231229599259249d0b0a00be9dd95b64d9d9a48c max Tue Dec 15 01:58:10 2020 -0800 adding VCF test case to chromToUcsc, no new feature or code change, so no redmine diff --git src/utils/chromToUcsc/tests/in/hg19.vcf src/utils/chromToUcsc/tests/in/hg19.vcf new file mode 100644 index 0000000..dde2a8e --- /dev/null +++ src/utils/chromToUcsc/tests/in/hg19.vcf @@ -0,0 +1,500 @@ +##fileformat=VCFv4.1 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##ALT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##reference=GRCh37 +#CHROM POS ID REF ALT QUAL FILTER INFO +1 10583 rs58108140 G A 100 PASS AVGPOST=0.7707;RSQ=0.4319;LDAF=0.2327;ERATE=0.0161;AN=2184;VT=SNP;AA=.;THETA=0.0046;AC=314;SNPSOURCE=LOWCOV;AF=0.14;ASN_AF=0.13;AMR_AF=0.17;AFR_AF=0.04;EUR_AF=0.21 +1 10611 rs189107123 C G 100 PASS AN=2184;THETA=0.0077;VT=SNP;AA=.;AC=41;ERATE=0.0048;SNPSOURCE=LOWCOV;AVGPOST=0.9330;LDAF=0.0479;RSQ=0.3475;AF=0.02;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.02 +1 13302 rs180734498 C T 100 PASS THETA=0.0048;AN=2184;AC=249;VT=SNP;AA=.;RSQ=0.6281;LDAF=0.1573;SNPSOURCE=LOWCOV;AVGPOST=0.8895;ERATE=0.0058;AF=0.11;ASN_AF=0.02;AMR_AF=0.08;AFR_AF=0.21;EUR_AF=0.14 +1 13327 rs144762171 G C 100 PASS AVGPOST=0.9698;AN=2184;VT=SNP;AA=.;RSQ=0.6482;AC=59;SNPSOURCE=LOWCOV;ERATE=0.0012;LDAF=0.0359;THETA=0.0204;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 13957 rs201747181 TC T 28 PASS AA=TC;AC=35;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.8711;ERATE=0.0065;EUR_AF=0.02;LDAF=0.0788;RSQ=0.2501;THETA=0.0100;VT=INDEL +1 13980 rs151276478 T C 100 PASS AN=2184;AC=45;ERATE=0.0034;THETA=0.0139;RSQ=0.3603;LDAF=0.0525;VT=SNP;AA=.;AVGPOST=0.9221;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02 +1 30923 rs140337953 G T 100 PASS AC=1584;AA=T;AN=2184;RSQ=0.5481;VT=SNP;THETA=0.0162;SNPSOURCE=LOWCOV;ERATE=0.0183;LDAF=0.6576;AVGPOST=0.7335;AF=0.73;ASN_AF=0.89;AMR_AF=0.80;AFR_AF=0.48;EUR_AF=0.73 +1 46402 rs199681827 C CTGT 31 PASS AA=.;AC=8;AF=0.0037;AFR_AF=0.01;AN=2184;ASN_AF=0.0017;AVGPOST=0.8325;ERATE=0.0072;LDAF=0.0903;RSQ=0.0960;THETA=0.0121;VT=INDEL +1 47190 rs200430748 G GA 192 PASS AA=G;AC=29;AF=0.01;AFR_AF=0.06;AMR_AF=0.0028;AN=2184;AVGPOST=0.9041;ERATE=0.0041;LDAF=0.0628;RSQ=0.2883;THETA=0.0153;VT=INDEL +1 51476 rs187298206 T C 100 PASS ERATE=0.0021;AA=C;AC=18;AN=2184;VT=SNP;THETA=0.0103;LDAF=0.0157;SNPSOURCE=LOWCOV;AVGPOST=0.9819;RSQ=0.5258;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 51479 rs116400033 T A 100 PASS RSQ=0.7414;AVGPOST=0.9085;AA=T;AN=2184;THETA=0.0131;AC=235;VT=SNP;LDAF=0.1404;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.03;EUR_AF=0.22 +1 51914 rs190452223 T G 100 PASS ERATE=0.0004;AVGPOST=0.9985;THETA=0.0159;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4089;LDAF=0.0012;AF=0.0005;ASN_AF=0.0017 +1 51935 rs181754315 C T 100 PASS THETA=0.0126;AA=C;AN=2184;RSQ=0.1888;AVGPOST=0.9972;LDAF=0.0015;VT=SNP;AC=0;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0 +1 51954 rs185832753 G C 100 PASS LDAF=0.0021;AA=G;AN=2184;RSQ=0.4692;AVGPOST=0.9975;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0029;ERATE=0.0006;AC=2;AF=0.0009;AMR_AF=0.01 +1 52058 rs62637813 G C 100 PASS AA=C;ERATE=0.0057;AN=2184;AVGPOST=0.9264;VT=SNP;RSQ=0.4882;AC=64;SNPSOURCE=LOWCOV;LDAF=0.0620;THETA=0.0069;AF=0.03;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.05 +1 52144 rs190291950 T A 100 PASS THETA=0.0093;ERATE=0.0013;LDAF=0.0156;AA=T;AN=2184;VT=SNP;RSQ=0.5220;AVGPOST=0.9811;SNPSOURCE=LOWCOV;AC=21;AF=0.01;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 52185 rs201374420 TTAA T 244 PASS AA=.;AC=10;AF=0.0046;AFR_AF=0.0020;AMR_AF=0.02;AN=2184;ASN_AF=0.0035;AVGPOST=0.9840;ERATE=0.0037;LDAF=0.0124;RSQ=0.4271;THETA=0.0232;VT=INDEL +1 52238 rs150021059 T G 100 PASS THETA=0.0132;AA=G;AN=2184;RSQ=0.6256;VT=SNP;ERATE=0.0026;AVGPOST=0.8617;SNPSOURCE=LOWCOV;AC=1941;LDAF=0.8423;AF=0.89;ASN_AF=0.99;AMR_AF=0.93;AFR_AF=0.64;EUR_AF=0.95 +1 53234 rs199502715 CAT C 227 PASS AA=CAT;AC=10;AF=0.0046;AFR_AF=0.02;AMR_AF=0.0028;AN=2184;AVGPOST=0.9936;ERATE=0.0007;LDAF=0.0074;RSQ=0.6237;THETA=0.0119;VT=INDEL +1 54353 rs140052487 C A 100 PASS THETA=0.0026;AA=C;AN=2184;AC=16;VT=SNP;RSQ=0.5074;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0146;ERATE=0.0058;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.02;EUR_AF=0.0013 +1 54421 rs146477069 A G 100 PASS ERATE=0.0013;AN=2184;AC=220;VT=SNP;RSQ=0.7869;AVGPOST=0.9461;AA=A;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.1190;AF=0.10;ASN_AF=0.25;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.02 +1 54490 rs141149254 G A 100 PASS ERATE=0.0004;THETA=0.0074;AA=G;AN=2184;VT=SNP;RSQ=0.8366;AVGPOST=0.9646;AC=175;SNPSOURCE=LOWCOV;LDAF=0.0929;AF=0.08;ASN_AF=0.0035;AMR_AF=0.12;AFR_AF=0.03;EUR_AF=0.15 +1 54676 rs2462492 C T 100 PASS LDAF=0.1528;RSQ=0.6989;AA=T;AN=2184;AC=267;VT=SNP;AVGPOST=0.8998;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0037;AF=0.12;ASN_AF=0.02;AMR_AF=0.20;AFR_AF=0.09;EUR_AF=0.18 +1 54753 rs143174675 T G 100 PASS AA=T;AN=2184;RSQ=0.6820;AC=65;VT=SNP;THETA=0.0080;ERATE=0.0016;SNPSOURCE=LOWCOV;AVGPOST=0.9697;LDAF=0.0399;AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.03 +1 55164 rs3091274 C A 100 PASS AN=2184;VT=SNP;ERATE=0.0045;AA=A;THETA=0.0162;SNPSOURCE=LOWCOV;AC=1955;RSQ=0.6373;AVGPOST=0.8686;LDAF=0.8489;AF=0.90;ASN_AF=0.99;AMR_AF=0.94;AFR_AF=0.65;EUR_AF=0.96 +1 55249 rs200769871 C CTATGG 443 PASS AA=C;AC=151;AF=0.07;AFR_AF=0.03;AMR_AF=0.08;AN=2184;ASN_AF=0.16;AVGPOST=0.9073;ERATE=0.0063;EUR_AF=0.02;LDAF=0.0968;RSQ=0.5891;THETA=0.0038;VT=INDEL +1 55299 rs10399749 C T 100 PASS RSQ=0.7602;LDAF=0.2954;AN=2184;VT=SNP;ERATE=0.0051;AA=c;AC=554;SNPSOURCE=LOWCOV;AVGPOST=0.8845;THETA=0.0070;AF=0.25;ASN_AF=0.33;AMR_AF=0.21;AFR_AF=0.39;EUR_AF=0.13 +1 55313 rs182462964 A T 100 PASS ERATE=0.0004;RSQ=0.6112;AVGPOST=0.9994;AN=2184;VT=SNP;THETA=0.0057;AA=A;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020 +1 55326 rs3107975 T C 100 PASS AA=C;ERATE=0.0074;AN=2184;THETA=0.0085;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9622;AC=90;RSQ=0.6901;LDAF=0.0562;AF=0.04;ASN_AF=0.07;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.01 +1 55330 rs185215913 G A 100 PASS ERATE=0.0005;AA=G;AN=2184;VT=SNP;THETA=0.0086;AVGPOST=0.9988;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4701;AF=0.0005;AFR_AF=0.0020 +1 55367 rs190850374 G A 100 PASS ERATE=0.0004;THETA=0.0044;AA=G;AN=2184;VT=SNP;LDAF=0.0029;RSQ=0.3860;SNPSOURCE=LOWCOV;AVGPOST=0.9961;AC=2;AF=0.0009;AMR_AF=0.01 +1 55388 rs182711216 C T 100 PASS THETA=0.0102;ERATE=0.0005;AA=C;AVGPOST=0.9983;AN=2184;LDAF=0.0010;VT=SNP;RSQ=0.2348;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017 +1 55394 rs2949420 T A 100 PASS AC=18;AN=2184;VT=SNP;AA=A;RSQ=0.4995;AVGPOST=0.9784;LDAF=0.0171;SNPSOURCE=LOWCOV;ERATE=0.0012;THETA=0.0063;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02 +1 55416 rs193242050 G A 100 PASS AA=G;AN=2184;AVGPOST=0.9944;VT=SNP;LDAF=0.0064;AC=9;THETA=0.0019;RSQ=0.6553;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0041;AFR_AF=0.02 +1 55427 rs183189405 T C 100 PASS THETA=0.0054;AA=T;AN=2184;VT=SNP;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2759;ERATE=0.0007;AF=0.0005;AFR_AF=0.0020 +1 55816 rs187434873 G A 100 PASS AN=2184;THETA=0.0119;VT=SNP;AC=10;RSQ=0.4578;AA=A;SNPSOURCE=LOWCOV;AVGPOST=0.9844;LDAF=0.0108;ERATE=0.0007;AF=0.0046;AMR_AF=0.01;EUR_AF=0.01 +1 55850 rs191890754 C G 100 PASS