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Record with empty list of samples instead of None

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commit 10b26fc4d5733d7e7f97336009449ec12160c1c2 1 parent 1dbe5b5
Martijn Vermaat martijnvermaat authored
2  vcf/model.py
@@ -133,7 +133,7 @@ def __init__(self, CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT,
133 133 self.alleles = [self.REF]
134 134 self.alleles.extend(self.ALT)
135 135 #: list of ``_Calls`` for each sample ordered as in source VCF
136   - self.samples = samples
  136 + self.samples = samples or []
137 137 self._sample_indexes = sample_indexes
138 138
139 139 def __eq__(self, other):
200 vcf/test/1kg.sites.vcf
... ... @@ -0,0 +1,200 @@
  1 +##fileformat=VCFv4.1
  2 +##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
  3 +##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
  4 +##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
  5 +##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
  6 +##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
  7 +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
  8 +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
  9 +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
  10 +##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
  11 +##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
  12 +##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
  13 +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
  14 +##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
  15 +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
  16 +##ALT=<ID=DEL,Description="Deletion">
  17 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
  18 +##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
  19 +##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
  20 +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README">
  21 +##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
  22 +##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
  23 +##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
  24 +##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
  25 +##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
  26 +##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
  27 +##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
  28 +##reference=GRCh37
  29 +#CHROM POS ID REF ALT QUAL FILTER INFO
  30 +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
  31 +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
  32 +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
  33 +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
  34 +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
  35 +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
  36 +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
  37 +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
  38 +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
  39 +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
  40 +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
  41 +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
  42 +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
  43 +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
  44 +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
