npm - @jbrowse/plugin-spreadsheet-view - Versions diffs - 2.6.1 → 2.6.3 - Mend

@jbrowse/plugin-spreadsheet-view 2.6.1 → 2.6.3

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package/src/SpreadsheetView/test_data/1801160099-N32519_26611_S51_56704.hard-filtered.vcf DELETED Viewed

@@ -1,174 +0,0 @@
-##fileformat=VCFv4.1
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
-##DRAGENCommandLine=<ID=dragen,Date="Mon Mar 05 02:30:12 PST 2018",CommandLineOptions=" -r human/reference/human_GRCh37.p13.RefSeq/defaults --vc-reference human/reference/human_GRCh37.p13.RefSeq/defaults/genome.fa -1 /data/c10185/analysis/run_56704/1801160099-N32519_26611_S51_R1_001.fastq.gz -2 /data/c10185/analysis/run_56704/1801160099-N32519_26611_S51_R2_001.fastq.gz -f --output-file-prefix 1801160099-N32519_26611_S51_56704 --output-directory jobout --RGID 1801160099-N32519_26611_S51_56704 --RGPL illumina --RGSM 1801160099-N32519 --enable-duplicate-marking true --enable-bam-indexing true --lic-no-print --intermediate-results-dir /staging/tmp --enable-variant-caller true --enable-map-align-output true --vc-sample-name 1801160099-N32519_26611_S51_56704 --vc-enable-depth-of-coverage true --vc-hard-filter=QDFilter:snp:QD<2.0;MQFilter:snp:MQ<40.0;FSFilter:snp:FS>60.0 --dbsnp human/reference/dbSNP/dbsnp_147.b37.vcf --vc-target-bed /ref/extra/targets/LS_coding_exon.b37.pad50.bed">
-##DRAGENVersion=<ID=dragen,Version="SW: 01.011.099.02.03.02.32154, HW: 01.011.099">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
-##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##FILTER=<ID=QDFilter,Description="Set if true:QD<2.0">
-##FILTER=<ID=MQFilter,Description="Set if true:MQ<40.0">
-##FILTER=<ID=FSFilter,Description="Set if true:FS>60.0">
-##contig=<ID=1,length=249250621>
-##contig=<ID=2,length=243199373>
-##contig=<ID=3,length=198022430>
-##contig=<ID=4,length=191154276>
-##contig=<ID=5,length=180915260>
-##contig=<ID=6,length=171115067>
-##contig=<ID=7,length=159138663>
-##contig=<ID=8,length=146364022>
-##contig=<ID=9,length=141213431>
-##contig=<ID=10,length=135534747>
-##contig=<ID=11,length=135006516>
-##contig=<ID=12,length=133851895>
-##contig=<ID=13,length=115169878>
-##contig=<ID=14,length=107349540>
-##contig=<ID=15,length=102531392>
-##contig=<ID=16,length=90354753>
-##contig=<ID=17,length=81195210>
-##contig=<ID=18,length=78077248>
-##contig=<ID=19,length=59128983>
-##contig=<ID=20,length=63025520>
-##contig=<ID=21,length=48129895>
-##contig=<ID=22,length=51304566>
-##contig=<ID=X,length=155270560>
-##contig=<ID=Y,length=59373566>
-##contig=<ID=MT,length=16569>
-##reference=file:///staging/human/reference/human_GRCh37.75/defaults/reference.bin
-##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
-##SnpSiftCmd="SnpSift Annotate /opt/ras/ref/extra/gme_allele.vcf.gz 1801160099-N32519_26611_S51_56704.hard-filtered.vcf"
-##INFO=<ID=GMEAF,Number=1,Type=String,Description="GME Allele Frequency">
-##INFO=<ID=GMEAC,Number=1,Type=String,Description="GME Allele Count">
-##SnpSiftCmd="SnpSift Annotate /opt/ras/ref/extra/hgmd/hgmd.vcf.gz 1801160099-N32519_26611_S51_56704.hard-filtered.vcf"
-##INFO=<ID=HGMD_CLASSIFICATION,Number=1,Type=String,Description="HGMD Class Information">
-##INFO=<ID=HGMD_ACCESSION,Number=1,Type=String,Description="HGMD Accession ID">
-##SnpSiftCmd="SnpSift Annotate /opt/ras/ref/extra/emvclass/emvclass_2016.vcf.gz 1801160099-N32519_26611_S51_56704.hard-filtered.vcf"
-##INFO=<ID=EMV_CLASSIFICATION,Number=1,Type=String,Description="Emory Variant Class Information">
-##INFO=<ID=HGVS,Number=1,Type=String,Description="HGVS notations">
-##SnpSiftCmd="SnpSift Annotate /opt/ras/ref/extra/gnomAD/release-170228/exomes/vcf/gnomad.exomes.r2.0.1.sites.vcf.gz 1801160099-N32519_26611_S51_56704.hard-filtered.vcf -info AC,AC_POPMAX,AF,AF_POPMAX,AN,AN_POPMAX,POPMAX,Hom,Hemi,InbreedingCoeff,AC_OTH,AF_OTH,AN_OTH,AS_FilterStatus"
-##INFO=<ID=Hom,Number=A,Type=Integer,Description="Count of homozygous individuals">
-##INFO=<ID=POPMAX,Number=A,Type=String,Description="Population with max AF">
-##INFO=<ID=AN_OTH,Number=1,Type=Integer,Description="Total number of alleles in Other (population not assigned) called genotypes">
-##INFO=<ID=AF_OTH,Number=A,Type=Float,Description="Allele Frequency among Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=Hemi,Number=A,Type=Integer,Description="Count of hemizygous individuals">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=AC_OTH,Number=A,Type=Integer,Description="Allele count in Other (population not assigned) genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF_POPMAX,Number=A,Type=Float,Description="Maximum Allele Frequency across populations (excluding OTH)">
-##INFO=<ID=AN_POPMAX,Number=A,Type=Integer,Description="AN in the population with the max AF">
-##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Random Forests filter status for each allele">
-##INFO=<ID=AC_POPMAX,Number=A,Type=Integer,Description="AC in the population with the max AF">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	1801160099-N32519_26611_S51_56704
-1	156845492	rs144271100	A	AGTGT	1241.01	PASS	DP=98;FS=0.000;MQ=60.00;QD=12.66;SOR=3.912;FractionInformativeReads=0.306;DB	GT:AD:DP:GQ:PL:SB	1/1:0,30:30:89:1278,89,0:0,0,3,27
