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##fileformat=VCFv4.0
##problem1=The first base of the second ALT allele at 20:1234567 does not match the reference.
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AC,Number=-1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=-1,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description=Genotype>
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0\1:3,3
19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0\1:3,3
20 14370 rs6054257 G A 29 0 NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:-1,-1
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:-1,-1
20 1110696 rs6040355 A G,T 67 0 NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:-1,-1
20 1230237 . T . 47 0 NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:-1:56,60 0|0:48:4:51,51 0/0:61:2:-1,-1
20 1234567 microsat1 G GA,AAC 50 0 NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:-1:4 0/2:17:2 1/1:40:3
20 1235237 . T . -1 . . GT 0\0 0|0 ./.
X 10 rsTest AC A,ATG 10 . . GT 0 0/1 0|2
X 11 rsTest2 T A,G 10 q10;s50 . GT:DP:GQ 0:3:10 .:5:20 0:3:10
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