  45 +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
  46 +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
  47 +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
  48 +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
  49 +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
  50 +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
  51 +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
  52 +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
  53 +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
  54 +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
  55 +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
  56 +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
  57 +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
  58 +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
  59 +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
  60 +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
  61 +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
  62 +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
  63 +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
  64 +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
  65 +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
  66 +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
  67 +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
  68 +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
  69 +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
  70 +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
  71 +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
  72 +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
  73 +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
  74 +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
  75 +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
  76 +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
  77 +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
  78 +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
  79 +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
  80 +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
  81 +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
  82 +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
  83 +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
  84 +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
  85 +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
  86 +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
  87 +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
  88 +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
  89 +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
  90 +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
  91 +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
  92 +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
  93 +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
  94 +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
  95 +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
  96 +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
  97 +1 69534 rs190717287 T C 100 PASS AVGPOST=0.9986;LDAF=0.0013;AN=2184;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4002;THETA=0.0016;ERATE=0.0006;AF=0.0005;ASN_AF=0.0017
  98 +1 69536 rs200013390 C T 100 PASS AA=.;AC=0;AF=0;AN=2184;AVGPOST=0.9986;ERATE=0.0006;LDAF=0.0008;RSQ=0.0677;SNPSOURCE=EXOME;THETA=0.0087;VT=SNP
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  100 +1 72148 rs182862337 C T 100 PASS AN=2184;RSQ=0.2794;THETA=0.0130;VT=SNP;AA=.;LDAF=0.0019;AVGPOST=0.9971;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0007;AF=0.0005;AMR_AF=0.0028
  101 +1 72297 rs200651397 G GTAT 160 PASS AA=G;AC=19;AF=0.01;AMR_AF=0.02;AN=2184;ASN_AF=0.01;AVGPOST=0.9383;ERATE=0.0055;EUR_AF=0.01;LDAF=0.0399;RSQ=0.3194;THETA=0.0064;VT=INDEL
  102 +1 73841 rs143773730 C T 100 PASS ERATE=0.0303;THETA=0.0044;AN=2184;AVGPOST=0.8178;RSQ=0.5832;VT=SNP;AA=.;SNPSOURCE=LOWCOV;LDAF=0.2588;AC=425;AF=0.19;ASN_AF=0.15;AMR_AF=0.22;AFR_AF=0.17;EUR_AF=0.23
  103 +1 77462 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
  104 +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
  105 +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
  106 +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
  107 +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
  108 +1 79050 rs62641299 G T 100 PASS AC=1871;AN=2184;THETA=0.0031;RSQ=0.3928;VT=SNP;AA=.;AVGPOST=0.6803;SNPSOURCE=LOWCOV;LDAF=0.7318;ERATE=0.0107;AF=0.86;ASN_AF=0.98;AMR_AF=0.93;AFR_AF=0.54;EUR_AF=0.94
  109 +1 79137 rs143777184 A T 100 PASS AN=2184;AC=55;ERATE=0.0009;AVGPOST=0.9773;LDAF=0.0324;VT=SNP;AA=.;THETA=0.0091;SNPSOURCE=LOWCOV;RSQ=0.7309;AF=0.03;AMR_AF=0.01;AFR_AF=0.10
  110 +1 79417 rs184768190 C T 100 PASS ERATE=0.0005;THETA=0.0166;AN=2184;RSQ=0.5026;AVGPOST=0.9975;VT=SNP;AA=.;LDAF=0.0022;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;ASN_AF=0.0035
  111 +1 79772 rs147215883 C G 100 PASS LDAF=0.1066;AN=2184;THETA=0.0138;RSQ=0.7199;VT=SNP;AA=.;AVGPOST=0.9271;AC=176;ERATE=0.0011;SNPSOURCE=LOWCOV;AF=0.08;ASN_AF=0.07;AMR_AF=0.06;AFR_AF=0.10;EUR_AF=0.09
  112 +1 79872 rs189224661 T G 100 PASS THETA=0.0054;AN=2184;LDAF=0.0057;VT=SNP;AA=.;ERATE=0.0017;AC=9;AVGPOST=0.9956;SNPSOURCE=LOWCOV;RSQ=0.6548;AF=0.0041;AFR_AF=0.02
  113 +1 80454 rs144226842 G C 100 PASS RSQ=0.6549;LDAF=0.0035;AN=2184;AVGPOST=0.9975;VT=SNP;AA=.;AC=5;SNPSOURCE=LOWCOV;THETA=0.0110;ERATE=0.0015;AF=0.0023;ASN_AF=0.01
  114 +1 81949 rs181567186 T C 100 PASS AN=2184;ERATE=0.0009;VT=SNP;AA=.;AVGPOST=0.9948;LDAF=0.0030;SNPSOURCE=LOWCOV;AC=1;THETA=0.0052;RSQ=0.2129;AF=0.0005;ASN_AF=0.0017
  115 +1 82163 rs139113303 G A 100 PASS AN=2184;LDAF=0.0375;ERATE=0.0009;VT=SNP;AA=.;RSQ=0.7842;AC=66;THETA=0.0053;SNPSOURCE=LOWCOV;AVGPOST=0.9761;AF=0.03;ASN_AF=0.0017;AMR_AF=0.01;AFR_AF=0.0020;EUR_AF=0.08
  116 +1 82249 rs1851945 A G 100 PASS THETA=0.0137;LDAF=0.0712;AVGPOST=0.9150;AN=2184;VT=SNP;AA=.;RSQ=0.4689;AC=75;ERATE=0.0116;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.03;AMR_AF=0.04;AFR_AF=0.02;EUR_AF=0.04
  117 +1 82609 rs149189449 C G 100 PASS ERATE=0.0005;AN=2184;LDAF=0.0364;VT=SNP;AA=.;AC=68;AVGPOST=0.9822;RSQ=0.8408;SNPSOURCE=LOWCOV;THETA=0.0024;AF=0.03;AMR_AF=0.02;AFR_AF=0.0020;EUR_AF=0.08
  118 +1 82676 rs185237834 T G 100 PASS LDAF=0.1144;AN=2184;AVGPOST=0.9264;VT=SNP;AA=.;RSQ=0.7176;AC=198;THETA=0.0025;SNPSOURCE=LOWCOV;ERATE=0.0056;AF=0.09;ASN_AF=0.07;AMR_AF=0.08;AFR_AF=0.12;EUR_AF=0.10
  119 +1 82734 rs4030331 T C 100 PASS AN=2184;THETA=0.0008;VT=SNP;AA=.;ERATE=0.0158;RSQ=0.6316;AVGPOST=0.8280;LDAF=0.2433;SNPSOURCE=LOWCOV;AC=435;AF=0.20;ASN_AF=0.15;AMR_AF=0.28;AFR_AF=0.24;EUR_AF=0.17