-1	156848995	rs6337	C	T	2209.0	PASS	DP=150;FS=2.049;MQ=60.00;MQRankSum=1.664;QD=14.73;ReadPosRankSum=1.580;SOR=0.543;FractionInformativeReads=0.993;DB;GMEAC=1089893;GMEAF=0.549445;AC=141461;AC_OTH=3473;AC_POPMAX=7385;AF=5.80610e-01;AF_OTH=6.37716e-01;AF_POPMAX=7.51425e-01;AN=243642;AN_OTH=5446;AN_POPMAX=9828;AS_FilterStatus=PASS;Hom=46764;InbreedingCoeff=1.90900e-01;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:70,79:149:99:2237,0,2064:41,29,43,36
-2	47601106	rs1126497	T	C	1551.63	PASS	DP=119;FS=4.625;MQ=60.00;MQRankSum=-2.215;QD=13.04;ReadPosRankSum=0.818;SOR=0.379;FractionInformativeReads=1.000;DB;GMEAC=8441142;GMEAF=0.424975;HGMD_ACCESSION=CM1110060;HGMD_CLASSIFICATION=DP;AC=126143;AC_OTH=2587;AC_POPMAX=12929;AF=5.12364e-01;AF_OTH=4.71736e-01;AF_POPMAX=8.44812e-01;AN=246198;AN_OTH=5484;AN_POPMAX=15304;AS_FilterStatus=PASS;Hom=34881;InbreedingCoeff=7.92000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	0/1:55,64:119:99:1580,0,1515:37,18,37,27
-2	47630550	rs2303426	C	G	413.7	PASS	DP=38;FS=5.329;MQ=60.00;MQRankSum=1.439;QD=10.89;ReadPosRankSum=-1.116;SOR=0.204;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000251:c.211+9C>G;AC=98964;AC_OTH=2024;AC_POPMAX=12433;AF=4.73557e-01;AF_OTH=4.28995e-01;AF_POPMAX=8.15600e-01;AN=208980;AN_OTH=4718;AN_POPMAX=15244;AS_FilterStatus=PASS;Hom=25312;InbreedingCoeff=9.87000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:21,17:38:99:442,0,688:4,17,6,11
-2	47641559	rs768805063	TAAAAA	T,TAA	1196.95	PASS	DP=116;FS=0.000;MQ=60.00;MQRankSum=-1.701;QD=10.32;ReadPosRankSum=0.444;SOR=1.314;FractionInformativeReads=0.379;DB	GT:AD:DP:GQ:PL:SB	1/2:5,17,22:44:99:1234,463,591,370,0,278:1,4,7,32
-2	47693959	rs3732183	G	A	2335.12	PASS	DP=176;FS=1.184;MQ=60.00;MQRankSum=0.712;QD=13.27;ReadPosRankSum=-1.278;SOR=0.585;FractionInformativeReads=1.000;DB;HGMD_ACCESSION=CS045476;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_000251:c.1661+12G>A;AC=84217;AC_OTH=1722;AC_POPMAX=11331;AF=3.42599e-01;AF_OTH=3.14923e-01;AF_POPMAX=6.57251e-01;AN=245818;AN_OTH=5468;AN_POPMAX=17240;AS_FilterStatus=PASS;Hom=16411;InbreedingCoeff=7.10000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:84,92:176:99:2363,0,2204:35,49,41,51
-2	48010558	rs1042820	C	A	1518.37	PASS	DP=137;FS=1.367;MQ=60.00;MQRankSum=-0.446;QD=11.08;ReadPosRankSum=-1.028;SOR=0.830;FractionInformativeReads=1.000;DB;GMEAC=2741672;GMEAF=0.140802;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.186C>A;AC=15976;AC_OTH=403;AC_POPMAX=9525;AF=1.43863e-01;AF_OTH=1.49038e-01;AF_POPMAX=2.10945e-01;AN=111050;AN_OTH=2704;AN_POPMAX=45154;AS_FilterStatus=PASS;Hom=1366;InbreedingCoeff=7.69000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:72,65:137:99:1547,0,1848:30,42,25,40
-2	48010654	rs55927047	C	G	367.61	PASS	DP=29;FS=1.744;MQ=60.00;MQRankSum=1.129;QD=12.68;ReadPosRankSum=-0.155;SOR=0.368;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.260+22C>G;AC=3934;AC_OTH=100;AC_POPMAX=1890;AF=1.36238e-01;AF_OTH=1.40449e-01;AF_POPMAX=2.04811e-01;AN=28876;AN_OTH=712;AN_POPMAX=9228;AS_FilterStatus=PASS;Hom=347;InbreedingCoeff=8.02000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:17,12:29:99:396,0,494:3,14,3,9
-2	48018030	rs1800931	A	G	531.18	PASS	DP=30;FS=7.141;MQ=60.00;MQRankSum=0.445;QD=17.71;ReadPosRankSum=-0.402;SOR=0.091;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.261-36A>G;AC=9183;AC_OTH=201;AC_POPMAX=6011;AF=3.73931e-02;AF_OTH=3.67325e-02;AF_POPMAX=5.41015e-02;AN=245580;AN_OTH=5472;AN_POPMAX=111106;AS_FilterStatus=PASS;Hom=225;InbreedingCoeff=1.14000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:12,18:30:99:559,0,359:11,1,12,6
-2	48018081	rs1800932	A	G	1300.89	PASS	DP=102;FS=0.882;MQ=60.00;MQRankSum=-0.349;QD=12.75;ReadPosRankSum=-0.060;SOR=0.818;FractionInformativeReads=1.000;DB;GMEAC=3001684;GMEAF=0.151210;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.276A>G;AC=33198;AC_OTH=777;AC_POPMAX=21264;AF=1.34814e-01;AF_OTH=1.41633e-01;AF_POPMAX=1.90367e-01;AN=246250;AN_OTH=5486;AN_POPMAX=111700;AS_FilterStatus=PASS;Hom=2758;InbreedingCoeff=3.40000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:55,47:102:99:1329,0,1787:42,13,37,10
-2	48023115	rs1800935	T	C	1844.25	PASS	DP=166;FS=1.241;MQ=60.00;MQRankSum=-0.761;QD=11.11;ReadPosRankSum=-1.542;SOR=0.832;FractionInformativeReads=1.000;DB;GMEAC=3641620;GMEAF=0.183468;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.540T>C;AC=52613;AC_OTH=1182;AC_POPMAX=33558;AF=2.13778e-01;AF_OTH=2.15615e-01;AF_POPMAX=3.00699e-01;AN=246110;AN_OTH=5482;AN_POPMAX=111600;AS_FilterStatus=PASS;Hom=7023;InbreedingCoeff=6.20000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:93,73:166:99:1872,0,2655:40,53,29,44
-2	48030838	rs2020911	A	T	3310.84	PASS	DP=92;FS=0.000;MQ=60.00;QD=29.23;SOR=3.209;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.3438+14A>T;AC=101116;AC_OTH=2153;AC_POPMAX=10767;AF=4.11134e-01;AF_OTH=3.93170e-01;AF_POPMAX=6.24391e-01;AN=245944;AN_OTH=5476;AN_POPMAX=17244;AS_FilterStatus=PASS;Hom=22061;InbreedingCoeff=4.05000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,92:92:99:3339,275,0:0,0,15,77
-2	48032874	rs2234731;rs767177736	ACTAT	A	2095.58	PASS	DP=124;FS=3.035;MQ=60.00;MQRankSum=-0.513;QD=16.90;ReadPosRankSum=0.987;SOR=0.430;FractionInformativeReads=0.871;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000179:c.3646+33_3646+36delCTAT;AC=167729;AC_OTH=3696;AC_POPMAX=14962;AF=6.84061e-01;AF_OTH=6.77419e-01;AF_POPMAX=8.69884e-01;AN=245196;AN_OTH=5456;AN_POPMAX=17200;AS_FilterStatus=PASS;Hom=58425;InbreedingCoeff=3.36000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:52,56:108:99:2133,0,2672:10,42,14,42