AVGPOST=0.9921;AA=G;AN=2184;VT=SNP;RSQ=0.4083;THETA=0.0045;LDAF=0.0056;AC=5;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0023;EUR_AF=0.01 +1 55852 rs184233019 G C 100 PASS THETA=0.0137;AA=G;AN=2184;RSQ=0.5433;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;EUR_AF=0.0013 +1 56644 rs143342222 A C 100 PASS AN=2184;AVGPOST=0.9962;LDAF=0.0040;ERATE=0.0024;VT=SNP;AA=A;RSQ=0.5700;AC=5;SNPSOURCE=LOWCOV;THETA=0.0117;AF=0.0023;AFR_AF=0.01 +1 57952 rs189727433 A C 100 PASS AA=C;ERATE=0.0085;AN=2184;LDAF=0.7878;VT=SNP;THETA=0.0076;RSQ=0.4712;AC=1902;SNPSOURCE=LOWCOV;AVGPOST=0.7578;AF=0.87;ASN_AF=0.98;AMR_AF=0.91;AFR_AF=0.64;EUR_AF=0.91 +1 58814 rs114420996 G A 100 PASS AC=223;THETA=0.0032;AA=G;AN=2184;RSQ=0.9087;LDAF=0.1074;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9777;AF=0.10;ASN_AF=0.03;AMR_AF=0.17;AFR_AF=0.20;EUR_AF=0.06 +1 59040 rs149755937 T C 100 PASS AVGPOST=0.9710;AC=115;AA=T;AN=2184;RSQ=0.8248;VT=SNP;ERATE=0.0017;THETA=0.0025;SNPSOURCE=LOWCOV;LDAF=0.0613;AF=0.05;ASN_AF=0.03;AMR_AF=0.15;AFR_AF=0.0041;EUR_AF=0.06 +1 60726 rs192328835 C A 100 PASS AVGPOST=0.9092;AN=2184;RSQ=0.5988;ERATE=0.0081;AC=144;VT=SNP;THETA=0.0045;AA=A;SNPSOURCE=LOWCOV;LDAF=0.0959;AF=0.07;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.11;EUR_AF=0.03 +1 61442 rs74970982 A G 100 PASS LDAF=0.9152;AA=G;AN=2184;VT=SNP;ERATE=0.0026;RSQ=0.4867;AVGPOST=0.9004;SNPSOURCE=LOWCOV;THETA=0.0013;AC=2084;AF=0.95;ASN_AF=1.00;AMR_AF=0.97;AFR_AF=0.84;EUR_AF=0.99 +1 61462 rs56992750 T A 100 PASS THETA=0.0023;LDAF=0.0378;RSQ=0.7396;AA=T;AN=2184;AVGPOST=0.9773;VT=SNP;AC=68;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.03;AMR_AF=0.02;AFR_AF=0.13 +1 61743 rs184286948 G C 100 PASS AVGPOST=0.9939;LDAF=0.0047;AA=G;AN=2184;VT=SNP;ERATE=0.0011;SNPSOURCE=LOWCOV;AC=4;THETA=0.0016;RSQ=0.4838;AF=0.0018;AMR_AF=0.01;EUR_AF=0.0026 +1 61987 rs76735897 A G 100 PASS THETA=0.0015;AN=2184;AC=569;VT=SNP;AA=A;RSQ=0.7192;AVGPOST=0.8533;LDAF=0.2944;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.26;ASN_AF=0.07;AMR_AF=0.31;AFR_AF=0.25;EUR_AF=0.39 +1 61989 rs77573425 G C 100 PASS RSQ=0.7254;AVGPOST=0.8584;AA=G;AN=2184;LDAF=0.2849;VT=SNP;AC=555;THETA=0.0019;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.25;ASN_AF=0.07;AMR_AF=0.31;AFR_AF=0.22;EUR_AF=0.39 +1 61993 rs190553843 C T 100 PASS AC=7;RSQ=0.6106;AA=C;THETA=0.0143;AN=2184;ERATE=0.0009;VT=SNP;AVGPOST=0.9953;SNPSOURCE=LOWCOV;LDAF=0.0050;AF=0.0032;AFR_AF=0.01 +1 62156 rs181864839 C T 100 PASS ERATE=0.0005;AA=C;AN=2184;AVGPOST=0.9979;LDAF=0.0015;VT=SNP;THETA=0.0094;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4561;AF=0.0005;AFR_AF=0.0020 +1 62157 rs10399597 G A 100 PASS AVGPOST=0.9945;AA=G;AN=2184;ERATE=0.0025;VT=SNP;RSQ=0.5217;AC=5;THETA=0.0066;SNPSOURCE=LOWCOV;LDAF=0.0050;AF=0.0023;AFR_AF=0.01 +1 62162 rs140556834 G A 100 PASS AA=G;AN=2184;AC=8;LDAF=0.0057;VT=SNP;THETA=0.0018;ERATE=0.0017;RSQ=0.6089;AVGPOST=0.9948;SNPSOURCE=LOWCOV;AF=0.0037;AMR_AF=0.0028;AFR_AF=0.01;EUR_AF=0.0013 +1 63276 rs185977555 G A 100 PASS RSQ=0.2744;AA=G;AN=2184;AVGPOST=0.9947;VT=SNP;ERATE=0.0010;SNPSOURCE=LOWCOV;AC=1;THETA=0.0010;LDAF=0.0031;AF=0.0005;AFR_AF=0.0020 +1 63297 rs188886746 G A 100 PASS ERATE=0.0005;AVGPOST=0.9986;AA=G;AN=2184;VT=SNP;AC=0;SNPSOURCE=LOWCOV;RSQ=0.2459;THETA=0.0024;LDAF=0.0008;AF=0 +1 63671 rs116440577 G A 100 PASS AA=G;AN=2184;ERATE=0.0047;LDAF=0.1773;VT=SNP;THETA=0.0072;AC=369;SNPSOURCE=LOWCOV;RSQ=0.8980;AVGPOST=0.9652;AF=0.17;ASN_AF=0.05;AMR_AF=0.22;AFR_AF=0.35;EUR_AF=0.11 +1 63735 rs201888535 CCTA C 455 PASS AA=CCTA;AC=829;AF=0.38;AFR_AF=0.13;AMR_AF=0.33;AN=2184;ASN_AF=0.69;AVGPOST=0.7654;ERATE=0.0047;EUR_AF=0.34;LDAF=0.4128;RSQ=0.6424;THETA=0.0062;VT=INDEL +1 64649 rs181431124 A C 100 PASS RSQ=0.6975;AN=2184;VT=SNP;AA=.;ERATE=0.0008;AVGPOST=0.9918;SNPSOURCE=LOWCOV;AC=21;THETA=0.0024;LDAF=0.0114;AF=0.01;AMR_AF=0.01;EUR_AF=0.03 +1 66162 rs62639105 A T 100 PASS THETA=0.0026;ERATE=0.0166;LDAF=0.3089;AN=2184;VT=SNP;AA=.;AC=544;SNPSOURCE=LOWCOV;RSQ=0.5681;AVGPOST=0.7777;AF=0.25;ASN_AF=0.07;AMR_AF=0.30;AFR_AF=0.23;EUR_AF=0.38 +1 66176 rs28552463 T A 100 PASS AN=2184;RSQ=0.4451;VT=SNP;AA=.;THETA=0.0095;LDAF=0.0631;AC=70;SNPSOURCE=LOWCOV;ERATE=0.0061;AVGPOST=0.9210;AF=0.03;ASN_AF=0.0017;AMR_AF=0.01;AFR_AF=0.13;EUR_AF=0.0013 +1 66219 rs181028663 A T 100 PASS LDAF=0.1137;ERATE=0.0074;AN=2184;VT=SNP;AA=.;AC=68;THETA=0.0059;RSQ=0.2946;AVGPOST=0.8268;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.08;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.01 +1 66331 rs186063952 A C 100 PASS THETA=0.0126;AVGPOST=0.7656;RSQ=0.1616;AN=2184;LDAF=0.1387;ERATE=0.0093;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=42;AF=0.02;ASN_AF=0.0035;AMR_AF=0.01;AFR_AF=0.07 +1 66442 rs192044252 T A 100 PASS RSQ=0.1763;AVGPOST=0.7894;AN=2184;THETA=0.0031;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=36;ERATE=0.0107;LDAF=0.1241;AF=0.02;ASN_AF=0.0035;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.01 +1 66457 rs13328655 T A 100 PASS ERATE=0.0085;AN=2184;VT=SNP;AA=.;AC=31;AVGPOST=0.8340;LDAF=0.0957;RSQ=0.1836;SNPSOURCE=LOWCOV;THETA=0.0024;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.03;EUR_AF=0.01 +1 66507 rs12401368 T A 100 PASS ERATE=0.0197;AN=2184;VT=SNP;AA=.;THETA=0.0122;SNPSOURCE=LOWCOV;AC=170;RSQ=0.2110;LDAF=0.2457;AVGPOST=0.6536;AF=0.08;ASN_AF=0.07;AMR_AF=0.09;AFR_AF=0.05;EUR_AF=0.09 +1 67179 rs149952626 C G 100 PASS AVGPOST=0.9946;AN=2184;VT=SNP;AA=.;THETA=0.0046;SNPSOURCE=LOWCOV;ERATE=0.0012;AC=11;RSQ=0.6333;LDAF=0.0069;AF=0.01;ASN_AF=0.02 +1 67181 rs77662731 A G 100 PASS AVGPOST=0.9817;THETA=0.0096;ERATE=0.0013;AN=2184;RSQ=0.8542;AC=104;LDAF=0.0529;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AF=0.05;AMR_AF=0.02;AFR_AF=0.20 +1 69511 rs75062661 A G 100 PASS LDAF=0.6051;AC=1424;ERATE=0.0237;AN=2184;RSQ=0.5669;VT=SNP;AA=.;AVGPOST=0.7173;SNPSOURCE=LOWCOV;THETA=0.0052;AF=0.65;ASN_AF=0.87;AMR_AF=0.65;AFR_AF=0.33;EUR_AF=0.70 +1 69534 rs190717287 T C 100 PASS 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rs188023513 G A 100 PASS LDAF=0.1685;AN=2184;AVGPOST=0.8149;VT=SNP;AA=.;RSQ=0.4624;AC=198;THETA=0.0100;SNPSOURCE=LOWCOV;ERATE=0.0222;AF=0.09;ASN_AF=0.11;AMR_AF=0.12;AFR_AF=0.08;EUR_AF=0.07 +1 77470 rs192898053 T C 100 PASS LDAF=0.0047;AN=2184;VT=SNP;AA=.;ERATE=0.0011;AVGPOST=0.9918;THETA=0.0025;RSQ=0.1818;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AFR_AF=0.0020 +1 77874 rs184538873 G A 100 PASS THETA=0.0068;LDAF=0.0516;AN=2184;VT=SNP;AA=.;AVGPOST=0.9594;ERATE=0.0011;AC=87;SNPSOURCE=LOWCOV;RSQ=0.6970;AF=0.04;ASN_AF=0.01;AMR_AF=0.12;AFR_AF=0.0041;EUR_AF=0.04 +1 77961 rs78385339 G A 100 PASS AVGPOST=0.9114;AN=2184;VT=SNP;AA=.;THETA=0.0072;RSQ=0.6667;ERATE=0.0011;SNPSOURCE=LOWCOV;AC=192;LDAF=0.1180;AF=0.09;ASN_AF=0.20;AMR_AF=0.14;AFR_AF=0.01;EUR_AF=0.03 +1 79033 rs62641298 A G 100 PASS AVGPOST=0.7371;THETA=0.0022;LDAF=0.7962;AN=2184;ERATE=0.0054;VT=SNP;AA=.;AC=1961;SNPSOURCE=LOWCOV;RSQ=0.3963;AF=0.90;ASN_AF=0.98;AMR_AF=0.95;AFR_AF=0.65;EUR_AF=0.97 +1 79050 rs62641299 G T 100 PASS 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ERATE=0.0021;AN=2184;AC=6;VT=SNP;AA=.;LDAF=0.0049;AVGPOST=0.9956;RSQ=0.5906;SNPSOURCE=LOWCOV;THETA=0.0016;AF=0.0027;AMR_AF=0.0028;AFR_AF=0.01 +1 84139 rs183605470 A T 100 PASS THETA=0.0023;AC=28;AN=2184;RSQ=0.6469;VT=SNP;AA=.;LDAF=0.0180;SNPSOURCE=LOWCOV;AVGPOST=0.9835;ERATE=0.0006;AF=0.01;ASN_AF=0.0017;AMR_AF=0.07;AFR_AF=0.0041 +1 84156 rs188652299 A C 100 PASS THETA=0.0009;AVGPOST=0.9936;ERATE=0.0014;RSQ=0.3359;AN=2184;VT=SNP;AA=.;LDAF=0.0044;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AMR_AF=0.0028;AFR_AF=0.0041 +1 84244 rs191297051 A C 100 PASS LDAF=0.1204;AN=2184;VT=SNP;AA=.;AVGPOST=0.9398;RSQ=0.7828;THETA=0.0025;ERATE=0.0018;SNPSOURCE=LOWCOV;AC=222;AF=0.10;ASN_AF=0.08;AMR_AF=0.08;AFR_AF=0.14;EUR_AF=0.11 +1 84295 rs183209871 G A 100 PASS LDAF=0.0067;AVGPOST=0.9946;AN=2184;THETA=0.0038;VT=SNP;AA=.;AC=9;SNPSOURCE=LOWCOV;ERATE=0.0007;RSQ=0.6599;AF=0.0041;AMR_AF=0.01;EUR_AF=0.01 +1 84346 rs187855973 T C 100 PASS THETA=0.0044;AN=2184;AVGPOST=0.9981;VT=SNP;AA=.;LDAF=0.0014;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0007;RSQ=0.3659;AF=0.0005;EUR_AF=0.0013 +1 84453 rs191379015 C G 100 PASS LDAF=0.0021;RSQ=0.2866;AN=2184;VT=SNP;AA=.;THETA=0.0018;ERATE=0.0008;SNPSOURCE=LOWCOV;AC=1;AVGPOST=0.9968;AF=0.0005;AMR_AF=0.0028 +1 84705 rs183470350 T G 100 PASS LDAF=0.0033;AVGPOST=0.9943;AN=2184;VT=SNP;AA=.;THETA=0.0030;RSQ=0.2658;SNPSOURCE=LOWCOV;AC=2;ERATE=0.0007;AF=0.0009;AMR_AF=0.0028;EUR_AF=0.0013 +1 85063 rs187802690 T C 100 PASS THETA=0.0093;AN=2184;VT=SNP;AA=.;ERATE=0.0051;LDAF=0.0255;RSQ=0.6868;AVGPOST=0.9806;AC=38;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02 +1 85597 rs192472955 A C 100 PASS AC=145;AVGPOST=0.9322;AN=2184;LDAF=0.0880;VT=SNP;AA=.;RSQ=0.6993;SNPSOURCE=LOWCOV;THETA=0.0020;ERATE=0.0022;AF=0.07;AMR_AF=0.07;AFR_AF=0.11;EUR_AF=0.09 +1 85622 rs185273034 A T 100 PASS ERATE=0.0005;AVGPOST=0.9963;AN=2184;RSQ=0.5194;VT=SNP;AA=.;THETA=0.0174;LDAF=0.0034;SNPSOURCE=LOWCOV;AC=4;AF=0.0018;AFR_AF=0.01 +1 85892 rs147185795 A G 100 PASS AVGPOST=0.9936;RSQ=0.7759;AN=2184;VT=SNP;AA=.;LDAF=0.0122;SNPSOURCE=LOWCOV;AC=21;THETA=0.0116;ERATE=0.0007;AF=0.01;AMR_AF=0.0028;AFR_AF=0.04 +1 86000 rs140628094 A C 100 PASS AN=2184;LDAF=0.0062;VT=SNP;AA=.;AC=10;THETA=0.0018;ERATE=0.0008;RSQ=0.7700;SNPSOURCE=LOWCOV;AVGPOST=0.9968;AF=0.0046;AFR_AF=0.02 +1 86018 rs142878000 C G 100 PASS ERATE=0.0036;RSQ=0.7867;AVGPOST=0.9429;AN=2184;AC=213;LDAF=0.1166;VT=SNP;AA=.;THETA=0.0030;SNPSOURCE=LOWCOV;AF=0.10;ASN_AF=0.08;AMR_AF=0.08;AFR_AF=0.12;EUR_AF=0.11 +1 86028 rs114608975 T C 100 PASS ERATE=0.0005;AC=73;AN=2184;RSQ=0.8713;VT=SNP;AA=.;THETA=0.0108;SNPSOURCE=LOWCOV;AVGPOST=0.9841;LDAF=0.0388;AF=0.03;AMR_AF=0.02;AFR_AF=0.0041;EUR_AF=0.08 +1 86064 rs190167736 G A 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;THETA=0.0081;SNPSOURCE=LOWCOV;AC=1;RSQ=0.5628;AVGPOST=0.9992;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020 +1 86065 rs116504101 G C 100 PASS ERATE=0.0005;LDAF=0.0398;AN=2184;AVGPOST=0.9846;VT=SNP;AA=.;AC=76;THETA=0.0057;RSQ=0.8725;SNPSOURCE=LOWCOV;AF=0.03;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.09 +1 86282 rs192830046 T G 100 PASS LDAF=0.0036;AN=2184;VT=SNP;AA=.;SNPSOURCE=LOWCOV;ERATE=0.0012;RSQ=0.2764;AVGPOST=0.9941;AC=2;THETA=0.0034;AF=0.0009;AMR_AF=0.0028;EUR_AF=0.0013 +1 86303 rs2949417 G T 100 PASS THETA=0.0021;RSQ=0.8008;LDAF=0.1194;AN=2184;AC=214;VT=SNP;AA=.;AVGPOST=0.9465;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.10;ASN_AF=0.08;AMR_AF=0.08;AFR_AF=0.12;EUR_AF=0.11 +1 86331 rs115209712 A G 100 PASS THETA=0.0047;AN=2184;VT=SNP;AA=.;AC=216;LDAF=0.1195;RSQ=0.8119;ERATE=0.0008;AVGPOST=0.9495;SNPSOURCE=LOWCOV;AF=0.10;ASN_AF=0.08;AMR_AF=0.08;AFR_AF=0.12;EUR_AF=0.11 +1 86982 rs184970101 G A 100 PASS 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AN=2184;AC=80;RSQ=0.8364;AVGPOST=0.9797;THETA=0.0075;VT=SNP;AA=.;ERATE=0.0011;SNPSOURCE=LOWCOV;LDAF=0.0438;AF=0.04;ASN_AF=0.0017;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.09 +1 87590 rs185279164 G A 100 PASS THETA=0.0068;ERATE=0.0005;AN=2184;VT=SNP;AA=.;LDAF=0.0026;RSQ=0.6866;SNPSOURCE=LOWCOV;AC=4;AVGPOST=0.9982;AF=0.0018;AFR_AF=0.01 +1 87647 rs146836579 T C 100 PASS AN=2184;AC=111;THETA=0.0041;VT=SNP;AA=.;LDAF=0.0558;AVGPOST=0.9811;SNPSOURCE=LOWCOV;ERATE=0.0015;RSQ=0.8636;AF=0.05;AMR_AF=0.03;AFR_AF=0.20 +1 87755 rs140735660 G A 100 PASS ERATE=0.0027;RSQ=0.5060;AN=2184;AC=16;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AVGPOST=0.9847;LDAF=0.0138;THETA=0.0069;AF=0.01;AFR_AF=0.03 +1 87970 rs189643077 T C 100 PASS ERATE=0.0005;AN=2184;RSQ=0.5846;VT=SNP;AA=.;AVGPOST=0.9976;THETA=0.0053;LDAF=0.0025;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AFR_AF=0.01 +1 87978 rs182297743 G A 100 PASS AVGPOST=0.9963;THETA=0.0074;AN=2184;VT=SNP;AA=.;LDAF=0.0023;RSQ=0.2883;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0006;AF=0.0005;AMR_AF=0.0028 +1 88136 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AA=G;AC=63;AF=0.03;AFR_AF=0.01;AMR_AF=0.04;AN=2184;ASN_AF=0.03;AVGPOST=0.8840;ERATE=0.0122;EUR_AF=0.04;LDAF=0.0890;RSQ=0.3660;THETA=0.0210;VT=INDEL +1 111513 rs199911222 C CTA 249 PASS AA=.;AC=58;AF=0.03;AFR_AF=0.09;AMR_AF=0.03;AN=2184;ASN_AF=0.0017;AVGPOST=0.9145;ERATE=0.0024;EUR_AF=0.0013;LDAF=0.0665;RSQ=0.4694;THETA=0.0292;VT=INDEL +1 111516 rs201010400 TG T 164 PASS AA=.;AC=55;AF=0.03;AFR_AF=0.09;AMR_AF=0.02;AN=2184;AVGPOST=0.9267;ERATE=0.0012;LDAF=0.0589;RSQ=0.5011;THETA=0.0098;VT=INDEL +1 114699 rs187571096 A G 100 PASS AVGPOST=0.9936;ERATE=0.0014;RSQ=0.4063;AN=2184;THETA=0.0220;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=4;LDAF=0.0050;AF=0.0018;AFR_AF=0.01 +1 114828 rs201824320 GA G 71 PASS AA=GA;AC=37;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=2184;ASN_AF=0.04;AVGPOST=0.8268;ERATE=0.0091;LDAF=0.1072;RSQ=0.2067;THETA=0.0057;VT=INDEL +1 115729 rs199999500 GCACA G 117 PASS AA=.;AC=15;AF=0.01;AMR_AF=0.02;AN=2184;AVGPOST=0.9970;ERATE=0.0007;EUR_AF=0.01;LDAF=0.0088;RSQ=0.8387;THETA=0.0214;VT=INDEL +1 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LDAF=0.1947;AN=2184;AC=133;RSQ=0.3091;VT=SNP;AA=.;ERATE=0.0122;AVGPOST=0.7375;SNPSOURCE=LOWCOV;THETA=0.0225;AF=0.06;ASN_AF=0.03;AMR_AF=0.09;AFR_AF=0.04;EUR_AF=0.09 +1 121009 rs1851943 C T 100 PASS AC=464;ERATE=0.0237;AN=2184;RSQ=0.3182;VT=SNP;AA=.;AVGPOST=0.6419;SNPSOURCE=LOWCOV;LDAF=0.3572;THETA=0.0113;AF=0.21;ASN_AF=0.13;AMR_AF=0.27;AFR_AF=0.26;EUR_AF=0.22 +1 126108 rs146756510 G A 100 PASS ERATE=0.0023;AC=126;RSQ=0.6899;AN=2184;THETA=0.0038;VT=SNP;AA=.;LDAF=0.0781;SNPSOURCE=LOWCOV;AVGPOST=0.9469;AF=0.06;ASN_AF=0.01;AMR_AF=0.13;AFR_AF=0.08;EUR_AF=0.04 +1 126113 rs79114531 C A 100 PASS RSQ=0.6875;AC=2069;AN=2184;ERATE=0.0024;VT=SNP;AA=.;SNPSOURCE=LOWCOV;THETA=0.0151;AVGPOST=0.9450;LDAF=0.9281;AF=0.95;ASN_AF=1.00;AMR_AF=0.97;AFR_AF=0.79;EUR_AF=1.00 +1 128658 rs185320873 G A 100 PASS AVGPOST=0.9994;RSQ=0.5869;AN=2184;THETA=0.0245;VT=SNP;AA=.;LDAF=0.0007;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;AF=0.0005;EUR_AF=0.0013 +1 133013 rs149496965 C T 100 PASS LDAF=0.0133;AN=2184;THETA=0.0131;RSQ=0.5517;AVGPOST=0.9869;VT=SNP;AA=.;ERATE=0.0011;AC=15;SNPSOURCE=LOWCOV;AF=0.01;AFR_AF=0.03 +1 135032 rs148209574 G A 100 PASS ERATE=0.0036;AVGPOST=0.9468;THETA=0.0181;LDAF=0.0898;AN=2184;VT=SNP;AA=.;AC=155;RSQ=0.7186;SNPSOURCE=LOWCOV;AF=0.07;ASN_AF=0.01;AMR_AF=0.14;AFR_AF=0.10;EUR_AF=0.07 +1 135040 rs141523926 T C 100 PASS AVGPOST=0.9321;AN=2184;VT=SNP;AA=.;ERATE=0.0075;LDAF=0.0716;RSQ=0.5453;SNPSOURCE=LOWCOV;AC=96;THETA=0.0248;AF=0.04;ASN_AF=0.07;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.04 +1 135203 rs147502335 G A 100 PASS ERATE=0.0005;AVGPOST=0.9868;AC=28;RSQ=0.7032;AN=2184;VT=SNP;AA=.;THETA=0.0066;SNPSOURCE=LOWCOV;LDAF=0.0179;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.03 +1 137801 rs191107331 G A 100 PASS AN=2184;VT=SNP;AA=.;AVGPOST=0.9976;RSQ=0.5379;THETA=0.0086;ERATE=0.0008;LDAF=0.0023;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AFR_AF=0.01 +1 137825 rs147252685 G A 100 PASS ERATE=0.0021;AVGPOST=0.9146;AC=226;THETA=0.0317;AN=2184;LDAF=0.1383;VT=SNP;AA=.;RSQ=0.7019;SNPSOURCE=LOWCOV;AF=0.10;ASN_AF=0.02;AMR_AF=0.17;AFR_AF=0.01;EUR_AF=0.19 +1 139479 rs182357477 C T 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9997;RSQ=0.7805;VT=SNP;AA=.;LDAF=0.0006;SNPSOURCE=LOWCOV;AC=1;THETA=0.0101;AF=0.0005;EUR_AF=0.0013 +1 161483 rs189086610 C G 100 PASS AVGPOST=0.8457;AN=2184;THETA=0.0338;RSQ=0.2084;VT=SNP;AA=.;LDAF=0.0952;SNPSOURCE=LOWCOV;AC=36;ERATE=0.0041;AF=0.02;ASN_AF=0.02;AMR_AF=0.01;AFR_AF=0.02;EUR_AF=0.01 +1 161488 rs193081027 C T 100 PASS AC=30;ERATE=0.0063;AN=2184;AVGPOST=0.8463;THETA=0.0206;VT=SNP;AA=.;LDAF=0.0911;SNPSOURCE=LOWCOV;RSQ=0.1885;AF=0.01;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.01 +1 162463 rs143399298 T C 100 PASS ERATE=0.0027;AVGPOST=0.9658;AN=2184;LDAF=0.0760;THETA=0.0234;VT=SNP;AA=.;RSQ=0.8017;SNPSOURCE=LOWCOV;AC=142;AF=0.07;ASN_AF=0.0035;AMR_AF=0.09;AFR_AF=0.07;EUR_AF=0.09 +1 165954 rs200989943 GAATA G 64 PASS AA=GAATA;AC=41;AF=0.02;AFR_AF=0.0020;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.6517;ERATE=0.0113;EUR_AF=0.03;LDAF=0.2128;RSQ=0.0998;THETA=0.0393;VT=INDEL +1 168373 rs183198872 C T 100 PASS RSQ=0.1972;ERATE=0.0057;THETA=0.0229;AN=2184;VT=SNP;AA=.;AC=51;LDAF=0.1487;AVGPOST=0.7604;SNPSOURCE=LOWCOV;AF=0.02;ASN_AF=0.03;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.03 +1 168964 rs187450123 A G 100 PASS AVGPOST=0.6568;AN=2184;ERATE=0.0115;VT=SNP;AA=.;AC=54;THETA=0.0201;SNPSOURCE=LOWCOV;LDAF=0.2153;RSQ=0.1400;AF=0.02;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03 +1 171529 rs191891026 A G 100 PASS RSQ=0.1588;THETA=0.0180;AN=2184;VT=SNP;AA=.;LDAF=0.0972;SNPSOURCE=LOWCOV;ERATE=0.0040;AVGPOST=0.8299;AC=25;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02 +1 171841 rs184235219 A G 100 PASS LDAF=0.1067;ERATE=0.0073;AN=2184;AC=8;VT=SNP;AA=.;AVGPOST=0.8061;SNPSOURCE=LOWCOV;RSQ=0.1101;THETA=0.0152;AF=0.0037;ASN_AF=0.0035;AMR_AF=0.0028;AFR_AF=0.0020;EUR_AF=0.01 +1 172595 rs187071114 G A 100 PASS RSQ=0.2299;AN=2184;THETA=0.0191;VT=SNP;AA=.;LDAF=0.3463;AVGPOST=0.5901;SNPSOURCE=LOWCOV;AC=375;ERATE=0.0109;AF=0.17;ASN_AF=0.19;AMR_AF=0.19;AFR_AF=0.06;EUR_AF=0.22 +1 173709 rs192722547 A C 100 PASS THETA=0.0285;AN=2184;AC=159;RSQ=0.2308;ERATE=0.0126;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AVGPOST=0.6564;LDAF=0.2510;AF=0.07;ASN_AF=0.07;AMR_AF=0.07;AFR_AF=0.05;EUR_AF=0.09 +1 227622 rs184145725 C T 100 PASS THETA=0.0184;AN=2184;RSQ=0.5273;VT=SNP;AA=.;AVGPOST=0.9799;SNPSOURCE=LOWCOV;AC=21;ERATE=0.0022;LDAF=0.0179;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 230433 rs190807317 T C 100 PASS ERATE=0.0042;AN=2184;VT=SNP;AA=.;THETA=0.0140;SNPSOURCE=LOWCOV;AVGPOST=0.9559;AC=21;RSQ=0.3424;LDAF=0.0300;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 233473 rs115354837 C G 100 PASS AN=2184;AC=390;ERATE=0.0025;AVGPOST=0.9128;VT=SNP;AA=.;LDAF=0.2047;SNPSOURCE=LOWCOV;RSQ=0.7996;THETA=0.0107;AF=0.18;ASN_AF=0.12;AMR_AF=0.12;AFR_AF=0.40;EUR_AF=0.11 +1 233476 rs141415251 G A 100 PASS THETA=0.0199;LDAF=0.0078;AN=2184;AVGPOST=0.9935;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=11;ERATE=0.0022;RSQ=0.6319;AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 233586 rs202245468 CCT C 219 PASS AA=CCT;AC=51;AF=0.02;AFR_AF=0.02;AMR_AF=0.02;AN=2184;ASN_AF=0.03;AVGPOST=0.9297;ERATE=0.0092;EUR_AF=0.02;LDAF=0.0586;RSQ=0.4246;THETA=0.0185;VT=INDEL +1 234432 rs8179455 A G 100 PASS RSQ=0.7901;ERATE=0.0168;AN=2184;LDAF=0.1339;VT=SNP;AA=.;THETA=0.0217;SNPSOURCE=LOWCOV;AC=252;AVGPOST=0.9437;AF=0.12;ASN_AF=0.08;AMR_AF=0.17;AFR_AF=0.19;EUR_AF=0.07 +1 237877 rs181999503 C T 100 PASS ERATE=0.0005;AN=2184;THETA=0.0038;VT=SNP;AA=.;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;AVGPOST=0.9987;RSQ=0.4509;AF=0.0005;ASN_AF=0.0017 +1 238369 rs200500460 G GT 117 PASS AA=G;AC=7;AF=0.0032;AFR_AF=0.01;AMR_AF=0.01;AN=2184;AVGPOST=0.9691;ERATE=0.0032;LDAF=0.0188;RSQ=0.2293;THETA=0.0249;VT=INDEL +1 239339 rs184451216 A G 100 PASS AN=2184;THETA=0.0060;VT=SNP;AA=.;AVGPOST=0.9840;LDAF=0.0170;SNPSOURCE=LOWCOV;ERATE=0.0012;AC=25;RSQ=0.6024;AF=0.01;ASN_AF=0.02;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.01 +1 239599 rs201588983 CTAAAA C 28 PASS AA=CTAAAA;AC=6;AF=0.0027;AFR_AF=0.01;AN=2184;AVGPOST=0.9255;ERATE=0.0049;LDAF=0.0407;RSQ=0.1292;THETA=0.0230;VT=INDEL +1 240789 rs147589465 T G 100 PASS AN=2184;VT=SNP;AA=.;THETA=0.0108;AVGPOST=0.9671;ERATE=0.0035;AC=41;SNPSOURCE=LOWCOV;RSQ=0.5423;LDAF=0.0309;AF=0.02;ASN_AF=0.04;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 241320 rs79974410 A G 100 PASS AVGPOST=0.8177;AN=2184;ERATE=0.0126;VT=SNP;AA=.;THETA=0.0084;RSQ=0.4889;SNPSOURCE=LOWCOV;LDAF=0.1931;AC=252;AF=0.12;ASN_AF=0.16;AMR_AF=0.16;AFR_AF=0.10;EUR_AF=0.07 +1 243782 rs181434479 C A 100 PASS AC=7;AN=2184;LDAF=0.0043;RSQ=0.6806;VT=SNP;AA=.;THETA=0.0142;SNPSOURCE=LOWCOV;ERATE=0.0007;AVGPOST=0.9965;AF=0.0032;ASN_AF=0.01 +1 246060 rs185479292 G A 100 PASS ERATE=0.0005;AN=2184;THETA=0.0038;VT=SNP;AA=.;AVGPOST=0.9993;SNPSOURCE=LOWCOV;AC=1;RSQ=0.5771;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020 +1 247916 rs202029170 CAGG C 163 PASS AA=CAGG;AC=162;AF=0.07;AFR_AF=0.14;AMR_AF=0.04;AN=2184;ASN_AF=0.09;AVGPOST=0.7947;ERATE=0.0018;EUR_AF=0.04;LDAF=0.1696;RSQ=0.3977;THETA=0.0176;VT=INDEL +1 249275 rs200079338 G GT 129 PASS AA=.;AC=300;AF=0.14;AFR_AF=0.03;AMR_AF=0.10;AN=2184;ASN_AF=0.24;AVGPOST=0.8811;ERATE=0.0053;EUR_AF=0.15;LDAF=0.1723;RSQ=0.6986;THETA=0.0050;VT=INDEL +1 249276 rs115018998 T C 100 PASS AVGPOST=0.9903;THETA=0.0118;AN=2184;AC=13;VT=SNP;AA=.;ERATE=0.0010;SNPSOURCE=LOWCOV;RSQ=0.5651;LDAF=0.0104;AF=0.01;AMR_AF=0.01;EUR_AF=0.01 +1 251627 rs72502741 AC A 359 PASS AA=AC;AC=302;AF=0.14;AFR_AF=0.02;AMR_AF=0.11;AN=2184;ASN_AF=0.24;AVGPOST=0.8997;ERATE=0.0033;EUR_AF=0.16;LDAF=0.1728;RSQ=0.7565;THETA=0.0144;VT=INDEL +1 252144 rs191013370 T C 100 PASS ERATE=0.0004;LDAF=0.0009;AN=2184;THETA=0.0131;RSQ=0.5389;VT=SNP;AA=.;AVGPOST=0.9991;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017 +1 254186 rs148663102 T C 100 PASS RSQ=0.6519;AN=2184;AC=40;LDAF=0.0275;VT=SNP;AA=.;SNPSOURCE=LOWCOV;THETA=0.0079;ERATE=0.0007;AVGPOST=0.9780;AF=0.02;ASN_AF=0.06;AFR_AF=0.0020;EUR_AF=0.0026 +1 255923 rs199745078 G GTC 358 PASS AA=.;AC=776;AF=0.36;AFR_AF=0.40;AMR_AF=0.32;AN=2184;ASN_AF=0.38;AVGPOST=0.7344;ERATE=0.0210;EUR_AF=0.32;LDAF=0.4077;RSQ=0.5159;THETA=0.0199;VT=INDEL +1 256022 rs181053586 A G 100 PASS AN=2184;LDAF=0.0040;VT=SNP;AA=.;AVGPOST=0.9953;RSQ=0.4743;SNPSOURCE=LOWCOV;AC=4;THETA=0.0107;ERATE=0.0007;AF=0.0018;AMR_AF=0.01 +1 256586 rs140435168 T G 100 PASS AN=2184;AC=40;AVGPOST=0.9893;VT=SNP;AA=.;RSQ=0.8083;THETA=0.0358;ERATE=0.0016;LDAF=0.0231;SNPSOURCE=LOWCOV;AF=0.02;AMR_AF=0.01;AFR_AF=0.07 +1 258589 rs185940535 C A 100 PASS LDAF=0.0035;AN=2184;VT=SNP;AA=.;THETA=0.0146;RSQ=0.5577;SNPSOURCE=LOWCOV;AC=4;ERATE=0.0006;AVGPOST=0.9965;AF=0.0018;AMR_AF=0.0028;EUR_AF=0.0040 +1 259207 rs143738566 A C 100 PASS AC=7;RSQ=0.6249;AN=2184;LDAF=0.0054;VT=SNP;AA=.;THETA=0.0247;AVGPOST=0.9956;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0032;ASN_AF=0.01 +1 261542 rs192416692 T C 100 PASS RSQ=0.3631;THETA=0.0239;AN=2184;VT=SNP;AA=.;AC=9;SNPSOURCE=LOWCOV;ERATE=0.0040;AVGPOST=0.9850;LDAF=0.0108;AF=0.0041;AMR_AF=0.0028;AFR_AF=0.0041;EUR_AF=0.01 +1 356537 rs183318141 G A 100 PASS THETA=0.0207;ERATE=0.0013;RSQ=0.1472;AN=2184;LDAF=0.0124;VT=SNP;AA=.;AVGPOST=0.9771;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AFR_AF=0.01 +1 358440 rs187762289 T A 100 PASS AC=12;AN=2184;LDAF=0.1166;VT=SNP;AA=.;THETA=0.0066;SNPSOURCE=LOWCOV;AVGPOST=0.7896;ERATE=0.0135;RSQ=0.1099;AF=0.01;ASN_AF=0.0017;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.0013 +1 362895 rs190726048 A G 100 PASS AC=7;LDAF=0.0237;AN=2184;THETA=0.0090;VT=SNP;AA=.;RSQ=0.1566;SNPSOURCE=LOWCOV;ERATE=0.0053;AVGPOST=0.9570;AF=0.0032;AMR_AF=0.0028;AFR_AF=0.01;EUR_AF=0.0013 +1 362905 rs182870673 T G 100 PASS AC=205;AN=2184;RSQ=0.4530;VT=SNP;AA=.;LDAF=0.1882;SNPSOURCE=LOWCOV;THETA=0.0169;ERATE=0.0109;AVGPOST=0.7977;AF=0.09;ASN_AF=0.07;AMR_AF=0.07;AFR_AF=0.26;EUR_AF=0.02 +1 362907 rs138802168 G C 100 PASS AVGPOST=0.9154;THETA=0.0143;RSQ=0.4127;AN=2184;ERATE=0.0047;VT=SNP;AA=.;LDAF=0.0676;SNPSOURCE=LOWCOV;AC=63;AF=0.03;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.08;EUR_AF=0.01 +1 416202 rs150426163 G T 100 PASS LDAF=0.0141;AA=G;AN=2184;THETA=0.0242;RSQ=0.3187;AC=8;ERATE=0.0044;AVGPOST=0.9791;VT=SNP;SNPSOURCE=LOWCOV;AF=0.0037;AFR_AF=0.02 +1 522476 rs188307237 A T 100 PASS ERATE=0.0005;AVGPOST=0.9986;AN=2184;VT=SNP;RSQ=0.4304;AA=A;THETA=0.0142;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AFR_AF=0.0020 +1 523471 rs192687139 T C 100 PASS LDAF=0.3603;AA=C;AN=2184;RSQ=0.1770;VT=SNP;ERATE=0.0134;THETA=0.0203;SNPSOURCE=LOWCOV;AVGPOST=0.5701;AC=326;AF=0.15;ASN_AF=0.15;AMR_AF=0.21;AFR_AF=0.13;EUR_AF=0.13 +1 525698 rs2808353 A G 100 PASS ERATE=0.0023;AN=2184;THETA=0.0138;VT=SNP;RSQ=0.4998;LDAF=0.0044;SNPSOURCE=LOWCOV;AC=4;AA=a;AVGPOST=0.9950;AF=0.0018;ASN_AF=0.0017;AFR_AF=0.0020;EUR_AF=0.0026 +1 526057 rs141459107 T C 100 PASS AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0154;ERATE=0.0012;RSQ=0.3949;AC=11;AVGPOST=0.9800;LDAF=0.0146;AF=0.01;ASN_AF=0.0017;AMR_AF=0.01;EUR_AF=0.01 +1 526692 rs143629215 C T 100 PASS AA=C;AN=2184;VT=SNP;AC=10;THETA=0.0033;LDAF=0.0072;ERATE=0.0008;RSQ=0.6954;AVGPOST=0.9938;SNPSOURCE=LOWCOV;AF=0.0046;AFR_AF=0.02 +1 526735 rs187540194 C T 100 PASS ERATE=0.0004;AA=C;AN=2184;THETA=0.0191;RSQ=0.5965;LDAF=0.0015;VT=SNP;SNPSOURCE=LOWCOV;AVGPOST=0.9987;AC=2;AF=0.0009;AFR_AF=0.0041 +1 526771 rs140972083 G C 100 PASS RSQ=0.6603;AA=G;AN=2184;VT=SNP;LDAF=0.0072;ERATE=0.0011;THETA=0.0292;SNPSOURCE=LOWCOV;AC=11;AVGPOST=0.9932;AF=0.01;AFR_AF=0.02;EUR_AF=0.0013 +1 526832 rs192574259 G C 100 PASS AA=g;AVGPOST=0.9552;AN=2184;RSQ=0.3500;VT=SNP;AC=22;ERATE=0.0011;SNPSOURCE=LOWCOV;THETA=0.0110;LDAF=0.0318;AF=0.01;AMR_AF=0.02;EUR_AF=0.02 +1 526840 rs60396226 T C 100 PASS AN=2184;RSQ=0.5535;AVGPOST=0.8399;VT=SNP;THETA=0.0087;AC=230;SNPSOURCE=LOWCOV;LDAF=0.1660;AA=t;ERATE=0.0091;AF=0.11;ASN_AF=0.06;AMR_AF=0.04;AFR_AF=0.35;EUR_AF=0.01 +1 526970 rs60791385 T C 100 PASS LDAF=0.0666;AVGPOST=0.9085;AN=2184;THETA=0.0242;AC=57;ERATE=0.0089;VT=SNP;RSQ=0.3868;SNPSOURCE=LOWCOV;AA=N;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.07;EUR_AF=0.01 +1 527038 rs189135631 C T 100 PASS THETA=0.0048;RSQ=0.3706;AN=2184;VT=SNP;AA=c;ERATE=0.0050;SNPSOURCE=LOWCOV;AC=53;LDAF=0.0702;AVGPOST=0.9006;AF=0.02;ASN_AF=0.02;AMR_AF=0.01;AFR_AF=0.07;EUR_AF=0.0013 +1 527157 rs143773298 A G 100 PASS AVGPOST=0.9758;RSQ=0.5148;AN=2184;VT=SNP;AC=22;AA=A;LDAF=0.0194;SNPSOURCE=LOWCOV;THETA=0.0058;ERATE=0.0022;AF=0.01;AFR_AF=0.04 +1 527186 rs111227194 A G 100 PASS RSQ=0.8105;AN=2184;LDAF=0.0503;AC=93;VT=SNP;AA=A;ERATE=0.0008;SNPSOURCE=LOWCOV;AVGPOST=0.9739;THETA=0.0135;AF=0.04;AMR_AF=0.01;AFR_AF=0.18;EUR_AF=0.0040 +1 527207 rs112901516 A G 100 PASS AVGPOST=0.9749;AC=94;AN=2184;THETA=0.0218;VT=SNP;AA=A;LDAF=0.0508;SNPSOURCE=LOWCOV;RSQ=0.8208;ERATE=0.0007;AF=0.04;AMR_AF=0.01;AFR_AF=0.18;EUR_AF=0.0026 +1 527219 rs181574093 G A 100 PASS AC=12;AA=G;AN=2184;RSQ=0.6006;VT=SNP;AVGPOST=0.9922;LDAF=0.0087;ERATE=0.0011;SNPSOURCE=LOWCOV;THETA=0.0042;AF=0.01;AMR_AF=0.01;AFR_AF=0.02 +1 529782 rs144425991 C T 100 PASS AA=C;RSQ=0.6854;AN=2184;THETA=0.0234;VT=SNP;LDAF=0.0747;SNPSOURCE=LOWCOV;AC=114;ERATE=0.0056;AVGPOST=0.9456;AF=0.05;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.17;EUR_AF=0.01 +1 532051 rs184296032 A C 100 PASS AN=2184;RSQ=0.8251;ERATE=0.0032;VT=SNP;AA=A;SNPSOURCE=LOWCOV;LDAF=0.0244;THETA=0.0233;AVGPOST=0.9885;AC=42;AF=0.02;AMR_AF=0.01;AFR_AF=0.08 +1 532258 rs200842330 AAAT A 58 PASS AA=.;AC=32;AF=0.01;AFR_AF=0.01;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.9511;ERATE=0.0025;EUR_AF=0.02;LDAF=0.0375;RSQ=0.4287;THETA=0.0336;VT=INDEL +1 532413 rs190029356 G A 100 PASS RSQ=0.5650;AA=G;AN=2184;ERATE=0.0009;LDAF=0.0046;VT=SNP;AVGPOST=0.9953;AC=5;THETA=0.0203;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.01;AFR_AF=0.0020;EUR_AF=0.0026 +1 532447 rs181202492 A G 100 PASS ERATE=0.0005;AVGPOST=0.9986;LDAF=0.0016;AN=2184;VT=SNP;AA=A;RSQ=0.5987;THETA=0.0081;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;AMR_AF=0.01 +1 533162 rs112369404 C T 100 PASS AC=7;ERATE=0.0005;AA=C;RSQ=0.6012;THETA=0.0118;AN=2184;VT=SNP;LDAF=0.0063;SNPSOURCE=LOWCOV;AVGPOST=0.9937;AF=0.0032;AFR_AF=0.01 +1 533163 rs186223690 G A 100 PASS LDAF=0.0021;AA=G;AN=2184;AVGPOST=0.9967;VT=SNP;THETA=0.0146;ERATE=0.0008;SNPSOURCE=LOWCOV;AC=1;RSQ=0.2877;AF=0.0005;ASN_AF=0.0017 +1 533170 rs114617477 G T 100 PASS RSQ=0.6798;AVGPOST=0.9512;AC=94;AA=T;AN=2184;LDAF=0.0609;ERATE=0.0047;VT=SNP;THETA=0.0091;SNPSOURCE=LOWCOV;AF=0.04;ASN_AF=0.01;AMR_AF=0.04;AFR_AF=0.13;EUR_AF=0.02 +1 533179 rs111501994 A G 100 PASS AC=52;AN=2184;LDAF=0.0394;VT=SNP;AVGPOST=0.9627;THETA=0.0262;RSQ=0.6274;ERATE=0.0059;SNPSOURCE=LOWCOV;AA=a;AF=0.02;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.09;EUR_AF=0.0026 +1 533187 rs190848289 C T 100 PASS THETA=0.0096;AA=C;AN=2184;VT=SNP;RSQ=0.6451;AVGPOST=0.9879;ERATE=0.0020;SNPSOURCE=LOWCOV;AC=21;LDAF=0.0144;AF=0.01;AMR_AF=0.0028;AFR_AF=0.04 +1 533198 rs78497331 C T 100 PASS AA=C;THETA=0.0229;RSQ=0.6218;AN=2184;LDAF=0.1290;VT=SNP;AC=194;AVGPOST=0.8972;SNPSOURCE=LOWCOV;ERATE=0.0135;AF=0.09;ASN_AF=0.08;AMR_AF=0.06;AFR_AF=0.20;EUR_AF=0.03 +1 534192 rs6680723 C T 100 PASS 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AA=G;AN=2184;AVGPOST=0.8580;VT=SNP;THETA=0.0059;SNPSOURCE=LOWCOV;LDAF=0.2147;ERATE=0.0087;AC=355;RSQ=0.6386;AF=0.16;ASN_AF=0.23;AMR_AF=0.19;AFR_AF=0.21;EUR_AF=0.07 +1 534547 rs188376087 G A 100 PASS AA=G;AN=2184;AC=49;VT=SNP;THETA=0.0280;RSQ=0.6395;LDAF=0.0351;ERATE=0.0033;AVGPOST=0.9733;SNPSOURCE=LOWCOV;AF=0.02;AMR_AF=0.03;AFR_AF=0.0020;EUR_AF=0.05 +1 535696 rs151048542 G A 100 PASS AC=17;RSQ=0.6258;AA=G;AN=2184;ERATE=0.0009;VT=SNP;THETA=0.0089;LDAF=0.0143;SNPSOURCE=LOWCOV;AVGPOST=0.9860;AF=0.01;AFR_AF=0.03 +1 540345 rs201534199 AATTGT A 219 PASS AA=.;AC=78;AF=0.04;AFR_AF=0.05;AMR_AF=0.02;AN=2184;ASN_AF=0.07;AVGPOST=0.7057;ERATE=0.0169;EUR_AF=0.01;LDAF=0.1937;RSQ=0.2031;THETA=0.0111;VT=INDEL +1 540540 rs199511579 GC G 5 PASS AA=.;AC=20;AF=0.01;AFR_AF=0.01;AMR_AF=0.01;AN=2184;AVGPOST=0.8972;ERATE=0.0095;EUR_AF=0.01;LDAF=0.0615;RSQ=0.1917;THETA=0.0037;VT=INDEL +1 540975 rs80246094 G A 100 PASS THETA=0.0238;AA=G;AN=2184;VT=SNP;LDAF=0.1157;ERATE=0.0114;RSQ=0.6122;AVGPOST=0.9121;SNPSOURCE=LOWCOV;AC=170;AF=0.08;ASN_AF=0.08;AMR_AF=0.07;AFR_AF=0.07;EUR_AF=0.08 +1 549548 rs191550559 T G 100 PASS AA=T;AN=2184;VT=SNP;ERATE=0.0010;LDAF=0.0023;AC=0;THETA=0.0162;RSQ=0.0868;AVGPOST=0.9954;SNPSOURCE=LOWCOV;AF=0 +1 553346 rs183055671 C G 100 PASS ERATE=0.0004;AA=C;AN=2184;AVGPOST=0.9979;THETA=0.0175;VT=SNP;LDAF=0.0014;SNPSOURCE=LOWCOV;AC=1;RSQ=0.3911;AF=0.0005;EUR_AF=0.0013 +1 559081 rs188144421 G C 100 PASS