  120 +1 82957 rs189774606 C T 100 PASS RSQ=0.5163;AN=2184;VT=SNP;AA=.;LDAF=0.0072;THETA=0.0028;AC=9;AVGPOST=0.9918;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.0041;AMR_AF=0.01;AFR_AF=0.01
  121 +1 83084 rs181193408 T A 100 PASS AN=2184;AVGPOST=0.8261;VT=SNP;AA=.;RSQ=0.5750;AC=1914;LDAF=0.8278;SNPSOURCE=LOWCOV;ERATE=0.0061;THETA=0.0064;AF=0.88;ASN_AF=0.99;AMR_AF=0.92;AFR_AF=0.58;EUR_AF=0.96
  122 +1 83088 rs186081601 G C 100 PASS ERATE=0.0013;AN=2184;LDAF=0.0043;VT=SNP;AA=.;AVGPOST=0.9922;RSQ=0.1618;THETA=0.0019;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AFR_AF=0.0020
  123 +1 83771 rs189906733 T G 100 PASS RSQ=0.6473;AN=2184;AVGPOST=0.9871;VT=SNP;AA=.;AC=24;ERATE=0.0011;SNPSOURCE=LOWCOV;THETA=0.0043;LDAF=0.0158;AF=0.01;AMR_AF=0.01;AFR_AF=0.04;EUR_AF=0.0013
  124 +1 83977 rs180759811 A G 100 PASS AN=2184;ERATE=0.0009;VT=SNP;AA=.;THETA=0.0059;LDAF=0.0038;RSQ=0.2074;SNPSOURCE=LOWCOV;AC=1;AVGPOST=0.9932;AF=0.0005;AFR_AF=0.0020
  125 +1 84002 rs28850140 G A 100 PASS THETA=0.0050;ERATE=0.0211;AN=2184;AC=236;VT=SNP;AA=.;AVGPOST=0.8144;LDAF=0.1921;SNPSOURCE=LOWCOV;RSQ=0.4810;AF=0.11;ASN_AF=0.12;AMR_AF=0.15;AFR_AF=0.07;EUR_AF=0.11
  126 +1 84005 rs202079949 AG A 78 PASS AA=.;AC=52;AF=0.02;AFR_AF=0.02;AMR_AF=0.03;AN=2184;ASN_AF=0.01;AVGPOST=0.9360;ERATE=0.0049;EUR_AF=0.04;LDAF=0.0514;RSQ=0.4690;THETA=0.0005;VT=INDEL
  127 +1 84010 rs186443818 G A 100 PASS AVGPOST=0.9169;AN=2184;VT=SNP;AA=.;AC=97;THETA=0.0087;LDAF=0.0789;SNPSOURCE=LOWCOV;ERATE=0.0061;RSQ=0.5318;AF=0.04;ASN_AF=0.03;AMR_AF=0.05;AFR_AF=0.03;EUR_AF=0.06
  128 +1 84079 rs190867312 T C 100 PASS 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
  129 +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
  130 +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
  131 +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
  132 +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
  133 +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
  134 +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
  135 +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
  136 +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
  137 +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
  138 +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
  139 +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
  140 +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
  141 +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
  142 +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
  143 +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
  144 +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
  145 +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
  146 +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
  147 +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
  148 +1 86982 rs184970101 G A 100 PASS THETA=0.0050;AN=2184;AVGPOST=0.9979;LDAF=0.0015;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0006;RSQ=0.3541;AF=0.0005;AFR_AF=0.0020
  149 +1 87021 rs188486692 T C 100 PASS AN=2184;RSQ=0.4348;VT=SNP;AA=.;THETA=0.0112;AVGPOST=0.9687;ERATE=0.0011;SNPSOURCE=LOWCOV;AC=19;LDAF=0.0221;AF=0.01;AMR_AF=0.01;AFR_AF=0.0041;EUR_AF=0.02
  150 +1 87114 rs200095900 CT C 192 PASS AA=.;AC=8;AF=0.0037;AFR_AF=0.02;AN=2184;AVGPOST=0.9976;ERATE=0.0010;LDAF=0.0042;RSQ=0.7479;THETA=0.0149;VT=INDEL