-2	48033551	rs3136367	C	G	8769.99	PASS	DP=264;FS=0.000;MQ=60.00;QD=33.22;SOR=0.788;FractionInformativeReads=1.000;DB;AC=180221;AC_OTH=3919;AC_POPMAX=14043;AF=7.33261e-01;AF_OTH=7.15930e-01;AF_POPMAX=9.18924e-01;AN=245780;AN_OTH=5474;AN_POPMAX=15282;AS_FilterStatus=PASS;Hom=66853;InbreedingCoeff=3.00000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,264:264:99:8798,793,0:0,0,126,138
-2	48033890	rs771393147	C	CT	202.42	PASS	DP=110;FS=0.933;MQ=60.00;MQRankSum=0.641;QD=1.84;ReadPosRankSum=-0.266;SOR=0.538;FractionInformativeReads=0.818;DB	GT:AD:DP:GQ:PL:SB	0/1:62,28:90:99:240,0,833:44,18,19,9
-2	215632256	rs2070093	A	G	3403.61	PASS	DP=113;FS=0.000;MQ=60.00;QD=30.12;SOR=0.747;FractionInformativeReads=1.000;DB;GMEAC=1446540;GMEAF=0.728097;AC=201220;AC_OTH=4353;AC_POPMAX=16435;AF=8.17708e-01;AF_OTH=7.95504e-01;AF_POPMAX=9.52864e-01;AN=246078;AN_OTH=5472;AN_POPMAX=17248;AS_FilterStatus=PASS;Hom=83030;InbreedingCoeff=3.63000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,113:113:99:3432,338,0:0,0,55,58
-2	215645545	rs2070096	C	G	582.45	PASS	DP=55;FS=1.075;MQ=60.00;MQRankSum=0.060;QD=10.59;ReadPosRankSum=0.537;SOR=0.936;FractionInformativeReads=1.000;DB;GMEAC=4131573;GMEAF=0.207956;AC=50713;AC_OTH=1148;AC_POPMAX=2391;AF=2.06149e-01;AF_OTH=2.09566e-01;AF_POPMAX=2.42840e-01;AN=246002;AN_OTH=5478;AN_POPMAX=9846;AS_FilterStatus=PASS;Hom=5414;InbreedingCoeff=9.10000e-03;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:32,23:55:99:611,0,987:19,13,15,8
-2	215657182	rs56130510	TA	T	396.01	PASS	DP=75;FS=13.488;MQ=60.00;MQRankSum=3.098;QD=5.28;ReadPosRankSum=0.282;SOR=2.430;FractionInformativeReads=0.813;DB	GT:AD:DP:GQ:PL:SB	0/1:32,29:61:99:433,0,516:12,20,4,25
-2	215674090	rs35933323	T	G	2007.68	PASS	DP=147;FS=1.315;MQ=60.00;MQRankSum=0.409;QD=13.66;ReadPosRankSum=0.750;SOR=0.580;FractionInformativeReads=1.000;DB;AC=169036;AC_OTH=3753;AC_POPMAX=27084;AF=7.39382e-01;AF_OTH=7.23958e-01;AF_POPMAX=8.21275e-01;AN=228618;AN_OTH=5184;AN_POPMAX=32978;AS_FilterStatus=PASS;Hom=62885;InbreedingCoeff=3.07000e-02;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	0/1:70,77:147:99:2036,0,1855:43,27,45,32
-2	215674323	rs1129804	C	G	332.08	PASS	DP=30;FS=1.527;MQ=60.00;MQRankSum=0.953;QD=11.07;ReadPosRankSum=-1.334;SOR=1.034;FractionInformativeReads=1.000;DB;AC=98896;AC_OTH=2647;AC_POPMAX=19564;AF=7.34031e-01;AF_OTH=7.20076e-01;AF_POPMAX=8.15847e-01;AN=134730;AN_OTH=3676;AN_POPMAX=23980;AS_FilterStatus=PASS;Hom=36588;InbreedingCoeff=1.18000e-01;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	0/1:18,12:30:99:360,0,1014:6,12,3,9
-2	215674341	rs17489363	A	G	187.5	PASS	DP=23;FS=0.000;MQ=60.00;MQRankSum=-2.766;QD=8.15;ReadPosRankSum=1.155;SOR=0.904;FractionInformativeReads=1.000;DB;AC=96141;AC_OTH=2588;AC_POPMAX=19360;AF=7.33464e-01;AF_OTH=7.18490e-01;AF_POPMAX=8.15914e-01;AN=131078;AN_OTH=3602;AN_POPMAX=23728;AS_FilterStatus=PASS;Hom=35543;InbreedingCoeff=1.27400e-01;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	0/1:17,6:23:99:216,0,956:7,10,2,4
-3	10191523	.	T	G	109.43	QDFilter	DP=166;FS=48.789;MQ=60.00;MQRankSum=0.926;QD=0.66;ReadPosRankSum=0.004;SOR=5.693;FractionInformativeReads=1.000	GT:AD:DP:GQ:PL:SB	0/1:131,35:166:99:138,0,3431:89,42,35,0
-3	37083740	rs9876116	A	G	2712.47	PASS	DP=203;FS=0.000;MQ=60.00;MQRankSum=-1.370;QD=13.36;ReadPosRankSum=-0.860;SOR=0.662;FractionInformativeReads=0.995;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000249:c.1668-19A>G;AC=91015;AC_OTH=2066;AC_POPMAX=49473;AF=3.71126e-01;AF_OTH=3.78388e-01;AF_POPMAX=4.45679e-01;AN=245240;AN_OTH=5460;AN_POPMAX=111006;AS_FilterStatus=PASS;Hom=18383;InbreedingCoeff=5.16000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:103,99:202:99:2741,0,2764:46,57,45,54
-5	112103135	.	T	C	353.83	PASS	DP=25;FS=0.000;MQ=60.00;MQRankSum=-1.341;QD=14.15;ReadPosRankSum=-0.301;SOR=0.495;FractionInformativeReads=1.000;AC=1;AC_OTH=0;AC_POPMAX=1;AF=4.34628e-06;AF_OTH=0.00000e+00;AF_POPMAX=9.66277e-06;AN=230082;AN_OTH=5148;AN_POPMAX=103490;AS_FilterStatus=PASS;Hom=0;InbreedingCoeff=3.20000e-03;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:14,11:25:99:382,0,510:0,14,0,11
-5	112162854	rs2229992	T	C	5179.7	PASS	DP=156;FS=0.000;MQ=60.00;QD=33.20;SOR=1.186;FractionInformativeReads=1.000;DB;GMEAC=1130856;GMEAF=0.568983;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.1458T>C;AC=143908;AC_OTH=3317;AC_POPMAX=23443;AF=5.85411e-01;AF_OTH=6.07064e-01;AF_POPMAX=6.99499e-01;AN=245824;AN_OTH=5464;AN_POPMAX=33514;AS_FilterStatus=PASS;Hom=43904;InbreedingCoeff=5.69000e-02;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	1/1:0,156:156:99:5208,467,0:0,0,62,94
-5	112164561	rs351771	G	A	5919.51	PASS	DP=167;FS=0.000;MQ=60.00;QD=27.67;SOR=2.046;FractionInformativeReads=1.000;DB;GMEAC=1255729;GMEAF=0.632560;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.1635G>A;AC=159619;AC_OTH=3586;AC_POPMAX=14130;AF=6.49301e-01;AF_OTH=6.55097e-01;AF_POPMAX=8.21798e-01;AN=245832;AN_OTH=5474;AN_POPMAX=17194;AS_FilterStatus=PASS;Hom=52792;InbreedingCoeff=3.25000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,167:167:99:5948,500,0:0,0,121,46
