annotate test-data/gemini_load_input.vcf @ 2:9872131c2377 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0

##fileformat=VCFv4.1
##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
##ALT=<ID=DEL,Description="Deletion">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
##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">
##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
##reference=GRCh37
##SnpEffVersion="SnpEff 3.0f (build 2012-08-23), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh37.66 -i vcf -o vcf -c /Users/arq5x/src/other/snpEff_3_0/snpEff.config ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	10583	rs58108140	G	A	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
1	10611	rs189107123	C	G	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),UPSTREAM(MODIFIER|||||DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),UPSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
1	13302	rs180734498	C	T	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
1	13327	rs144762171	G	C	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||209|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|),INTRON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|)
1	13957	.	TC	T	28.0	PASS	AA=TC;AC=35;AN=2184;VT=INDEL;AVGPOST=0.8711;RSQ=0.2501;LDAF=0.0788;THETA=0.0100;ERATE=0.0065;AF=0.02;ASN_AF=0.01;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.02;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
1	13980	rs151276478	T	C	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000450305|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000537342|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|),DOWNSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000541675|),EXON(MODIFIER||||493|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000518655|),EXON(MODIFIER||||550|DDX11L1|transcribed_unprocessed_pseudogene|NON_CODING|ENST00000515242|),EXON(MODIFIER||||551|DDX11L1|processed_transcript|NON_CODING|ENST00000456328|)
1	30923	rs140337953	G	T	100.0	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;EFF=DOWNSTREAM(MODIFIER|||||FAM138A|processed_transcript|CODING|ENST00000461467|),DOWNSTREAM(MODIFIER|||||FAM138A|protein_coding|CODING|ENST00000417324|),DOWNSTREAM(MODIFIER|||||MIR1302-10|miRNA|NON_CODING|ENST00000408384|),INTRON(MODIFIER||||177|MIR1302-10|antisense|NON_CODING|ENST00000469289|),INTRON(MODIFIER||||236|MIR1302-10|antisense|NON_CODING|ENST00000473358|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000423562|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000430492|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000438504|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000488147|),UPSTREAM(MODIFIER|||||WASH7P|unprocessed_pseudogene|NON_CODING|ENST00000538476|)
1	46402	.	C	CTGT	31.0	PASS	AA=.;RSQ=0.0960;AN=2184;AC=8;VT=INDEL;AVGPOST=0.8325;THETA=0.0121;ERATE=0.0072;LDAF=0.0903;AF=0.0037;ASN_AF=0.0017;AFR_AF=0.01;EFF=INTERGENIC(MODIFIER|||||||||)
1	47190	.	G	GA	192.0	PASS	AA=G;AVGPOST=0.9041;AN=2184;AC=29;VT=INDEL;LDAF=0.0628;THETA=0.0153;RSQ=0.2883;ERATE=0.0041;AF=0.01;AMR_AF=0.0028;AFR_AF=0.06;EFF=INTERGENIC(MODIFIER|||||||||)
1	51476	rs187298206	T	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	51479	rs116400033	T	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	51914	rs190452223	T	G	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	51935	rs181754315	C	T	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	51954	rs185832753	G	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	52058	rs62637813	G	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	52144	rs190291950	T	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	52185	.	TTAA	T	244.0	PASS	AA=.;AN=2184;LDAF=0.0124;VT=INDEL;AC=10;THETA=0.0232;RSQ=0.4271;AVGPOST=0.9840;ERATE=0.0037;AF=0.0046;ASN_AF=0.0035;AMR_AF=0.02;AFR_AF=0.0020;EFF=INTERGENIC(MODIFIER|||||||||)
1	52238	rs150021059	T	G	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	53234	.	CAT	C	227.0	PASS	AA=CAT;AVGPOST=0.9936;AN=2184;VT=INDEL;THETA=0.0119;AC=10;LDAF=0.0074;RSQ=0.6237;ERATE=0.0007;AF=0.0046;AMR_AF=0.0028;AFR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
1	54353	rs140052487	C	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	54421	rs146477069	A	G	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	54490	rs141149254	G	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	54676	rs2462492	C	T	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	54753	rs143174675	T	G	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55164	rs3091274	C	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55249	.	C	CTATGG	443.0	PASS	AA=C;AVGPOST=0.9073;ERATE=0.0063;RSQ=0.5891;AN=2184;THETA=0.0038;VT=INDEL;AC=151;LDAF=0.0968;AF=0.07;ASN_AF=0.16;AMR_AF=0.08;AFR_AF=0.03;EUR_AF=0.02;EFF=INTERGENIC(MODIFIER|||||||||)
1	55299	rs10399749	C	T	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55313	rs182462964	A	T	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55326	rs3107975	T	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55330	rs185215913	G	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55367	rs190850374	G	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55388	rs182711216	C	T	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55394	rs2949420	T	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55416	rs193242050	G	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55427	rs183189405	T	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55816	rs187434873	G	A	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55850	rs191890754	C	G	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)
1	55852	rs184233019	G	C	100.0	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;EFF=INTERGENIC(MODIFIER|||||||||)