  151 +1 87190 rs1524602 G A 100 PASS AN=2184;LDAF=0.2822;VT=SNP;AA=.;RSQ=0.7549;THETA=0.0148;AC=540;SNPSOURCE=LOWCOV;ERATE=0.0096;AVGPOST=0.8739;AF=0.25;ASN_AF=0.29;AMR_AF=0.35;AFR_AF=0.38;EUR_AF=0.08
  152 +1 87360 rs180907504 C T 100 PASS THETA=0.0014;AN=2184;ERATE=0.0025;RSQ=0.3869;VT=SNP;AA=.;AC=14;LDAF=0.0170;SNPSOURCE=LOWCOV;AVGPOST=0.9768;AF=0.01;ASN_AF=0.02;AMR_AF=0.0028;AFR_AF=0.01
  153 +1 87409 rs139490478 C T 100 PASS 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
  154 +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
  155 +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
  156 +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
  157 +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
  158 +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
  159 +1 88136 rs59529791 G A 100 PASS RSQ=0.8406;AN=2184;VT=SNP;AA=.;ERATE=0.0010;THETA=0.0059;AVGPOST=0.9778;SNPSOURCE=LOWCOV;AC=106;LDAF=0.0548;AF=0.05;AMR_AF=0.03;AFR_AF=0.20
  160 +1 88169 rs940550 C T 100 PASS RSQ=0.7811;AN=2184;VT=SNP;AA=.;THETA=0.0055;LDAF=0.2576;ERATE=0.0018;SNPSOURCE=LOWCOV;AC=506;AVGPOST=0.8932;AF=0.23;ASN_AF=0.29;AMR_AF=0.33;AFR_AF=0.33;EUR_AF=0.08
  161 +1 88172 rs940551 G A 100 PASS RSQ=0.7703;AVGPOST=0.9669;LDAF=0.0483;AN=2184;ERATE=0.0009;VT=SNP;AA=.;THETA=0.0027;SNPSOURCE=LOWCOV;AC=86;AF=0.04;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.09
  162 +1 88177 rs143215837 G C 100 PASS ERATE=0.0004;AN=2184;LDAF=0.0456;VT=SNP;AA=.;AVGPOST=0.9686;AC=82;THETA=0.0089;SNPSOURCE=LOWCOV;RSQ=0.7787;AF=0.04;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.09
  163 +1 88188 rs148331237 C A 100 PASS THETA=0.0039;AN=2184;VT=SNP;AA=.;AC=9;LDAF=0.0085;SNPSOURCE=LOWCOV;ERATE=0.0007;RSQ=0.5212;AVGPOST=0.9910;AF=0.0041;AMR_AF=0.0028;EUR_AF=0.01
  164 +1 88236 rs186918018 C T 100 PASS AVGPOST=0.9904;AN=2184;ERATE=0.0031;RSQ=0.5511;VT=SNP;AA=.;THETA=0.0087;LDAF=0.0097;SNPSOURCE=LOWCOV;AC=11;AF=0.01;AMR_AF=0.02;AFR_AF=0.0041;EUR_AF=0.0026
  165 +1 88250 rs191950833 T A 100 PASS LDAF=0.0013;AN=2184;RSQ=0.1387;VT=SNP;AA=.;AC=0;THETA=0.0019;SNPSOURCE=LOWCOV;ERATE=0.0007;AVGPOST=0.9974;AF=0
  166 +1 88316 rs113759966 G A 100 PASS LDAF=0.0531;AN=2184;VT=SNP;AA=.;THETA=0.0071;RSQ=0.7791;AVGPOST=0.9644;ERATE=0.0008;AC=87;SNPSOURCE=LOWCOV;AF=0.04;ASN_AF=0.0017;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.09
  167 +1 88324 rs183326616 A G 100 PASS ERATE=0.0004;AN=2184;AVGPOST=0.9996;VT=SNP;AA=.;RSQ=0.7073;LDAF=0.0006;SNPSOURCE=LOWCOV;AC=1;THETA=0.0092;AF=0.0005;AFR_AF=0.0020
  168 +1 88338 rs55700207 G A 100 PASS THETA=0.0035;RSQ=0.7967;AN=2184;ERATE=0.0034;LDAF=0.1019;VT=SNP;AA=.;AC=186;SNPSOURCE=LOWCOV;AVGPOST=0.9507;AF=0.09;ASN_AF=0.03;AMR_AF=0.15;AFR_AF=0.14;EUR_AF=0.05
  169 +1 88370 rs185487977 G A 100 PASS AVGPOST=0.9957;LDAF=0.0035;AN=2184;ERATE=0.0009;RSQ=0.4507;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=4;THETA=0.0043;AF=0.0018;AMR_AF=0.0028;EUR_AF=0.0040
  170 +1 88376 rs189954431 T G 100 PASS RSQ=0.6404;AVGPOST=0.9994;AN=2184;VT=SNP;AA=.;THETA=0.0057;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;LDAF=0.0008;AF=0.0005;AFR_AF=0.0020
  171 +1 88388 rs182344336 C T 100 PASS THETA=0.0048;ERATE=0.0005;RSQ=0.3843;AVGPOST=0.9977;LDAF=0.0016;AN=2184;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;ASN_AF=0.0017