-5	112175770	rs41115	G	A	7515.59	PASS	DP=225;FS=0.000;MQ=60.00;QD=33.40;SOR=0.738;FractionInformativeReads=1.000;DB;GMEAC=1252734;GMEAF=0.630413;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.4479G>A;AC=159537;AC_OTH=3592;AC_POPMAX=14170;AF=6.49581e-01;AF_OTH=6.56673e-01;AF_POPMAX=8.21735e-01;AN=245600;AN_OTH=5470;AN_POPMAX=17244;AS_FilterStatus=PASS;Hom=52779;InbreedingCoeff=3.24000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,225:225:99:7544,675,0:0,0,110,115
-5	112176325	rs42427	G	A	4793.32	PASS	DP=144;FS=0.000;MQ=60.00;QD=33.29;SOR=1.179;FractionInformativeReads=0.993;DB;GMEAC=1267719;GMEAF=0.637966;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.5034G>A;AC=159652;AC_OTH=3594;AC_POPMAX=14128;AF=6.52440e-01;AF_OTH=6.59450e-01;AF_POPMAX=8.21873e-01;AN=244700;AN_OTH=5450;AN_POPMAX=17190;AS_FilterStatus=PASS;Hom=53006;InbreedingCoeff=3.11000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,143:143:99:4822,429,0:0,0,57,86
-5	112176559	rs866006	T	G	1758.52	PASS	DP=51;FS=0.000;MQ=60.00;QD=34.48;SOR=1.201;FractionInformativeReads=1.000;DB;GMEAC=1262724;GMEAF=0.635448;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.5268T>G;AC=159750;AC_OTH=3590;AC_POPMAX=14155;AF=6.51318e-01;AF_OTH=6.57028e-01;AF_POPMAX=8.21342e-01;AN=245272;AN_OTH=5464;AN_POPMAX=17234;AS_FilterStatus=PASS;Hom=52989;InbreedingCoeff=3.41000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,51:51:99:1787,153,0:0,0,31,20
-5	112176756	rs459552	T	A	5421.22	PASS	DP=156;FS=0.000;MQ=60.00;MQRankSum=1.598;QD=34.75;ReadPosRankSum=1.464;SOR=1.287;FractionInformativeReads=0.994;DB;GMEAC=1623361;GMEAF=0.818044;HGMD_ACCESSION=CM990164;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.5465T>A;AC=194769;AC_OTH=4307;AC_POPMAX=14646;AF=7.93764e-01;AF_OTH=7.89117e-01;AF_POPMAX=9.59513e-01;AN=245374;AN_OTH=5458;AN_POPMAX=15264;AS_FilterStatus=PASS;Hom=77927;InbreedingCoeff=2.93000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:1,154:155:99:5449,424,0:0,1,100,54
-5	112177171	rs465899	G	A	4173.79	PASS	DP=123;FS=0.000;MQ=60.00;MQRankSum=0.369;QD=33.93;ReadPosRankSum=1.221;SOR=0.324;FractionInformativeReads=0.992;DB;GMEAC=1261725;GMEAF=0.634945;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.5880G>A;AC=159530;AC_OTH=3595;AC_POPMAX=14150;AF=6.49732e-01;AF_OTH=6.56741e-01;AF_POPMAX=8.21814e-01;AN=245532;AN_OTH=5474;AN_POPMAX=17218;AS_FilterStatus=PASS;Hom=52777;InbreedingCoeff=3.22000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:1,121:122:99:4202,324,0:0,1,54,67
-5	112178795	rs2229995	G	A	3550.77	PASS	DP=264;FS=1.478;MQ=60.00;MQRankSum=1.783;QD=13.45;ReadPosRankSum=0.975;SOR=0.587;FractionInformativeReads=1.000;DB;GMEAC=311955;GMEAF=0.015609;HGMD_ACCESSION=CM042292;HGMD_CLASSIFICATION=DM?;EMV_CLASSIFICATION=Benign;HGVS=NM_000038:c.7504G>A;AC=4922;AC_OTH=128;AC_POPMAX=935;AF=2.00068e-02;AF_OTH=2.33491e-02;AF_POPMAX=4.19320e-02;AN=246016;AN_OTH=5482;AN_POPMAX=22298;AS_FilterStatus=PASS;Hom=70;InbreedingCoeff=8.60000e-03;POPMAX=FIN	GT:AD:DP:GQ:PL:SB	0/1:136,128:264:99:3579,0,3790:74,62,66,62
-5	131892979	rs4526098	G	A	1506.2	PASS	DP=45;FS=0.000;MQ=60.00;QD=33.47;SOR=1.280;FractionInformativeReads=1.000;DB;AC=241246;AC_OTH=5420;AC_POPMAX=17247;AF=9.79711e-01;AF_OTH=9.88690e-01;AF_POPMAX=9.99942e-01;AN=246242;AN_OTH=5482;AN_POPMAX=17248;AS_FilterStatus=PASS;Hom=118616;InbreedingCoeff=1.72100e-01;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,45:45:99:1534,135,0:0,0,28,17
-7	6022626	rs1805326	C	T	412.0	MQFilter	DP=38;FS=1.303;MQ=29.95;MQRankSum=-0.629;QD=10.84;ReadPosRankSum=-0.219;SOR=1.115;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000535:c.2007-4G>A;AC=24029;AC_OTH=576;AC_POPMAX=3080;AF=1.60084e-01;AF_OTH=1.51659e-01;AF_POPMAX=2.86992e-01;AN=150102;AN_OTH=3798;AN_POPMAX=10732;AS_FilterStatus=PASS;Hom=1952;InbreedingCoeff=2.80000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:18,20:38:99:440,0,386:10,8,13,7
-7	6026775	rs2228006	T	C	3683.33	PASS	DP=97;FS=0.000;MQ=56.02;QD=30.03;SOR=0.892;FractionInformativeReads=1.000;DB;GMEAC=1745241;GMEAF=0.878651;HGMD_ACCESSION=BM1497492;HGMD_CLASSIFICATION=R;EMV_CLASSIFICATION=Benign;HGVS=NM_000535:c.1621A>G;AC=206446;AC_OTH=4555;AC_POPMAX=13955;AF=8.40736e-01;AF_OTH=8.31812e-01;AF_POPMAX=9.25889e-01;AN=245554;AN_OTH=5476;AN_POPMAX=15072;AS_FilterStatus=PASS;Hom=87611;InbreedingCoeff=4.57000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,97:97:99:3712,291,0:0,0,44,53
-7	6026988	rs1805321	G	A	4337.15	PASS	DP=316;FS=6.666;MQ=58.33;MQRankSum=0.443;QD=13.73;ReadPosRankSum=-0.586;SOR=0.590;FractionInformativeReads=1.000;DB;GMEAC=9061080;GMEAF=0.456193;EMV_CLASSIFICATION=Benign;HGVS=NM_000535:c.1408C>T;AC=95521;AC_OTH=2155;AC_POPMAX=4438;AF=3.87906e-01;AF_OTH=3.92961e-01;AF_POPMAX=4.50558e-01;AN=246248;AN_OTH=5484;AN_POPMAX=9850;AS_FilterStatus=PASS;Hom=18823;InbreedingCoeff=1.21000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:160,156:316:99:4365,0,4571:89,71,75,81
-7	6036980	rs1805319	G	C	3018.02	PASS	DP=93;FS=0.000;MQ=60.00;QD=32.45;SOR=0.901;FractionInformativeReads=1.000;DB;GMEAC=1670316;GMEAF=0.840886;EMV_CLASSIFICATION=Benign;HGVS=NM_000535:c.780C>G;AC=196619;AC_OTH=4361;AC_POPMAX=15897;AF=8.01512e-01;AF_OTH=7.97549e-01;AF_POPMAX=9.23064e-01;AN=245310;AN_OTH=5468;AN_POPMAX=17222;AS_FilterStatus=PASS;Hom=79497;InbreedingCoeff=3.49000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,93:93:99:3046,279,0:0,0,51,42