AC=7;THETA=0.0238;AA=G;AN=2184;AVGPOST=0.9779;ERATE=0.0032;VT=SNP;LDAF=0.0134;RSQ=0.2658;SNPSOURCE=LOWCOV;AF=0.0032;ASN_AF=0.0017;AMR_AF=0.0028;AFR_AF=0.01;EUR_AF=0.0026 +1 559889 rs140313358 A G 100 PASS THETA=0.0159;LDAF=0.1597;AN=2184;AC=124;VT=SNP;AA=A;RSQ=0.3349;AVGPOST=0.7987;SNPSOURCE=LOWCOV;ERATE=0.0145;AF=0.06;ASN_AF=0.05;AMR_AF=0.07;AFR_AF=0.10;EUR_AF=0.03 +1 561200 rs141958416 C T 100 PASS AA=C;RSQ=0.5884;AN=2184;VT=SNP;AVGPOST=0.9647;THETA=0.0071;ERATE=0.0011;SNPSOURCE=LOWCOV;LDAF=0.0348;AC=39;AF=0.02;AMR_AF=0.01;AFR_AF=0.07 +1 563625 rs191286235 T C 100 PASS AA=C;ERATE=0.0152;AN=2184;AVGPOST=0.6693;VT=SNP;RSQ=0.1227;AC=2115;THETA=0.0122;LDAF=0.7973;SNPSOURCE=LOWCOV;AF=0.97;ASN_AF=0.98;AMR_AF=0.98;AFR_AF=0.95;EUR_AF=0.97 +1 566843 rs182069836 T C 100 PASS THETA=0.0088;LDAF=0.0052;AN=2184;AVGPOST=0.9934;VT=SNP;RSQ=0.4621;AA=-;ERATE=0.0008;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;ASN_AF=0.0035;EUR_AF=0.0040 +1 566847 rs187911910 T C 100 PASS ERATE=0.0005;LDAF=0.0013;RSQ=0.3895;AN=2184;VT=SNP;AA=-;SNPSOURCE=LOWCOV;AC=1;THETA=0.0152;AVGPOST=0.9984;AF=0.0005;AFR_AF=0.0020 +1 566939 rs192480211 C T 100 PASS AVGPOST=0.9945;LDAF=0.0041;AN=2184;RSQ=0.4393;VT=SNP;THETA=0.0104;AA=-;SNPSOURCE=LOWCOV;AC=4;ERATE=0.0006;AF=0.0018;AFR_AF=0.01 +1 567047 rs185393250 T C 100 PASS AVGPOST=0.9963;AN=2184;THETA=0.0175;VT=SNP;RSQ=0.4477;LDAF=0.0029;AA=-;ERATE=0.0008;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AFR_AF=0.01 +1 567098 rs189927567 C T 100 PASS LDAF=0.0058;AN=2184;AC=8;VT=SNP;THETA=0.0144;AA=-;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9951;RSQ=0.6352;AF=0.0037;AFR_AF=0.02 +1 568709 rs148329687 A G 100 PASS THETA=0.0255;ERATE=0.0132;AVGPOST=0.9114;AN=2184;LDAF=0.1251;VT=SNP;AA=-;AC=201;SNPSOURCE=LOWCOV;RSQ=0.6769;AF=0.09;ASN_AF=0.02;AMR_AF=0.06;AFR_AF=0.22;EUR_AF=0.08 +1 568745 rs200850333 C CCA 282 PASS AA=CCA;AC=197;AF=0.09;AFR_AF=0.21;AMR_AF=0.06;AN=2184;ASN_AF=0.04;AVGPOST=0.8910;ERATE=0.0093;EUR_AF=0.06;LDAF=0.1362;RSQ=0.6393;THETA=0.0239;VT=INDEL +1 570337 rs193042102 G T 100 PASS AA=G;AN=2184;ERATE=0.0009;VT=SNP;RSQ=0.2863;AVGPOST=0.9959;LDAF=0.0025;SNPSOURCE=LOWCOV;AC=1;THETA=0.0200;AF=0.0005;AMR_AF=0.0028 +1 570573 rs184868172 T G 100 PASS AVGPOST=0.9977;LDAF=0.0016;AA=T;AN=2184;VT=SNP;SNPSOURCE=LOWCOV;AC=1;THETA=0.0200;ERATE=0.0007;RSQ=0.3221;AF=0.0005;EUR_AF=0.0013 +1 570663 rs189669695 C T 100 PASS AA=C;AN=2184;ERATE=0.0009;THETA=0.0139;VT=SNP;LDAF=0.0038;RSQ=0.4536;SNPSOURCE=LOWCOV;AC=4;AVGPOST=0.9955;AF=0.0018;AMR_AF=0.01;AFR_AF=0.0041 +1 574151 rs74047006 A T 100 PASS AVGPOST=0.9106;AN=2184;AC=132;VT=SNP;AA=A;THETA=0.0153;RSQ=0.6125;SNPSOURCE=LOWCOV;ERATE=0.0056;LDAF=0.0961;AF=0.06;ASN_AF=0.03;AMR_AF=0.03;AFR_AF=0.16;EUR_AF=0.03 +1 574329 rs185282956 A G 100 PASS RSQ=0.2708;AA=G;AN=2184;VT=SNP;AVGPOST=0.9913;ERATE=0.0008;THETA=0.0049;SNPSOURCE=LOWCOV;LDAF=0.0051;AC=2;AF=0.0009;AFR_AF=0.0041 +1 580606 rs201531578 CT C 41 PASS AA=.;AC=21;AF=0.01;AFR_AF=0.03;AMR_AF=0.0028;AN=2184;ASN_AF=0.0017;AVGPOST=0.9539;ERATE=0.0041;EUR_AF=0.0026;LDAF=0.0314;RSQ=0.3531;THETA=0.0293;VT=INDEL +1 585859 rs189649164 G A 100 PASS 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AN=2184;VT=SNP;AA=.;ERATE=0.0019;LDAF=0.1250;RSQ=0.7146;AVGPOST=0.9296;SNPSOURCE=LOWCOV;AC=209;THETA=0.0182;AF=0.10;ASN_AF=0.09;AMR_AF=0.07;AFR_AF=0.16;EUR_AF=0.07 +1 600495 rs147241137 G C 100 PASS AC=47;AVGPOST=0.9745;AN=2184;VT=SNP;AA=.;THETA=0.0112;LDAF=0.0322;SNPSOURCE=LOWCOV;ERATE=0.0015;RSQ=0.6881;AF=0.02;AMR_AF=0.01;AFR_AF=0.09;EUR_AF=0.0013 +1 601055 rs183469249 T C 100 PASS AN=2184;THETA=0.0175;LDAF=0.0018;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0006;RSQ=0.2995;AVGPOST=0.9974;AF=0.0005;ASN_AF=0.0017 +1 601141 rs140845213 C T 100 PASS RSQ=0.6949;AN=2184;THETA=0.0242;VT=SNP;AA=.;AC=234;ERATE=0.0065;SNPSOURCE=LOWCOV;AVGPOST=0.9191;LDAF=0.1375;AF=0.11;ASN_AF=0.10;AMR_AF=0.07;AFR_AF=0.17;EUR_AF=0.09 +1 601583 rs79221329 G A 100 PASS AVGPOST=0.9718;AN=2184;LDAF=0.0320;VT=SNP;AA=.;ERATE=0.0043;AC=44;RSQ=0.6185;SNPSOURCE=LOWCOV;THETA=0.0109;AF=0.02;ASN_AF=0.0017;AMR_AF=0.02;AFR_AF=0.07;EUR_AF=0.0013 +1 601705 rs200489239 GCAAA G 167 PASS AA=GCAAA;AC=10;AF=0.0046;AFR_AF=0.02;AMR_AF=0.0028;AN=2184;AVGPOST=0.9602;ERATE=0.0066;LDAF=0.0247;RSQ=0.2370;THETA=0.0171;VT=INDEL +1 603331 rs186375515 T C 100 PASS THETA=0.0190;AN=2184;LDAF=0.0205;VT=SNP;AA=.;ERATE=0.0051;AVGPOST=0.9694;AC=15;SNPSOURCE=LOWCOV;RSQ=0.3377;AF=0.01;ASN_AF=0.01;AMR_AF=0.0028;AFR_AF=0.01;EUR_AF=0.0040 +1 603505 rs140832136 A C 100 PASS AC=28;AN=2184;ERATE=0.0009;VT=SNP;AA=.;RSQ=0.6254;THETA=0.0383;AVGPOST=0.9815;LDAF=0.0209;SNPSOURCE=LOWCOV;AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.03 +1 603515 rs190065153 C A 100 PASS AVGPOST=0.9718;AN=2184;RSQ=0.7790;VT=SNP;AA=.;AC=79;SNPSOURCE=LOWCOV;THETA=0.0107;ERATE=0.0006;LDAF=0.0475;AF=0.04;AMR_AF=0.01;AFR_AF=0.15 +1 603516 rs182349900 C A 100 PASS AN=2184;THETA=0.0335;LDAF=0.0477;ERATE=0.0009;RSQ=0.7782;VT=SNP;AA=.;AC=79;SNPSOURCE=LOWCOV;AVGPOST=0.9715;AF=0.04;AMR_AF=0.01;AFR_AF=0.15 +1 603589 rs149712121 A C 100 PASS RSQ=0.4843;AN=2184;LDAF=0.0040;VT=SNP;AA=.;THETA=0.0195;SNPSOURCE=LOWCOV;ERATE=0.0006;AC=3;AVGPOST=0.9951;AF=0.0014;ASN_AF=0.01 +1 603710 rs186580270 G C 100 PASS AN=2184;LDAF=0.0040;AVGPOST=0.9935;VT=SNP;AA=.;ERATE=0.0010;SNPSOURCE=LOWCOV;RSQ=0.3844;THETA=0.0271;AC=3;AF=0.0014;AFR_AF=0.01 +1 612688 rs201365517 TCTC T 406 PASS AA=TCTC;AC=77;AF=0.04;AFR_AF=0.01;AMR_AF=0.0028;AN=2184;ASN_AF=0.12;AVGPOST=0.8562;ERATE=0.0040;EUR_AF=0.01;LDAF=0.1048;RSQ=0.4011;THETA=0.0112;VT=INDEL +1 618463 rs114496243 G A 100 PASS AC=437;THETA=0.0285;AN=2184;AVGPOST=0.9066;VT=SNP;AA=.;RSQ=0.7682;SNPSOURCE=LOWCOV;ERATE=0.0107;LDAF=0.2272;AF=0.20;ASN_AF=0.24;AMR_AF=0.17;AFR_AF=0.34;EUR_AF=0.09 +1 626686 rs200090570 CCT C 106 PASS AA=CCT;AC=24;AF=0.01;AFR_AF=0.01;AMR_AF=0.01;AN=2184;ASN_AF=0.01;AVGPOST=0.9302;ERATE=0.0045;EUR_AF=0.01;LDAF=0.0444;RSQ=0.2666;THETA=0.0187;VT=INDEL +1 633582 rs192643069 C T 100 PASS 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AA=TC;AC=45;AF=0.02;AFR_AF=0.08;AMR_AF=0.01;AN=2184;ASN_AF=0.0017;AVGPOST=0.9753;ERATE=0.0030;LDAF=0.0278;RSQ=0.6781;THETA=0.0109;VT=INDEL +1 712583 rs142048655 T C 100 PASS THETA=0.0111;AN=2184;VT=SNP;AA=.;AVGPOST=0.9998;RSQ=0.7933;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;LDAF=0.0005;AF=0.0005;EUR_AF=0.0013 +1 712871 rs4311830 T C 100 PASS AC=73;AN=2184;VT=SNP;AA=.;THETA=0.0017;SNPSOURCE=LOWCOV;RSQ=0.7909;ERATE=0.0007;LDAF=0.0362;AVGPOST=0.9787;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.08;EUR_AF=0.01 +1 712930 rs28457007 T C 100 PASS ERATE=0.0004;AVGPOST=0.9902;AN=2184;LDAF=0.0186;VT=SNP;AA=.;RSQ=0.8130;SNPSOURCE=LOWCOV;AC=36;THETA=0.0010;AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03 +1 712991 rs192262181 G C 100 PASS AN=2184;VT=SNP;AA=.;LDAF=0.0059;ERATE=0.0019;THETA=0.0037;AVGPOST=0.9916;SNPSOURCE=LOWCOV;AC=4;RSQ=0.3783;AF=0.0018;AMR_AF=0.01;AFR_AF=0.0041 +1 713092 rs4565649 G A 100 PASS ERATE=0.0004;AN=2184;RSQ=0.9493;VT=SNP;AA=.;AC=59;SNPSOURCE=LOWCOV;THETA=0.0029;AVGPOST=0.9961;LDAF=0.0277;AF=0.03;AMR_AF=0.02;AFR_AF=0.11;EUR_AF=0.0013 +1 713111 rs138300141 C T 100 PASS ERATE=0.0005;RSQ=0.4288;AN=2184;LDAF=0.0010;VT=SNP;AA=.;THETA=0.0030;AVGPOST=0.9988;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017 +1 713131 rs200310424 A AT 157 PASS AA=A;AC=38;AF=0.02;AFR_AF=0.01;AMR_AF=0.02;AN=2184;AVGPOST=0.9928;ERATE=0.0004;EUR_AF=0.03;LDAF=0.0191;RSQ=0.8585;THETA=0.0014;VT=INDEL +1 713158 rs183634591 T A 