  172 +1 88429 rs146027550 T C 100 PASS LDAF=0.0083;AN=2184;AC=13;RSQ=0.6097;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9922;SNPSOURCE=LOWCOV;THETA=0.0069;AF=0.01;AMR_AF=0.01;AFR_AF=0.02;EUR_AF=0.0013
  173 +1 88710 rs186575039 C G 100 PASS ERATE=0.0005;AC=73;THETA=0.0022;AN=2184;VT=SNP;AA=.;AVGPOST=0.9774;LDAF=0.0389;SNPSOURCE=LOWCOV;RSQ=0.8058;AF=0.03;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.08
  174 +1 89165 rs192631277 A C 100 PASS RSQ=0.2647;AN=2184;ERATE=0.0009;VT=SNP;AA=.;AVGPOST=0.9969;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;THETA=0.0043;AF=0.0005;ASN_AF=0.0017
  175 +1 89744 rs184101761 A G 100 PASS THETA=0.0068;ERATE=0.0004;AVGPOST=0.9985;LDAF=0.0016;AN=2184;RSQ=0.5853;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=2;AF=0.0009;AFR_AF=0.0041
  176 +1 89794 rs188661839 T C 100 PASS AN=2184;THETA=0.0130;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0006;RSQ=0.3812;AVGPOST=0.9984;LDAF=0.0012;AF=0.0005;AFR_AF=0.0020
  177 +1 89946 rs138808727 A T 100 PASS RSQ=0.7414;LDAF=0.1417;AN=2184;ERATE=0.0009;AC=236;VT=SNP;AA=.;THETA=0.0100;AVGPOST=0.9001;SNPSOURCE=LOWCOV;AF=0.11;ASN_AF=0.0035;AMR_AF=0.16;AFR_AF=0.02;EUR_AF=0.22
  178 +1 91190 rs143856811 G A 100 PASS AN=2184;AC=77;ERATE=0.0009;VT=SNP;AA=.;LDAF=0.0447;SNPSOURCE=LOWCOV;RSQ=0.7517;THETA=0.0113;AVGPOST=0.9690;AF=0.04;ASN_AF=0.0017;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.08
  179 +1 91228 rs139873689 A G 100 PASS AN=2184;AVGPOST=0.9924;AC=8;RSQ=0.5097;VT=SNP;AA=.;ERATE=0.0010;THETA=0.0012;SNPSOURCE=LOWCOV;LDAF=0.0070;AF=0.0037;AFR_AF=0.02
  180 +1 91536 rs77418980 G T 100 PASS AC=695;AN=2184;ERATE=0.0025;AVGPOST=0.7792;VT=SNP;AA=.;THETA=0.0018;LDAF=0.3255;RSQ=0.6634;SNPSOURCE=LOWCOV;AF=0.32;ASN_AF=0.34;AMR_AF=0.30;AFR_AF=0.04;EUR_AF=0.50
  181 +1 91581 rs151118460 G A 100 PASS AVGPOST=0.7763;THETA=0.0078;AN=2184;VT=SNP;AA=.;AC=716;ERATE=0.0035;LDAF=0.3353;RSQ=0.6618;SNPSOURCE=LOWCOV;AF=0.33;ASN_AF=0.37;AMR_AF=0.30;AFR_AF=0.04;EUR_AF=0.50
  182 +1 91605 rs141083882 C T 100 PASS AC=105;LDAF=0.0597;AN=2184;RSQ=0.7792;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9660;SNPSOURCE=LOWCOV;THETA=0.0070;AF=0.05;AMR_AF=0.02;AFR_AF=0.20
  183 +1 92633 rs149776517 C T 100 PASS THETA=0.0054;AN=2184;VT=SNP;AA=.;AC=44;AVGPOST=0.9592;ERATE=0.0008;LDAF=0.0366;SNPSOURCE=LOWCOV;RSQ=0.5870;AF=0.02;AMR_AF=0.02;EUR_AF=0.05
  184 +1 92858 rs147061536 G T 100 PASS AC=248;THETA=0.0212;RSQ=0.7567;AN=2184;ERATE=0.0046;VT=SNP;AA=.;SNPSOURCE=LOWCOV;AVGPOST=0.9072;LDAF=0.1433;AF=0.11;ASN_AF=0.01;AMR_AF=0.15;AFR_AF=0.05;EUR_AF=0.22
  185 +1 92875 rs193157612 T C 100 PASS THETA=0.0048;AVGPOST=0.9957;AN=2184;LDAF=0.0040;ERATE=0.0009;VT=SNP;AA=.;RSQ=0.4901;SNPSOURCE=LOWCOV;AC=4;AF=0.0018;EUR_AF=0.01
  186 +1 94421 rs200856736 TC T 90 PASS AA=TC;AC=253;AF=0.12;AFR_AF=0.01;AMR_AF=0.20;AN=2184;ASN_AF=0.26;AVGPOST=0.7183;ERATE=0.0117;EUR_AF=0.03;LDAF=0.2244;RSQ=0.3175;THETA=0.0159;VT=INDEL
  187 +1 94986 rs185004859 C T 100 PASS ERATE=0.0166;AN=2184;AC=100;THETA=0.0227;VT=SNP;AA=.;LDAF=0.0872;AVGPOST=0.9040;SNPSOURCE=LOWCOV;RSQ=0.4650;AF=0.05;ASN_AF=0.03;AMR_AF=0.04;AFR_AF=0.07;EUR_AF=0.04
  188 +1 94991 rs188832636 G A 100 PASS THETA=0.0048;LDAF=0.0041;AN=2184;AVGPOST=0.9944;ERATE=0.0009;VT=SNP;AA=.;SNPSOURCE=LOWCOV;RSQ=0.4157;AC=3;AF=0.0014;AMR_AF=0.0028;EUR_AF=0.0026