-7	6037057	rs60794673	GA	G	309.11	PASS	DP=61;FS=9.310;MQ=60.00;MQRankSum=-2.073;QD=5.07;ReadPosRankSum=0.022;SOR=2.110;FractionInformativeReads=0.754;DB	GT:AD:DP:GQ:PL:SB	0/1:21,25:46:99:346,0,302:9,12,5,20
-7	6038722	rs62456182	T	C	1457.92	PASS	DP=89;FS=0.891;MQ=60.00;MQRankSum=-0.303;QD=16.38;ReadPosRankSum=1.099;SOR=0.571;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000535:c.705+17A>G;AC=90720;AC_OTH=2050;AC_POPMAX=4259;AF=3.68445e-01;AF_OTH=3.73951e-01;AF_POPMAX=4.32561e-01;AN=246224;AN_OTH=5482;AN_POPMAX=9846;AS_FilterStatus=PASS;Hom=17259;InbreedingCoeff=2.03000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:38,51:89:99:1486,0,1016:28,10,36,15
-7	116381121	rs112241458	GT	G	304.45	PASS	DP=68;FS=0.000;MQ=60.00;MQRankSum=-0.605;QD=4.48;ReadPosRankSum=-1.039;SOR=0.478;FractionInformativeReads=0.662;DB	GT:AD:DP:GQ:PL:SB	0/1:25,20:45:99:342,0,432:3,22,3,17
-7	116409675	rs753027677	CTT	C,CT	2783.76	PASS	DP=168;FS=1.665;MQ=60.00;MQRankSum=0.775;QD=16.57;ReadPosRankSum=0.569;SOR=0.333;FractionInformativeReads=0.792;DB	GT:AD:DP:GQ:PL:SB	1/2:6,44,83:133:99:2821,1731,1847,670,0,463:2,4,62,65
-9	21968199	rs11515	C	G	3297.05	PASS	DP=97;FS=0.000;MQ=60.00;QD=33.99;SOR=1.337;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000077:c.*29G>C;AC=216920;AC_OTH=4723;AC_POPMAX=16866;AF=8.81416e-01;AF_OTH=8.61233e-01;AF_POPMAX=9.77966e-01;AN=246104;AN_OTH=5484;AN_POPMAX=17246;AS_FilterStatus=PASS;Hom=95916;InbreedingCoeff=2.24000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	1/1:0,97:97:99:3325,289,0:0,0,61,36
-9	97873957	rs4647534	A	G	1294.56	PASS	DP=97;FS=4.043;MQ=60.00;MQRankSum=-2.205;QD=13.35;ReadPosRankSum=1.231;SOR=0.394;FractionInformativeReads=1.000;DB;AC=115676;AC_OTH=2443;AC_POPMAX=10749;AF=4.72954e-01;AF_OTH=4.46618e-01;AF_POPMAX=6.24506e-01;AN=244582;AN_OTH=5470;AN_POPMAX=17212;AS_FilterStatus=PASS;Hom=28309;InbreedingCoeff=2.68000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:47,50:97:99:1323,0,1273:13,34,18,32
-9	98221861	rs2236406	T	C	1046.9	PASS	DP=70;FS=0.943;MQ=60.00;MQRankSum=-0.121;QD=14.96;ReadPosRankSum=1.979;SOR=0.855;FractionInformativeReads=1.000;DB;AC=84563;AC_OTH=1849;AC_POPMAX=10248;AF=3.43869e-01;AF_OTH=3.37655e-01;AF_POPMAX=6.70330e-01;AN=245916;AN_OTH=5476;AN_POPMAX=15288;AS_FilterStatus=PASS;Hom=16079;InbreedingCoeff=4.81000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	0/1:27,43:70:99:1075,0,671:16,11,27,16
-9	98229389	rs2066829	C	G	1065.87	PASS	DP=78;FS=0.946;MQ=60.00;MQRankSum=0.610;QD=13.66;ReadPosRankSum=0.350;SOR=0.920;FractionInformativeReads=1.000;DB;AC=85078;AC_OTH=1874;AC_POPMAX=9977;AF=3.46440e-01;AF_OTH=3.42471e-01;AF_POPMAX=6.52433e-01;AN=245578;AN_OTH=5472;AN_POPMAX=15292;AS_FilterStatus=PASS;Hom=16169;InbreedingCoeff=4.39000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	0/1:41,37:78:99:1094,0,1053:28,13,27,10
-9	98238358	rs2066836	G	A	1367.39	PASS	DP=124;FS=3.283;MQ=60.00;MQRankSum=-0.080;QD=11.03;ReadPosRankSum=1.905;SOR=0.463;FractionInformativeReads=1.000;DB;GMEAC=3461638;GMEAF=0.174395;AC=42313;AC_OTH=1017;AC_POPMAX=2567;AF=1.72484e-01;AF_OTH=1.85584e-01;AF_POPMAX=2.61033e-01;AN=245316;AN_OTH=5480;AN_POPMAX=9834;AS_FilterStatus=PASS;Hom=4250;InbreedingCoeff=3.20000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:67,57:124:99:1396,0,1747:42,25,32,25
-9	98270646	rs587780530	T	TGCC	100.27	PASS	DP=21;FS=0.000;MQ=60.00;MQRankSum=-0.495;QD=4.77;ReadPosRankSum=-0.354;SOR=0.412;FractionInformativeReads=0.667;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000264:c.-6_-4dupGGC	GT:AD:DP:GQ:PL:SB	0/1:10,4:14:99:138,0,398:4,6,2,2
-10	43595968	rs1800858	A	G	10224.38	PASS	DP=313;FS=0.000;MQ=60.00;QD=32.67;SOR=1.005;FractionInformativeReads=1.000;DB;GMEAC=1471515;GMEAF=0.740685;HGMD_ACCESSION=CM020759;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_020975:c.135A>G;AC=178746;AC_OTH=4000;AC_POPMAX=14521;AF=7.30852e-01;AF_OTH=7.32064e-01;AF_POPMAX=9.53823e-01;AN=244572;AN_OTH=5464;AN_POPMAX=15224;AS_FilterStatus=PASS;Hom=66092;InbreedingCoeff=2.99000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,313:313:99:10253,940,0:0,0,178,135
-10	43606687	rs1800860	A	G	3993.6	PASS	DP=305;FS=1.397;MQ=60.00;MQRankSum=3.528;QD=13.09;ReadPosRankSum=-0.092;SOR=0.783;FractionInformativeReads=1.000;DB;GMEAC=1558428;GMEAF=0.784491;HGMD_ACCESSION=CM033447;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_020975:c.1296A>G;AC=171112;AC_OTH=3826;AC_POPMAX=13219;AF=6.95594e-01;AF_OTH=6.97920e-01;AF_POPMAX=8.63987e-01;AN=245994;AN_OTH=5482;AN_POPMAX=15300;AS_FilterStatus=PASS;Hom=60395;InbreedingCoeff=3.08000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	0/1:151,154:305:99:4022,0,3555:92,59,97,57
-10	43612226	rs760466	C	T	1076.0	PASS	DP=35;FS=0.000;MQ=60.00;MQRankSum=0.612;QD=30.74;ReadPosRankSum=1.019;SOR=1.609;FractionInformativeReads=0.971;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_020975:c.2284+47C>T;AC=46019;AC_OTH=1031;AC_POPMAX=28193;AF=2.07609e-01;AF_OTH=2.16870e-01;AF_POPMAX=2.77665e-01;AN=221662;AN_OTH=4754;AN_POPMAX=101536;AS_FilterStatus=PASS;Hom=5697;InbreedingCoeff=9.23000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	1/1:1,33:34:90:1104,90,0:0,1,6,27
-10	43613843	rs1800861	G	T	5478.15	PASS	DP=166;FS=0.000;MQ=60.00;MQRankSum=0.981;QD=33.00;ReadPosRankSum=0.167;SOR=0.562;FractionInformativeReads=1.000;DB;GMEAC=1524462;GMEAF=0.767372;HGMD_ACCESSION=CM014825;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_020975:c.2307G>T;AC=181651;AC_OTH=4158;AC_POPMAX=13540;AF=7.39176e-01;AF_OTH=7.59313e-01;AF_POPMAX=8.86010e-01;AN=245748;AN_OTH=5476;AN_POPMAX=15282;AS_FilterStatus=PASS;Hom=68119;InbreedingCoeff=3.86000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:1,165:166:99:5506,456,0:1,0,105,60