100 PASS ERATE=0.0005;RSQ=0.9018;AN=2184;VT=SNP;AA=.;AC=24;THETA=0.0104;SNPSOURCE=LOWCOV;AVGPOST=0.9968;LDAF=0.0114;AF=0.01;ASN_AF=0.04;EUR_AF=0.0013 +1 713189 rs187454950 G A 100 PASS AN=2184;RSQ=0.6996;VT=SNP;AA=.;AC=10;ERATE=0.0008;SNPSOURCE=LOWCOV;LDAF=0.0065;THETA=0.0016;AVGPOST=0.9958;AF=0.0046;AFR_AF=0.02 +1 713190 rs191899145 G A 100 PASS LDAF=0.0053;THETA=0.0015;RSQ=0.8268;AN=2184;VT=SNP;AA=.;AC=10;AVGPOST=0.9980;SNPSOURCE=LOWCOV;ERATE=0.0006;AF=0.0046;AFR_AF=0.02 +1 713250 rs149143617 G C 100 PASS AN=2184;VT=SNP;AA=.;THETA=0.0017;RSQ=0.9754;SNPSOURCE=LOWCOV;ERATE=0.0003;AC=25;LDAF=0.0115;AVGPOST=0.9992;AF=0.01;ASN_AF=0.04;EUR_AF=0.0013 +1 713337 rs184249808 G A 100 PASS ERATE=0.0005;RSQ=0.6269;AN=2184;VT=SNP;AA=.;AVGPOST=0.9969;LDAF=0.0038;THETA=0.0037;AC=5;SNPSOURCE=LOWCOV;AF=0.0023;AMR_AF=0.0028;EUR_AF=0.01 +1 713977 rs74512038 C T 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;AC=155;THETA=0.0019;AVGPOST=0.9916;SNPSOURCE=LOWCOV;LDAF=0.0723;RSQ=0.9544;AF=0.07;ASN_AF=0.22;AMR_AF=0.07;AFR_AF=0.01;EUR_AF=0.0040 +1 713979 rs117217250 C G 100 PASS ERATE=0.0004;AVGPOST=0.9977;AN=2184;RSQ=0.5843;VT=SNP;AA=.;THETA=0.0046;LDAF=0.0025;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;ASN_AF=0.01 +1 714002 rs143219077 C G 100 PASS AC=17;LDAF=0.0095;AN=2184;VT=SNP;AA=.;AVGPOST=0.9930;ERATE=0.0008;SNPSOURCE=LOWCOV;THETA=0.0034;RSQ=0.6851;AF=0.01;ASN_AF=0.02;AFR_AF=0.0041;EUR_AF=0.0013 +1 714019 rs114983708 A G 100 PASS AC=257;ERATE=0.0013;AN=2184;THETA=0.0038;LDAF=0.1171;VT=SNP;AA=.;RSQ=0.9494;SNPSOURCE=LOWCOV;AVGPOST=0.9830;AF=0.12;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.37;EUR_AF=0.04 +1 714031 rs138896432 G A 100 PASS ERATE=0.0004;THETA=0.0044;RSQ=0.6753;AN=2184;AVGPOST=0.9990;VT=SNP;AA=.;LDAF=0.0014;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;ASN_AF=0.0035 +1 714189 rs186983562 A G 100 PASS LDAF=0.0067;AVGPOST=0.9943;AN=2184;VT=SNP;AA=.;AC=10;RSQ=0.6623;SNPSOURCE=LOWCOV;THETA=0.0013;ERATE=0.0007;AF=0.0046;AFR_AF=0.02 +1 714277 rs138660747 C A 100 PASS THETA=0.0014;AN=2184;RSQ=0.5096;VT=SNP;AA=.;LDAF=0.0019;AVGPOST=0.9980;ERATE=0.0008;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;EUR_AF=0.0026 +1 714310 rs141232927 C G 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;THETA=0.0028;RSQ=0.6634;SNPSOURCE=LOWCOV;LDAF=0.0111;AC=19;AVGPOST=0.9892;AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.02 +1 714427 rs12028261 G A 100 PASS 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ERATE=0.0005;AN=2184;RSQ=0.9203;VT=SNP;AA=.;AC=34;LDAF=0.0162;AVGPOST=0.9964;SNPSOURCE=LOWCOV;THETA=0.0013;AF=0.02;AMR_AF=0.01;AFR_AF=0.06 +1 718284 rs184458587 C T 100 PASS ERATE=0.0005;AN=2184;VT=SNP;AA=.;THETA=0.0006;AVGPOST=0.9823;SNPSOURCE=LOWCOV;AC=21;RSQ=0.5709;LDAF=0.0144;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 718336 rs188996809 T C 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9981;VT=SNP;AA=.;THETA=0.0028;LDAF=0.0022;RSQ=0.6163;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AMR_AF=0.0028;EUR_AF=0.0026 +1 718505 rs181440659 G A 100 PASS LDAF=0.0123;AN=2184;RSQ=0.6073;AC=16;VT=SNP;AA=.;THETA=0.0057;SNPSOURCE=LOWCOV;ERATE=0.0007;AVGPOST=0.9882;AF=0.01;AMR_AF=0.01;EUR_AF=0.02 +1 718555 rs10751453 T C 100 PASS RSQ=0.3711;AC=2169;AN=2184;AVGPOST=0.9713;VT=SNP;AA=.;THETA=0.0018;LDAF=0.9817;ERATE=0.0048;SNPSOURCE=LOWCOV;AF=0.99;ASN_AF=1.00;AMR_AF=0.99;AFR_AF=0.99;EUR_AF=1.00 +1 718638 rs185487076 G A 100 PASS ERATE=0.0004;AVGPOST=0.9986;AN=2184;RSQ=0.7525;VT=SNP;AA=.;THETA=0.0017;LDAF=0.0025;SNPSOURCE=LOWCOV;AC=4;AF=0.0018;AFR_AF=0.01 +1 719484 rs189950152 A G 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;THETA=0.0006;AC=0;RSQ=0.2640;SNPSOURCE=LOWCOV;AVGPOST=0.9987;LDAF=0.0008;AF=0 +1 719489 rs201939756 C CATAAT 469 PASS AA=.;AC=166;AF=0.08;AFR_AF=0.28;AMR_AF=0.04;AN=2184;ASN_AF=0.01;AVGPOST=0.9569;ERATE=0.0037;EUR_AF=0.01;LDAF=0.0808;RSQ=0.8249;THETA=0.0010;VT=INDEL +1 719511 rs181042612 A G 100 PASS THETA=0.0014;AN=2184;LDAF=0.0117;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AVGPOST=0.9968;RSQ=0.8970;AC=25;ERATE=0.0007;AF=0.01;ASN_AF=0.04;EUR_AF=0.0013 +1 719604 rs186078657 T C 100 PASS AC=7;LDAF=0.0053;AN=2184;VT=SNP;AA=.;RSQ=0.5887;THETA=0.0012;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9951;AF=0.0032;AMR_AF=0.01;EUR_AF=0.01 +1 719643 rs192061759 A G 100 PASS ERATE=0.0004;AVGPOST=0.9994;AN=2184;THETA=0.0005;VT=SNP;AA=.;RSQ=0.6730;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;ASN_AF=0.0017 +1 719809 rs184004884 T C 100 PASS ERATE=0.0004;LDAF=0.0009;THETA=0.0014;AN=2184;RSQ=0.5341;VT=SNP;AA=.;AVGPOST=0.9991;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AMR_AF=0.0028 +1 719854 rs200512186 CAG C 120 PASS AA=CAG;AC=9;AF=0.0041;AMR_AF=0.0028;AN=2184;AVGPOST=0.9972;ERATE=0.0004;EUR_AF=0.01;LDAF=0.0055;RSQ=0.7795;THETA=0.0029;VT=INDEL +1 719873 rs114149602 G T 100 PASS AN=2184;VT=SNP;AA=.;AVGPOST=0.9989;THETA=0.0019;LDAF=0.0014;SNPSOURCE=LOWCOV;ERATE=0.0006;AC=2;RSQ=0.6622;AF=0.0009;AFR_AF=0.0041 +1 719914 rs187772768 C G 100 PASS ERATE=0.0004;THETA=0.0039;AC=52;AN=2184;LDAF=0.0239;VT=SNP;AA=.;RSQ=0.9477;SNPSOURCE=LOWCOV;AVGPOST=0.9968;AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 720134 rs190637783 G A 100 PASS ERATE=0.0005;RSQ=0.4411;AVGPOST=0.9985;THETA=0.0022;AN=2184;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0012;AF=0.0005;AMR_AF=0.0028 +1 720223 rs149231255 G A 100 PASS ERATE=0.0004;LDAF=0.0116;AN=2184;RSQ=0.9729;VT=SNP;AA=.;THETA=0.0018;SNPSOURCE=LOWCOV;AC=25;AVGPOST=0.9992;AF=0.01;ASN_AF=0.04;EUR_AF=0.0013 +1 720240 rs3121393 T C 100 PASS THETA=0.0015;AN=2184;VT=SNP;AA=.;RSQ=0.9143;AC=2021;ERATE=0.0008;SNPSOURCE=LOWCOV;AVGPOST=0.9832;LDAF=0.9212;AF=0.93;ASN_AF=0.81;AMR_AF=0.93;AFR_AF=0.95;EUR_AF=0.99 +1 720381 rs116801199 G T 100 PASS ERATE=0.0005;AC=73;AN=2184;VT=SNP;AA=.;RSQ=0.9379;AVGPOST=0.9938;SNPSOURCE=LOWCOV;THETA=0.0036;LDAF=0.0338;AF=0.03;ASN_AF=0.04;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 720416 rs182878777 A T 100 PASS THETA=0.0032;AN=2184;AVGPOST=0.9996;VT=SNP;AA=.;LDAF=0.0006;SNPSOURCE=LOWCOV;AC=1;RSQ=0.7354;ERATE=0.0003;AF=0.0005;EUR_AF=0.0013 +1 720468 rs187315357 G A 100 PASS RSQ=0.4812;AN=2184;AVGPOST=0.9962;LDAF=0.0032;VT=SNP;AA=.;THETA=0.0028;ERATE=0.0011;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AMR_AF=0.0028;EUR_AF=0.0026 +1 720681 rs192903943 T C 100 PASS ERATE=0.0004;AN=2184;LDAF=0.0043;VT=SNP;AA=.;RSQ=0.7666;AC=9;THETA=0.0012;AVGPOST=0.9973;SNPSOURCE=LOWCOV;AF=0.0041;AFR_AF=0.02 +1 720797 rs75530702 G A 100 PASS RSQ=0.9089;THETA=0.0022;AN=2184;VT=SNP;AA=.;AC=2027;ERATE=0.0018;SNPSOURCE=LOWCOV;AVGPOST=0.9828;LDAF=0.9224;AF=0.93;ASN_AF=0.82;AMR_AF=0.93;AFR_AF=0.95;EUR_AF=1.00 +1 720968 rs184456771 G C 100 PASS ERATE=0.0004;AN=2184;AC=6;VT=SNP;AA=.;THETA=0.0011;AVGPOST=0.9971;LDAF=0.0038;RSQ=0.6797;SNPSOURCE=LOWCOV;AF=0.0027;AFR_AF=0.01 +1 721006 rs187802448 A G 100 PASS AN=2184;RSQ=0.5588;VT=SNP;AA=.;AC=10;AVGPOST=0.9919;THETA=0.0017;SNPSOURCE=LOWCOV;ERATE=0.0006;LDAF=0.0080;AF=0.0046;ASN_AF=0.02 +1 721104 rs201616474 TA T 80 PASS AA=TA;AC=66;AF=0.03;AFR_AF=0.03;AMR_AF=0.02;AN=2184;ASN_AF=0.03;AVGPOST=0.9868;ERATE=0.0031;EUR_AF=0.03;LDAF=0.0323;RSQ=0.8470;THETA=0.0016;VT=INDEL +1 721119 rs115019173 C T 100 PASS LDAF=0.0092;AN=2184;AC=20;THETA=0.0005;VT=SNP;AA=.;SNPSOURCE=LOWCOV;ERATE=0.0003;AVGPOST=0.9995;RSQ=0.9743;AF=0.01;AMR_AF=0.01;AFR_AF=0.04 +1 721237 rs192191435 T A 100 PASS