  189 +1 98583 rs141344361 T A 100 PASS AVGPOST=0.9463;AC=248;THETA=0.0099;AN=2184;VT=SNP;AA=.;RSQ=0.8090;LDAF=0.1336;ERATE=0.0008;SNPSOURCE=LOWCOV;AF=0.11;ASN_AF=0.30;AMR_AF=0.16;AFR_AF=0.01;EUR_AF=0.02
  190 +1 98929 rs12184306 A G 100 PASS RSQ=0.6226;AVGPOST=0.8784;AN=2184;VT=SNP;AA=.;ERATE=0.0045;LDAF=0.1723;SNPSOURCE=LOWCOV;AC=264;THETA=0.0070;AF=0.12;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.16;EUR_AF=0.09
  191 +1 98946 rs191775802 C G 100 PASS AVGPOST=0.9945;ERATE=0.0013;AN=2184;LDAF=0.0046;VT=SNP;AA=.;RSQ=0.4807;SNPSOURCE=LOWCOV;AC=4;THETA=0.0097;AF=0.0018;AFR_AF=0.01
  192 +1 98974 rs12184307 A G 100 PASS AVGPOST=0.8921;AN=2184;AC=224;THETA=0.0130;VT=SNP;AA=.;LDAF=0.1405;RSQ=0.6149;SNPSOURCE=LOWCOV;ERATE=0.0012;AF=0.10;ASN_AF=0.14;AMR_AF=0.07;AFR_AF=0.14;EUR_AF=0.06
  193 +1 99671 rs146209971 A T 100 PASS THETA=0.0199;AN=2184;AC=13;RSQ=0.4401;VT=SNP;AA=.;ERATE=0.0010;AVGPOST=0.9802;SNPSOURCE=LOWCOV;LDAF=0.0158;AF=0.01;AMR_AF=0.02;AFR_AF=0.0020;EUR_AF=0.01
  194 +1 99687 rs139153227 C T 100 PASS THETA=0.0211;LDAF=0.0470;AN=2184;VT=SNP;AA=.;ERATE=0.0010;RSQ=0.6276;AVGPOST=0.9548;AC=64;SNPSOURCE=LOWCOV;AF=0.03;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.07
  195 +1 99719 rs183898652 C T 100 PASS AN=2184;RSQ=0.5856;VT=SNP;AA=.;AC=10;ERATE=0.0018;SNPSOURCE=LOWCOV;LDAF=0.0076;AVGPOST=0.9925;THETA=0.0251;AF=0.0046;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.0013
  196 +1 100676 rs188226172 A T 100 PASS THETA=0.0212;LDAF=0.0047;AN=2184;VT=SNP;AA=.;RSQ=0.2646;SNPSOURCE=LOWCOV;ERATE=0.0012;AC=2;AVGPOST=0.9925;AF=0.0009;AMR_AF=0.0028;AFR_AF=0.0020
  197 +1 103905 rs142403309 A G 100 PASS AN=2184;THETA=0.0131;ERATE=0.0025;AVGPOST=0.8782;AC=220;VT=SNP;AA=.;LDAF=0.1434;SNPSOURCE=LOWCOV;RSQ=0.5994;AF=0.10;ASN_AF=0.10;AMR_AF=0.14;AFR_AF=0.15;EUR_AF=0.05
  198 +1 106544 rs180741296 C G 100 PASS AC=205;AVGPOST=0.5776;AN=2184;VT=SNP;AA=.;LDAF=0.3120;SNPSOURCE=LOWCOV;ERATE=0.0061;THETA=0.0372;RSQ=0.1442;AF=0.09;ASN_AF=0.11;AMR_AF=0.13;AFR_AF=0.11;EUR_AF=0.05
  199 +1 109107 rs201432136 G GT 67 PASS 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
  200 +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
12 vcf/test/test_vcf.py
@@ -205,6 +205,17 @@ def test_issue_49(self):
205 205 pass
206 206
207 207
  208 +class Test1kgSites(unittest.TestCase):
  209 +
  210 + def test_reader(self):
  211 + """The samples attribute should be the empty list."""
  212 + reader = vcf.Reader(fh('1kg.sites.vcf', 'r'))
  213 +
  214 + self.assertEqual(reader.samples, [])
  215 + for record in reader:
  216 + self.assertEqual(record.samples, [])
  217 +
  218 +
208 219 class TestGatkOutputWriter(unittest.TestCase):
209 220
210 221 def testWrite(self):
@@ -841,6 +852,7 @@ def test_trim(self):
841 852 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestOpenMethods))
842 853 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestFilter))
843 854 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(Test1kg))
  855 +suite.addTests(unittest.TestLoader().loadTestsFromTestCase(Test1kgSites))
844 856 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRecord))
845 857 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestCall))
846 858 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestRegression))

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