-10	43622217	rs2075912	T	C	8120.47	PASS	DP=264;FS=0.000;MQ=60.00;MQRankSum=1.078;QD=30.76;ReadPosRankSum=1.152;SOR=0.206;FractionInformativeReads=0.996;DB;HGMD_ACCESSION=CS032426;HGMD_CLASSIFICATION=DP;EMV_CLASSIFICATION=Benign;HGVS=NM_020975:c.3187+47T>C;AC=182343;AC_OTH=4249;AC_POPMAX=13051;AF=7.90877e-01;AF_OTH=8.10259e-01;AF_POPMAX=9.18567e-01;AN=230558;AN_OTH=5244;AN_POPMAX=14208;AS_FilterStatus=PASS;Hom=72912;InbreedingCoeff=5.10000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:2,261:263:99:8149,703,0:0,2,107,154
-10	89720633	rs771859047	CT	C	33.21	PASS	DP=123;FS=0.000;MQ=59.85;MQRankSum=-2.021;QD=0.27;ReadPosRankSum=0.174;SOR=0.605;FractionInformativeReads=0.967;DB	GT:AD:DP:GQ:PL:SB	0/1:101,18:119:70:70,0,2109:78,23,14,4
-10	89720907	rs555895	T	G	2326.73	PASS	DP=235;FS=1.035;MQ=58.27;MQRankSum=-3.395;QD=9.90;ReadPosRankSum=-0.559;SOR=0.780;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000314:c.1026+32T>G;AC=90864;AC_OTH=2055;AC_POPMAX=7438;AF=3.72580e-01;AF_OTH=3.78314e-01;AF_POPMAX=5.00538e-01;AN=243878;AN_OTH=5432;AN_POPMAX=14860;AS_FilterStatus=PASS;Hom=17524;InbreedingCoeff=2.05000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	0/1:141,94:235:99:2355,0,3902:60,81,38,56
-11	64572018	rs2959656	T	C	8940.87	PASS	DP=281;FS=0.000;MQ=60.00;QD=31.82;SOR=1.162;FractionInformativeReads=1.000;DB;GMEAC=190878;GMEAF=0.960725;HGMD_ACCESSION=CM085535;HGMD_CLASSIFICATION=DFP;EMV_CLASSIFICATION=Benign;HGVS=NM_130799:c.1621A>G;AC=230904;AC_OTH=5240;AC_POPMAX=111155;AF=9.39046e-01;AF_OTH=9.55856e-01;AF_POPMAX=9.95888e-01;AN=245892;AN_OTH=5482;AN_POPMAX=111614;AS_FilterStatus=PASS;Hom=109716;InbreedingCoeff=1.85000e-01;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	1/1:0,281:281:99:8969,842,0:0,0,113,168
-11	64572557	rs540012	A	G	9274.04	PASS	DP=256;FS=0.000;MQ=60.00;QD=29.46;SOR=0.825;FractionInformativeReads=1.000;DB;GMEAC=19797;GMEAF=0.996475;EMV_CLASSIFICATION=Benign;HGVS=NM_130799:c.1299T>C;AC=244692;AC_OTH=5467;AC_POPMAX=9848;AF=9.94351e-01;AF_OTH=9.96537e-01;AF_POPMAX=1.00000e+00;AN=246082;AN_OTH=5486;AN_POPMAX=9848;AS_FilterStatus=PASS;Hom=121701;InbreedingCoeff=5.93000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	1/1:0,256:256:99:9302,780,0:0,0,136,120
-11	64572602	rs2071313	G	A	2978.85	PASS	DP=278;FS=0.000;MQ=60.00;MQRankSum=-0.763;QD=10.72;ReadPosRankSum=-0.013;SOR=0.717;FractionInformativeReads=1.000;DB;GMEAC=7821204;GMEAF=0.393756;EMV_CLASSIFICATION=Benign;HGVS=NM_130799:c.1254C>T;AC=96630;AC_OTH=2160;AC_POPMAX=15114;AF=3.92968e-01;AF_OTH=3.94161e-01;AF_POPMAX=4.91033e-01;AN=245898;AN_OTH=5480;AN_POPMAX=30780;AS_FilterStatus=PASS;Hom=20211;InbreedingCoeff=3.80000e-02;POPMAX=SAS	GT:AD:DP:GQ:PL:SB	0/1:158,120:278:99:3007,0,4432:76,82,57,63
-11	64577620	rs509606	G	C	509.35	PASS	DP=28;FS=0.000;MQ=60.00;MQRankSum=0.376;QD=18.19;ReadPosRankSum=1.976;SOR=1.179;FractionInformativeReads=1.000;DB;AC=18976;AC_OTH=444;AC_POPMAX=6255;AF=1.81307e-01;AF_OTH=1.48495e-01;AF_POPMAX=3.02525e-01;AN=104662;AN_OTH=2990;AN_POPMAX=20676;AS_FilterStatus=PASS;Hom=2310;InbreedingCoeff=6.37000e-02;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	0/1:11,17:28:99:538,0,301:0,11,0,17
-11	94197260	rs641936	A	G	728.98	PASS	DP=54;FS=1.329;MQ=60.00;MQRankSum=1.802;QD=13.50;ReadPosRankSum=2.759;SOR=1.085;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_005591:c.1225+19T>C;AC=93588;AC_OTH=2085;AC_POPMAX=15012;AF=3.81553e-01;AF_OTH=3.82709e-01;AF_POPMAX=4.48334e-01;AN=245282;AN_OTH=5448;AN_POPMAX=33484;AS_FilterStatus=PASS;Hom=18125;InbreedingCoeff=1.32000e-02;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	0/1:30,24:54:99:757,0,907:7,23,4,20
-11	94225920	rs497763	C	T	706.94	PASS	DP=61;FS=3.505;MQ=60.00;MQRankSum=2.849;QD=11.59;ReadPosRankSum=-2.416;SOR=0.853;FractionInformativeReads=1.000;DB;AC=115336;AC_OTH=2524;AC_POPMAX=17470;AF=4.68750e-01;AF_OTH=4.60416e-01;AF_POPMAX=5.67872e-01;AN=246050;AN_OTH=5482;AN_POPMAX=30764;AS_FilterStatus=PASS;Hom=27472;InbreedingCoeff=1.49000e-02;POPMAX=SAS	GT:AD:DP:GQ:PL:SB	0/1:31,30:61:99:735,0,844:17,14,13,17
-11	108098459	rs2066734;rs766396464	TAA	T	4440.29	PASS	DP=100;FS=0.000;MQ=60.00;QD=32.38;SOR=1.681;FractionInformativeReads=1.000;DB;AC=107380;AC_OTH=2486;AC_POPMAX=19050;AF=4.36281e-01;AF_OTH=4.53484e-01;AF_POPMAX=5.67471e-01;AN=246126;AN_OTH=5482;AN_POPMAX=33570;AS_FilterStatus=PASS;Hom=24815;InbreedingCoeff=4.20000e-02;POPMAX=AMR	GT:AD:DP:GQ:PL:SB	1/1:0,100:100:99:4478,301,0:0,0,68,32
-11	108114661	rs779838075	AT	A	79.7	PASS	DP=40;FS=0.000;MQ=60.00;MQRankSum=0.483;QD=1.99;ReadPosRankSum=1.017;SOR=0.951;FractionInformativeReads=0.975;DB	GT:AD:DP:GQ:PL:SB	0/1:30,9:39:99:117,0,612:24,6,8,1
-11	108121410	rs34325032	C	CT	1716.13	PASS	DP=121;FS=3.094;MQ=60.00;MQRankSum=-2.194;QD=14.18;ReadPosRankSum=1.718;SOR=0.417;FractionInformativeReads=0.983;DB	GT:AD:DP:GQ:PL:SB	0/1:29,90:119:99:1753,0,339:22,7,61,29
-11	108141955	rs373881770	CT	C	229.74	PASS	DP=56;FS=1.190;MQ=60.00;MQRankSum=0.581;QD=4.10;ReadPosRankSum=0.848;SOR=0.955;FractionInformativeReads=0.946;DB	GT:AD:DP:GQ:PL:SB	0/1:36,17:53:99:267,0,676:23,13,12,5