ERATE=0.0004;THETA=0.0015;AN=2184;AVGPOST=0.9990;VT=SNP;AA=.;LDAF=0.0019;RSQ=0.7652;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;ASN_AF=0.01 +1 721243 rs184778694 A G 100 PASS AN=2184;VT=SNP;AA=.;RSQ=0.6929;LDAF=0.0007;SNPSOURCE=LOWCOV;AC=1;THETA=0.0013;ERATE=0.0003;AVGPOST=0.9995;AF=0.0005;EUR_AF=0.0013 +1 721290 rs12565286 G C 100 PASS AN=2184;RSQ=0.9811;LDAF=0.0352;VT=SNP;AA=.;AC=76;SNPSOURCE=LOWCOV;THETA=0.0013;ERATE=0.0003;AVGPOST=0.9982;AF=0.03;ASN_AF=0.04;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 721705 rs151072073 A G 100 PASS ERATE=0.0004;AN=2184;LDAF=0.0199;VT=SNP;AA=.;RSQ=0.8558;THETA=0.0019;SNPSOURCE=LOWCOV;AVGPOST=0.9920;AC=39;AF=0.02;AMR_AF=0.01;AFR_AF=0.08 +1 721757 rs189147642 T A 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9975;VT=SNP;AA=.;AC=51;LDAF=0.0238;SNPSOURCE=LOWCOV;THETA=0.0007;RSQ=0.9610;AF=0.02;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.04 +1 722361 rs181577596 A G 100 PASS LDAF=0.0027;AN=2184;RSQ=0.4393;VT=SNP;AA=.;ERATE=0.0008;SNPSOURCE=LOWCOV;THETA=0.0010;AC=2;AVGPOST=0.9965;AF=0.0009;ASN_AF=0.0017;AFR_AF=0.0020 +1 722519 rs140978157 A G 100 PASS ERATE=0.0004;AN=2184;LDAF=0.0032;AC=6;VT=SNP;AA=.;RSQ=0.8810;AVGPOST=0.9991;SNPSOURCE=LOWCOV;THETA=0.0036;AF=0.0027;AFR_AF=0.01 +1 722559 rs150361918 T C 100 PASS AN=2184;LDAF=0.0385;AC=83;VT=SNP;AA=.;ERATE=0.0008;SNPSOURCE=LOWCOV;THETA=0.0010;RSQ=0.9738;AVGPOST=0.9978;AF=0.04;AMR_AF=0.02;AFR_AF=0.15;EUR_AF=0.0013 +1 722603 rs138029171 T C 100 PASS THETA=0.0014;AC=48;LDAF=0.0240;AN=2184;VT=SNP;AA=.;AVGPOST=0.9908;ERATE=0.0008;SNPSOURCE=LOWCOV;RSQ=0.8482;AF=0.02;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.08;EUR_AF=0.0013 +1 722670 rs116030099 T C 100 PASS AC=120;THETA=0.0014;AN=2184;LDAF=0.0637;VT=SNP;AA=.;RSQ=0.8222;AVGPOST=0.9721;ERATE=0.0038;SNPSOURCE=LOWCOV;AF=0.05;AMR_AF=0.10;AFR_AF=0.01;EUR_AF=0.10 +1 722672 rs143583930 C T 100 PASS LDAF=0.0285;AN=2184;RSQ=0.8860;AC=65;VT=SNP;AA=.;SNPSOURCE=LOWCOV;THETA=0.0043;ERATE=0.0006;AVGPOST=0.9910;AF=0.03;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.03 +1 722711 rs184304920 A C 100 PASS ERATE=0.0005;AVGPOST=0.9994;AN=2184;RSQ=0.8141;LDAF=0.0015;VT=SNP;AA=.;THETA=0.0011;SNPSOURCE=LOWCOV;AC=3;AF=0.0014;AFR_AF=0.01 +1 722980 rs114222710 C T 100 PASS ERATE=0.0004;THETA=0.0026;RSQ=0.9871;AN=2184;AVGPOST=0.9990;VT=SNP;AA=.;LDAF=0.0326;SNPSOURCE=LOWCOV;AC=71;AF=0.03;AMR_AF=0.02;AFR_AF=0.13;EUR_AF=0.0013 +1 722981 rs146158714 G A 100 PASS THETA=0.0021;ERATE=0.0005;AN=2184;VT=SNP;AA=.;RSQ=0.9199;AVGPOST=0.9989;LDAF=0.0056;SNPSOURCE=LOWCOV;AC=11;AF=0.01;AFR_AF=0.02 +1 723307 rs28659788 C G 100 PASS ERATE=0.0005;LDAF=0.0328;AN=2184;RSQ=0.9424;AVGPOST=0.9947;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=69;THETA=0.0024;AF=0.03;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.04 +1 723329 rs189787166 A T 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9996;VT=SNP;AA=.;RSQ=0.7048;LDAF=0.0007;THETA=0.0025;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AFR_AF=0.0020 +1 723379 rs181223789 T A 100 PASS AN=2184;VT=SNP;AA=.;AVGPOST=0.9989;THETA=0.0012;LDAF=0.0014;SNPSOURCE=LOWCOV;ERATE=0.0006;RSQ=0.6424;AC=2;AF=0.0009;ASN_AF=0.0017;EUR_AF=0.0013 +1 723738 rs59776264 ACT A 223 PASS AA=.;AC=74;AF=0.03;AFR_AF=0.13;AMR_AF=0.02;AN=2184;AVGPOST=0.9973;ERATE=0.0004;LDAF=0.0338;RSQ=0.9746;THETA=0.0007;VT=INDEL +1 723741 rs200325929 CTG C 97 PASS AA=.;AC=73;AF=0.03;AFR_AF=0.13;AMR_AF=0.02;AN=2184;AVGPOST=0.9971;ERATE=0.0004;LDAF=0.0333;RSQ=0.9724;THETA=0.0012;VT=INDEL +1 723742 rs28375378 T C 100 PASS ERATE=0.0005;RSQ=0.9190;AN=2184;THETA=0.0031;VT=SNP;AA=.;LDAF=0.0303;SNPSOURCE=LOWCOV;AC=69;AVGPOST=0.9926;AF=0.03;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.04 +1 723819 rs11804171 T A 100 PASS RSQ=0.9858;AN=2184;LDAF=0.1202;AC=262;VT=SNP;AA=.;THETA=0.0006;ERATE=0.0008;SNPSOURCE=LOWCOV;AVGPOST=0.9955;AF=0.12;ASN_AF=0.04;AMR_AF=0.06;AFR_AF=0.37;EUR_AF=0.04 +1 723891 rs2977670 G C 100 PASS THETA=0.0009;LDAF=0.7873;AN=2184;RSQ=0.9857;VT=SNP;AA=.;AVGPOST=0.9930;AC=1720;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.79;ASN_AF=0.78;AMR_AF=0.86;AFR_AF=0.50;EUR_AF=0.95 +1 723918 rs144434834 G A 100 PASS ERATE=0.0004;RSQ=0.9840;AN=2184;VT=SNP;AA=.;AVGPOST=0.9988;SNPSOURCE=LOWCOV;THETA=0.0010;AC=71;LDAF=0.0327;AF=0.03;AMR_AF=0.02;AFR_AF=0.13;EUR_AF=0.0013 +1 724103 rs111533735 A G 100 PASS ERATE=0.0005;RSQ=0.9859;THETA=0.0061;AN=2184;VT=SNP;AA=.;AVGPOST=0.9988;SNPSOURCE=LOWCOV;LDAF=0.0341;AC=74;AF=0.03;AMR_AF=0.02;AFR_AF=0.13 +1 726449 rs145488171 T C 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9990;VT=SNP;AA=.;LDAF=0.0119;THETA=0.0028;SNPSOURCE=LOWCOV;AC=25;RSQ=0.9763;AF=0.01;ASN_AF=0.04;EUR_AF=0.0013 +1 726794 rs28454925 C G 100 PASS ERATE=0.0023;AN=2184;LDAF=0.0286;VT=SNP;AA=.;AC=56;SNPSOURCE=LOWCOV;THETA=0.0013;RSQ=0.8891;AVGPOST=0.9925;AF=0.03;AMR_AF=0.03;AFR_AF=0.03;EUR_AF=0.04 +1 727142 rs28641938 T C 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;AVGPOST=0.9980;THETA=0.0059;SNPSOURCE=LOWCOV;AC=53;RSQ=0.9652;LDAF=0.0248;AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 727212 rs186100254 G A 100 PASS AN=2184;LDAF=0.0105;RSQ=0.5746;VT=SNP;AA=.;AC=14;ERATE=0.0016;SNPSOURCE=LOWCOV;THETA=0.0016;AVGPOST=0.9885;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 +1 727655 rs12565110 C T 100 PASS THETA=0.0015;AVGPOST=0.9902;AN=2184;VT=SNP;AA=.;LDAF=0.0734;AC=156;SNPSOURCE=LOWCOV;RSQ=0.9485;ERATE=0.0006;AF=0.07;ASN_AF=0.18;AMR_AF=0.07;AFR_AF=0.05;EUR_AF=0.0026 +1 727841 rs116587930 G A 100 PASS ERATE=0.0004;AN=2184;AC=49;VT=SNP;AA=.;THETA=0.0030;LDAF=0.0223;SNPSOURCE=LOWCOV;RSQ=0.9658;AVGPOST=0.9982;AF=0.02;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.06 +1 728088 rs201276269 ACT A 70 PASS AA=ACT;AC=66;AF=0.03;AFR_AF=0.05;AMR_AF=0.03;AN=2184;ASN_AF=0.03;AVGPOST=0.9094;ERATE=0.0165;EUR_AF=0.01;LDAF=0.0712;RSQ=0.4139;THETA=0.0012;VT=INDEL +1 728159 rs3131978 C T 100 PASS AC=1995;THETA=0.0032;AVGPOST=0.9390;AN=2184;VT=SNP;AA=.;LDAF=0.8943;ERATE=0.0059;RSQ=0.7769;SNPSOURCE=LOWCOV;AF=0.91;ASN_AF=0.78;AMR_AF=0.92;AFR_AF=0.94;EUR_AF=0.99 +1 728242 rs3131977 C G 100 PASS THETA=0.0015;AN=2184;RSQ=0.8511;VT=SNP;AA=.;ERATE=0.0017;AVGPOST=0.9647;LDAF=0.9074;SNPSOURCE=LOWCOV;AC=2005;AF=0.92;ASN_AF=0.80;AMR_AF=0.92;AFR_AF=0.93;EUR_AF=1.00 +1 728606 rs145605014 G A 100 PASS AN=2184;AC=8;RSQ=0.9605;AVGPOST=0.9997;VT=SNP;AA=.;LDAF=0.0038;SNPSOURCE=LOWCOV;THETA=0.0007;ERATE=0.0003;AF=0.0037;AFR_AF=0.02 +1 728853 rs191103318 A G 100 PASS ERATE=0.0004;AN=2184;VT=SNP;AA=.;LDAF=0.0007;SNPSOURCE=LOWCOV;AC=1;THETA=0.0013;RSQ=0.4944;AVGPOST=0.9992;AF=0.0005;ASN_AF=0.0017 +1 728951 rs55744711 C T 100 PASS AC=73;AN=2184;RSQ=0.9879;AVGPOST=0.9990;VT=SNP;AA=.;THETA=0.0006;LDAF=0.0333;SNPSOURCE=LOWCOV;ERATE=0.0003;AF=0.03;AMR_AF=0.02;AFR_AF=0.13 +1 729358 rs142251181 GA G 119 PASS AA=GA;AC=24;AF=0.01;AN=2184;ASN_AF=0.04;AVGPOST=0.9971;ERATE=0.0004;EUR_AF=0.0013;LDAF=0.0122;RSQ=0.9290;THETA=0.0086;VT=INDEL +1 729632 rs116720794 C T 100 PASS ERATE=0.0004;LDAF=0.0246;RSQ=0.9316;AC=52;AN=2184;VT=SNP;AA=.;THETA=0.0018;SNPSOURCE=LOWCOV;AVGPOST=0.9958;AF=0.02;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 +1 729679 rs4951859 C G 100 PASS LDAF=0.6596;RSQ=0.9300;AN=2184;AC=1440;ERATE=0.0009;VT=SNP;AA=.;SNPSOURCE=LOWCOV;THETA=0.0010;AVGPOST=0.9514;AF=0.66;ASN_AF=0.65;AMR_AF=0.77;AFR_AF=0.31;EUR_AF=0.83 +1 729739 rs148932570 C T 100 PASS ERATE=0.0004;RSQ=0.6965;AN=2184;VT=SNP;AA=.;THETA=0.0017;LDAF=0.0020;SNPSOURCE=LOWCOV;AVGPOST=0.9987;AC=3;AF=0.0014;ASN_AF=0.01