=C;AF1000G=0.640575;phyloP=-0.16;CSQT=1|COL4A4|NM_000092.4|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,61:61:1.000:20:-100.0000:0.0000
chr2	227873028	rs13419076	A	G	100	PASS	DP=60;clinvar=1|benign,1|benign;EVS=0.454801|42|6228;GMAF=A|0.4844;AA=G;AF1000G=0.515575;phyloP=-1.917;CSQT=1|COL4A4|NM_000092.4|splice_region_variant&intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,60:60:1.000:20:-100.0000:0.0000
chr2	227874957	rs4423583	C	T	100	PASS	DP=39;GMAF=C|0.4834;AA=T;AF1000G=0.516573;phyloP=-0.859;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,39:39:1.000:20:-100.0000:0.0000
chr2	227877037	rs10188770	G	A	100	PASS	DP=24;cosmic=1|COSN8867960;EVS=0.471249|43|6191;GMAF=G|0.4794;AA=G;AF1000G=0.520567;phyloP=0.723;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:87:0,24:24:1.000:20:-100.0000:0.0000
chr2	227886773	rs3752895	A	G	100	PASS	DP=51;clinvar=1|benign,1|benign;cosmic=1|COSM3757993;EVS=0.478246|113|5976;GMAF=A|0.4738;AA=G;AF1000G=0.526158;phyloP=1.999;CSQT=1|COL4A4|NM_000092.4|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,50:51:0.980:20:-100.0000:0.0000
chr2	227886925	rs3752896	C	T	100	PASS	DP=28;cosmic=1|COSN8867961,1|COSN8867962;EVS=0.411268|92|6035;GMAF=T|0.4485;AA=C;AF1000G=0.448482;phyloP=-0.599;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:48:13,15:28:0.536:20:-97.3268:0.0000
chr2	227892619	rs2228556	C	T	100	PASS	DP=80;clinvar=1|benign,1|benign;cosmic=1|COSM1752390;EVS=0.454637|56|5952;GMAF=T|0.4918;AA=T;AF1000G=0.491813;phyloP=0.477;CSQT=1|COL4A4|NM_000092.4|splice_region_variant&synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:38,42:80:0.525:20:-91.6535:0.0000
chr2	227892658	rs16823077	T	C	100	PASS	DP=62;clinvar=1|benign,1|likely_benign;EVS=0.024841|47|5958;GMAF=C|0.02636;AA=T;AF1000G=0.026358;phyloP=-1.357;CSQT=1|COL4A4|NM_000092.4|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:33,29:62:0.468:20:-100.0000:0.0000
chr2	227892720	rs2229813	C	T	100	PASS	DP=62;clinvar=1|likely_pathogenic,1|benign,1|benign;cosmic=1|COSM1752392;EVS=0.454830|27|5911;GMAF=T|0.493;AA=T;AF1000G=0.493011;phyloP=0.077;CSQT=1|COL4A4|NM_000092.4|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:33,29:62:0.468:20:-100.0000:0.0000
chr2	227895125	rs1917127	A	G	100	PASS	DP=16;cosmic=1|COSN8867963,1|COSN8867964;EVS=0.454085|101|6022;GMAF=G|0.4966;AA=G;AF1000G=0.496605;phyloP=-0.061;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:11:6,10:16:0.625:20:-100.0000:0.0000
chr2	227896652	rs13423714	C	G	100	PASS	DP=60;clinvar=1|benign,1|benign;EVS=0.451309|34|6110;GMAF=G|0.496;AA=C;AF1000G=0.496006;phyloP=-0.301;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:59:24,36:60:0.600:20:-100.0000:0.0000
chr2	227896886	rs2229812	C	T	100	PASS	DP=27;clinvar=1|benign,1|benign;cosmic=1|COSM3757994;EVS=0.452558|76|5923;GMAF=T|0.4956;AA=T;AF1000G=0.495607;phyloP=-0.79;CSQT=1|COL4A4|NM_000092.4|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:29:10,16:27:0.593:20:-100.0000:0.0000
chr2	227896976	rs10203363	C	T	100	PASS	DP=27;clinvar=1|benign,1|benign;cosmic=1|COSM3757995;EVS=0.451201|36|5953;GMAF=T|0.495;AA=C;AF1000G=0.495008;phyloP=-0.718;CSQT=1|COL4A4|NM_000092.4|synonymous_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:29:11,16:27:0.593:20:-100.0000:0.0000
chr2	227915601	rs2272204	G	T	100	PASS	DP=30;GMAF=G|0.4527;AA=G;AF1000G=0.547324;phyloP=-0.534;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:29:12,18:30:0.600:20:-100.0000:0.0000
chr2	227915832	rs1800517	G	A	100	PASS	DP=56;clinvar=1|benign,1|benign;cosmic=1|COSM4001525;EVS=0.518593|111|5997;GMAF=G|0.4527;AA=G;AF1000G=0.547324;phyloP=2.772;CSQT=1|COL4A4|NM_000092.4|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:100:29,27:56:0.482:20:-100.0000:0.0000
chr2	227920474	rs1320406	G	A	100	PASS	DP=23;GMAF=A|0.4922;AA=G;AF1000G=0.492212;phyloP=-0.61;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:45:12,11:23:0.478:20:-100.0000:0.0000
chr2	227921977	rs4536647	A	G	100	PASS	DP=22;GMAF=A|0.3333;AA=G;AF1000G=0.666733;phyloP=-0.246;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:5:6,16:22:0.727:20:-100.0000:0.0000
chr2	227922015	rs4566357	A	G	100	PASS	DP=22;GMAF=A|0.3335;AA=a;AF1000G=0.666534;phyloP=0.103;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:5:6,16:22:0.727:20:-100.0000:0.0000