-11	108151707	rs3218681	T	TA	959.19	PASS	DP=27;FS=0.000;MQ=60.00;QD=31.68;SOR=3.180;FractionInformativeReads=1.000;DB	GT:AD:DP:GQ:PL:SB	1/1:0,27:27:84:996,84,0:0,0,23,4
-11	108183167	rs659243	A	G	1383.58	PASS	DP=44;FS=0.000;MQ=60.00;QD=31.45;SOR=0.990;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000051:c.5948A>G;AC=246114;AC_OTH=5482;AC_POPMAX=15288;AF=1.00000e+00;AF_OTH=1.00000e+00;AF_POPMAX=1.00000e+00;AN=246114;AN_OTH=5482;AN_POPMAX=15288;AS_FilterStatus=PASS;Hom=123057;InbreedingCoeff=0.00000e+00;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,44:44:99:1412,132,0:0,0,19,25
-12	58144665	rs2069502	C	T	1059.29	PASS	DP=67;FS=0.000;MQ=60.00;MQRankSum=1.126;QD=15.81;ReadPosRankSum=-2.026;SOR=0.674;FractionInformativeReads=1.000;DB;AC=87436;AC_OTH=1666;AC_POPMAX=10974;AF=3.55211e-01;AF_OTH=3.03793e-01;AF_POPMAX=6.36248e-01;AN=246152;AN_OTH=5484;AN_POPMAX=17248;AS_FilterStatus=PASS;Hom=17527;InbreedingCoeff=6.86000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:26,41:67:99:1088,0,650:18,8,28,13
-13	32890572	rs1799943	G	A	2119.61	PASS	DP=141;FS=0.000;MQ=60.00;MQRankSum=1.137;QD=15.03;ReadPosRankSum=-2.021;SOR=0.719;FractionInformativeReads=1.000;DB;HGMD_ACCESSION=CR068211;HGMD_CLASSIFICATION=DFP;AC=60139;AC_OTH=1326;AC_POPMAX=6437;AF=2.45513e-01;AF_OTH=2.42502e-01;AF_POPMAX=3.74854e-01;AN=244952;AN_OTH=5468;AN_POPMAX=17172;AS_FilterStatus=PASS;Hom=7831;InbreedingCoeff=2.21000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:67,74:141:99:2148,0,1934:23,44,25,49
-13	32906729	rs144848	A	C	1855.68	PASS	DP=186;FS=0.000;MQ=60.00;MQRankSum=0.082;QD=9.98;ReadPosRankSum=-2.795;SOR=0.657;FractionInformativeReads=1.000;DB;GMEAC=5531433;GMEAF=0.278449;HGMD_ACCESSION=CM002750;HGMD_CLASSIFICATION=DFP;EMV_CLASSIFICATION=Benign;HGVS=NM_000059:c.1114A>C;AC=68695;AC_OTH=1536;AC_POPMAX=3510;AF=2.79496e-01;AF_OTH=2.81010e-01;AF_POPMAX=3.57143e-01;AN=245782;AN_OTH=5466;AN_POPMAX=9828;AS_FilterStatus=PASS;Hom=10055;InbreedingCoeff=1.62000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	0/1:114,72:186:99:1884,0,3391:69,45,43,29
-13	32911888	rs1801406	A	G	2312.78	PASS	DP=168;FS=0.578;MQ=60.00;MQRankSum=-0.999;QD=13.77;ReadPosRankSum=0.183;SOR=0.778;FractionInformativeReads=1.000;DB;GMEAC=5181468;GMEAF=0.260826;EMV_CLASSIFICATION=Benign;HGVS=NM_000059:c.3396A>G;AC=72325;AC_OTH=1626;AC_POPMAX=6587;AF=2.94742e-01;AF_OTH=2.97584e-01;AF_POPMAX=3.81988e-01;AN=245384;AN_OTH=5464;AN_POPMAX=17244;AS_FilterStatus=PASS;Hom=11007;InbreedingCoeff=1.41000e-02;POPMAX=EAS	GT:AD:DP:GQ:PL:SB	0/1:88,80:168:99:2341,0,2499:51,37,48,32
-13	32913055	rs206075	A	G	4961.12	PASS	DP=144;FS=0.000;MQ=60.00;QD=34.45;SOR=0.971;FractionInformativeReads=1.000;DB;GMEAC=195234;GMEAF=0.982880;EMV_CLASSIFICATION=Benign;HGVS=NM_000059:c.4563A>G;AC=244277;AC_OTH=5453;AC_POPMAX=9822;AF=9.94476e-01;AF_OTH=9.96528e-01;AF_POPMAX=1.00000e+00;AN=245634;AN_OTH=5472;AN_POPMAX=9822;AS_FilterStatus=PASS;Hom=121497;InbreedingCoeff=5.60000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	1/1:0,144:144:99:4989,433,0:0,0,63,81
-13	32915005	rs206076	G	C	4870.04	PASS	DP=153;FS=0.000;MQ=60.00;QD=31.83;SOR=0.845;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_000059:c.6513G>C;AC=233536;AC_OTH=5175;AC_POPMAX=9194;AF=9.94303e-01;AF_OTH=9.96342e-01;AF_POPMAX=1.00000e+00;AN=234874;AN_OTH=5194;AN_POPMAX=9194;AS_FilterStatus=PASS;Hom=116135;InbreedingCoeff=5.87000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	1/1:0,153:153:99:4898,458,0:0,0,82,71
-13	32929387	rs169547	T	C	3233.42	PASS	DP=92;FS=0.000;MQ=60.00;QD=26.23;SOR=1.880;FractionInformativeReads=1.000;DB;GMEAC=195030;GMEAF=0.984848;HGMD_ACCESSION=CM960194;HGMD_CLASSIFICATION=DM?;EMV_CLASSIFICATION=Benign;HGVS=NM_000059:c.7397T>C;AC=244758;AC_OTH=5462;AC_POPMAX=9842;AF=9.94984e-01;AF_OTH=9.97443e-01;AF_POPMAX=1.00000e+00;AN=245992;AN_OTH=5476;AN_POPMAX=9842;AS_FilterStatus=PASS;Hom=121794;InbreedingCoeff=5.01000e-02;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	1/1:0,92:92:99:3262,276,0:0,0,27,65
-16	68771372	rs3743674	C	T	2968.67	PASS	DP=93;FS=0.000;MQ=60.00;QD=31.92;SOR=1.739;FractionInformativeReads=1.000;DB;EMV_CLASSIFICATION=Benign;HGVS=NM_004360:c.48+6C>T;AC=104774;AC_OTH=3000;AC_POPMAX=7309;AF=8.14956e-01;AF_OTH=8.41279e-01;AF_POPMAX=9.28009e-01;AN=128564;AN_OTH=3566;AN_POPMAX=7876;AS_FilterStatus=PASS;Hom=43188;InbreedingCoeff=1.87500e-01;POPMAX=ASJ	GT:AD:DP:GQ:PL:SB	1/1:0,93:93:99:2997,277,0:0,0,64,29
-16	68855966	rs35187787	G	A	1153.58	PASS	DP=114;FS=8.989;MQ=60.00;MQRankSum=-0.299;QD=10.12;ReadPosRankSum=-3.189;SOR=1.337;FractionInformativeReads=1.000;DB;GMEAC=71979;GMEAF=0.003525;HGMD_ACCESSION=CM994192;HGMD_CLASSIFICATION=DM?;AC=807;AC_OTH=20;AC_POPMAX=541;AF=3.27702e-03;AF_OTH=3.64697e-03;AF_POPMAX=4.84290e-03;AN=246260;AN_OTH=5484;AN_POPMAX=111710;AS_FilterStatus=PASS;Hom=4;InbreedingCoeff=4.30000e-03;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	0/1:67,47:114:99:1182,0,1597:32,35,30,17
-17	7579472	rs1042522	G	C	3947.32	PASS	DP=111;FS=0.000;MQ=60.00;QD=22.75;SOR=0.865;FractionInformativeReads=1.000;DB;HGMD_ACCESSION=CM961374;HGMD_CLASSIFICATION=DFP;EMV_CLASSIFICATION=Benign;HGVS=NM_000546:c.215C>G;AC=164592;AC_OTH=3856;AC_POPMAX=82396;AF=6.68584e-01;AF_OTH=7.02880e-01;AF_POPMAX=7.37813e-01;AN=246180;AN_OTH=5486;AN_POPMAX=111676;AS_FilterStatus=PASS;Hom=56629;InbreedingCoeff=5.57000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	1/1:0,111:111:99:3976,334,0:0,0,51,60
