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Homozygous VS Heterozygous

meharmehar Member ✭✭


I have two SNP calls as shown below:

chr1 86208198 . G C 903.25 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=0.117;DP=33;Dels=0.00;FS=6.463;HRun=0;HaplotypeScore=8.5544;MQ=43.69;MQ0=0;MQRankSum=-0.506;QD=27.37;ReadPosRankSum=0.272;SB=-414.82 GT:AD:DP:GQ:PL 1/1:2,30:33:18.60:936,19,0

chr16 14895239 . C T 671.60 . AC=1;AF=0.50;AN=2;BaseQRankSum=-0.582;DP=33;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=1.5317;MQ=53.44;MQ0=0;MQRankSum=0.970;QD=20.35;ReadPosRankSum=-0.711;SB=-292.79 GT:AD:DP:GQ:PL 0/1:3,30:33:6.39:701,0,6

The first SNP is categorized as 1/1 and the second SNP as 0/1. For both the SNP's the variant allele ratio are 30/32=0.9375 and 30/33=0.909 which are approximately equal and above 0.9. On what criteria one SNP is determined as 0/1 and the other as 1/1?

As per my knowledge both the SNPs should be 1/1. Could anyone comment the reason for this discrepancy?


Best Answer


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