chr2	227922104	rs7567789	T	C	100	PASS	DP=22;cosmic=1|COSN19692653;EVS=0.657633|10|5922;GMAF=T|0.3335;AA=T;AF1000G=0.666534;phyloP=-0.149;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:5:6,16:22:0.727:20:-100.0000:0.0000
chr2	227922109	rs7567796	T	A	100	PASS	DP=22;cosmic=1|COSN19692654;EVS=0.624452|11|5926;GMAF=T|0.3662;AA=T;AF1000G=0.633786;phyloP=0.119;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:5:6,16:22:0.727:20:-100.0000:0.0000
chr2	227924817	.	G	GA	60	LowDP	DP=7;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	./.:0:3,4:7:0.571:20:-100.0000:0.0000
chr2	227927189	rs35717623;rs398081120;rs796278870	GT	G	55	R5x9	DP=21;AF1000G=0.558307;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:1:16,5:21:0.238:20:-100.0000:0.0000
chr2	227942519	rs7597336	A	G	100	PASS	DP=64;GMAF=G|0.1416;AA=A;AF1000G=0.141573;phyloP=0.845;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:68:26,38:64:0.594:20:-100.0000:0.0000
chr2	227942778	rs75539253	C	T	100	PASS	DP=28;EVS=0.001428|37|5954;GMAF=T|0.001398;AA=C;AF1000G=0.001398;phyloP=2.347;CSQT=1|COL4A4|NM_000092.4|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:37:12,16:28:0.571:20:-100.0000:0.0000
chr2	227945181	rs35998949	T	C	100	PASS	DP=40;clinvar=1|conflicting_interpretations_of_pathogenicity,1|likely_benign;EVS=0.023334|128|5957;GMAF=C|0.02336;AA=T;AF1000G=0.023363;phyloP=0.612;CSQT=1|COL4A4|NM_000092.4|missense_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:28:15,25:40:0.625:20:-100.0000:0.0000
chr2	227954599	rs2229814	G	A	100	PASS	DP=54;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	0/1:91:30,24:54:0.444:20:-100.0000:0.0000
chr2	227966148	rs16823202	C	T	100	PASS	DP=53;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	0/1:77:31,22:53:0.415:20:-100.0000:0.0000
chr2	227966298	rs59443812;rs397724904	T	TA	100	PASS	DP=53;AF1000G=0.535343;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:70:32,21:53:0.396:20:-100.0000:0.0000
chr2	227967601	rs11274738;rs150877371	ACAATATTTCAGCAATAGGGAAAG	A	100	LowDP	DP=7;EVS=0.560269|98|5575;AF1000G=0.604832;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	./.:0:0,7:7:1.000:20:-100.0000:0.0000
chr2	227967830	rs398081123;rs573969560;rs796369993;rs10707643	GA	G	100	PASS	DP=39;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:41:8,31:39:0.795:20:-100.0000:0.0000
chr2	227973193	rs10174459	G	A	100	PASS	DP=21;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	0/1:16:8,13:21:0.619:20:-100.0000:0.0000
chr2	227973623	rs12475686	A	G	100	PASS	DP=54;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	1/1:100:0,54:54:1.000:20:-100.0000:0.0357
chr2	227973873	rs58363082	T	C	100	PASS	DP=22;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	0/1:1:7,15:22:0.682:20:-100.0000:0.0000
chr2	227973878	rs59938187	C	T	100	PASS	DP=22;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	0/1:1:7,15:22:0.682:20:-100.0000:0.0000
chr2	227973892	rs73082223	T	C	100	PASS	DP=22;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	0/1:1:7,15:22:0.682:20:-100.0000:0.0000
chr2	227976298	rs59888959	G	A	100	PASS	DP=31;GMAF=A|0.05831;AA=G;AF1000G=0.058307;phyloP=-0.521;CSQT=1|COL4A4|NM_000092.4|intron_variant	GT:GQ:AD:DP:VF:NL:SB:NC	0/1:26:12,19:31:0.613:20:-100.0000:0.0606
chr2	227979533	rs12465531	A	C	100	PASS	DP=52;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	0/1:100:27,25:52:0.481:20:-100.0000:0.0000
chr2	228012054	rs16823262	C	T	100	PASS	DP=50;EVS=0.098012|267|2867;GMAF=T|0.1012;AA=T;AF1000G=0.101238;phyloP=-0.323;CSQT=1|COL4A4|NM_000092.4|intron_variant;CSQR=1|ENSR00001552587|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,50:50:1.000:20:-100.0000:0.0000
chr2	228012183	rs16823264	A	G	100	PASS	DP=50;clinvar=1|benign,1|benign;EVS=0.101154|208|6065;GMAF=G|0.1042;AA=A;AF1000G=0.104233;phyloP=-0.336;CSQT=1|COL4A4|NM_000092.4|missense_variant;CSQR=1|ENSR00001552587|regulatory_region_variant	GT:GQ:AD:DP:VF:NL:SB:NC	1/1:100:0,50:50:1.000:20:-100.0000:0.0196
chr2	228012201	rs2228558	G	A	100	PASS	DP=49;clinvar=1|benign,1|benign;EVS=0.102401|167|6040;GMAF=A|0.1048;AA=A;AF1000G=0.104832;phyloP=-0.39;CSQT=1|COL4A4|NM_000092.4|5_prime_UTR_