-17	7579801	rs1642785	G	C	2883.77	PASS	DP=88;FS=0.000;MQ=60.00;MQRankSum=1.175;QD=32.77;ReadPosRankSum=1.713;SOR=3.307;FractionInformativeReads=0.989;DB;HGMD_ACCESSION=CR1413385;HGMD_CLASSIFICATION=FP;EMV_CLASSIFICATION=Benign;HGVS=NM_000546:c.74+38C>G;AC=163840;AC_OTH=3799;AC_POPMAX=80467;AF=6.73823e-01;AF_OTH=7.02218e-01;AF_POPMAX=7.32170e-01;AN=243150;AN_OTH=5410;AN_POPMAX=109902;AS_FilterStatus=PASS;Hom=56219;InbreedingCoeff=3.89000e-02;POPMAX=NFE	GT:AD:DP:GQ:PL:SB	1/1:2,85:87:99:2912,234,0:0,2,72,13
-17	29508819	rs765008499	AT	A	154.17	PASS	DP=44;FS=0.000;MQ=60.00;MQRankSum=0.017;QD=3.50;ReadPosRankSum=1.060;SOR=0.922;FractionInformativeReads=0.795;DB	GT:AD:DP:GQ:PL:SB	0/1:23,12:35:99:191,0,431:11,12,5,7
-17	29553485	rs2285892	G	A	1683.49	PASS	DP=58;FS=0.000;MQ=60.00;QD=29.03;SOR=0.914;FractionInformativeReads=1.000;DB;GMEAC=4951237;GMEAF=0.285797;AC=92408;AC_OTH=1822;AC_POPMAX=10451;AF=3.76862e-01;AF_OTH=3.33577e-01;AF_POPMAX=6.83787e-01;AN=245204;AN_OTH=5462;AN_POPMAX=15284;AS_FilterStatus=PASS;Hom=19270;InbreedingCoeff=5.90000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,58:58:99:1712,174,0:0,0,32,26
-17	29559932	rs2066736	C	A	2307.33	PASS	DP=64;FS=0.000;MQ=60.00;QD=31.10;SOR=1.402;FractionInformativeReads=1.000;DB;AC=89090;AC_OTH=1770;AC_POPMAX=9357;AF=3.64370e-01;AF_OTH=3.24890e-01;AF_POPMAX=6.16241e-01;AN=244504;AN_OTH=5448;AN_POPMAX=15184;AS_FilterStatus=PASS;Hom=17542;InbreedingCoeff=4.20000e-02;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,64:64:99:2336,192,0:0,0,23,41
-17	29563076	rs59745739	T	TG	1981.17	PASS	DP=48;FS=0.000;MQ=60.00;QD=28.50;SOR=2.160;FractionInformativeReads=0.979;DB;AC=52570;AC_OTH=955;AC_POPMAX=7188;AF=3.97920e-01;AF_OTH=3.61742e-01;AF_POPMAX=6.41442e-01;AN=132112;AN_OTH=2640;AN_POPMAX=11206;AS_FilterStatus=PASS;Hom=11882;InbreedingCoeff=-1.91700e-01;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,47:47:99:2018,144,0:0,0,12,35
-17	29563085	rs56874702;rs72813695	T	TG	1774.95	PASS	DP=40;FS=0.000;MQ=60.00;QD=31.95;SOR=2.191;FractionInformativeReads=1.000;DB;AC=47751;AC_OTH=853;AC_POPMAX=7580;AF=2.50414e-01;AF_OTH=1.99953e-01;AF_POPMAX=6.80309e-01;AN=190688;AN_OTH=4266;AN_POPMAX=11142;AS_FilterStatus=PASS;Hom=10151;InbreedingCoeff=2.63100e-01;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,40:40:99:1812,132,0:0,0,10,30
-17	29663625	rs553817239;rs7406039	T	TA	240.25	PASS	DP=11;FS=0.000;MQ=60.00;QD=21.84;SOR=0.859;FractionInformativeReads=1.000;DB;AC=33611;AC_OTH=732;AC_POPMAX=2867;AF=2.49577e-01;AF_OTH=2.29755e-01;AF_POPMAX=3.48783e-01;AN=134672;AN_OTH=3186;AN_POPMAX=8220;AS_FilterStatus=PASS;Hom=1300;InbreedingCoeff=-7.80000e-03;POPMAX=AFR	GT:AD:DP:GQ:PL:SB	1/1:0,11:11:33:278,33,0:0,0,6,5
-17	29670190	rs7405740	C	G	721.11	PASS	DP=18;FS=0.000;MQ=60.00;QD=29.73;SOR=2.833;FractionInformativeReads=1.000;DB;AC=217339;AC_OTH=4850;AC_POPMAX=28817;AF=9.08175e-01;AF_OTH=9.04176e-01;AF_POPMAX=9.48802e-01;AN=239314;AN_OTH=5364;AN_POPMAX=30372;AS_FilterStatus=PASS;Hom=98897;InbreedingCoeff=2.40000e-02;POPMAX=SAS	GT:AD:DP:GQ:PL:SB	1/1:0,18:18:54:749,54,0:0,0,3,15
-17	41223094	rs1799966	T	C	3335.67	PASS	DP=243;FS=0.983;MQ=60.00;MQRankSum=-1.539;QD=13.73;ReadPosRankSum=1.135;SOR=0.767;FractionInformativeReads=0.996;DB;GMEAC=7581228;GMEAF=0.381672;HGMD_ACCESSION=CM1210129;HGMD_CLASSIFICATION=R;EMV_CLASSIFICATION=Benign;HGVS=NM_007294:c.4837A>G;AC=87283;AC_OTH=1937;AC_POPMAX=15541;AF=3.54601e-01;AF_OTH=3.53209e-01;AF_POPMAX=5.04906e-01;AN=246144;AN_OTH=5484;AN_POPMAX=30780;AS_FilterStatus=PASS;Hom=16323;InbreedingCoeff=2.33000e-02;POPMAX=SAS	GT:AD:DP:GQ:PL:SB	0/1:123,119:242:99:3364,0,3433:66,57,66,53
-17	41234470	rs1060915	A	G	2475.24	PASS	DP=205;FS=1.733;MQ=60.00;MQRankSum=-1.765;QD=12.07;ReadPosRankSum=-0.876;SOR=0.855;FractionInformativeReads=1.000;DB;GMEAC=7351251;GMEAF=0.370091;EMV_CLASSIFICATION=Benign;HGVS=NM_007294:c.4308T>C;AC=85980;AC_OTH=1909;AC_POPMAX=15532;AF=3.49274e-01;AF_OTH=3.48231e-01;AF_POPMAX=5.04646e-01;AN=246168;AN_OTH=5482;AN_POPMAX=30778;AS_FilterStatus=PASS;Hom=15965;InbreedingCoeff=2.70000e-02;POPMAX=SAS	GT:AD:DP:GQ:PL:SB	0/1:112,93:205:99:2503,0,3075:50,62,38,55
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package/src/SpreadsheetView/test_data/breast_cancer.subset.csv DELETED Viewed

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package/src/SpreadsheetView/test_data/diabetes_target.csv.gz DELETED Viewed

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package/src/SpreadsheetView/test_data/foo.bed DELETED Viewed

@@ -1,11 +0,0 @@
-browser position chr7:127471196-127495720
-browser hide all
-track name='ClinGen Gene Curation Triplosensitivity Scores' db=hg19
-chr1	100652477	100715409	DBT	Not yet evaluated
-chr1	103342022	103574052	COL11A1 0
-chr1	10535002	10690815	PEX14	0
-chr1	10696660	10856733	CASZ1	0
-chr1	109419602	109476957	GPSM2	0
-chr1	109606997	109618624	TAF13	0
-chr1	110091185	110138465	GNAI3	0
-chr1	11072678	11085549	TARDBP	0

package/src/SpreadsheetView/test_data/location_test.csv DELETED Viewed

@@ -1,3 +0,0 @@
-"Random Number","Location","Location 2"
-12,"chr1:100..200","chr2:300-400"
-42,"chr2:10000-20000","chr2:40000-50000"

package/src/SpreadsheetView/test_data/location_test_2.csv DELETED Viewed

@@ -1,3 +0,0 @@
-ref1,start1,end1,ref2,start2,end2
-chr1,200,300,chr2,10000,40000
-chr4,20000,30000,chr12,80000,90000