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In the following vcf file, the AF allele frequency of ALT allele is 1.0. Does it mean that it is not a true SNP of interest? Does it also mean that ALT allele always occurs and REF allele never occurs in the population?

Also not sure how allele count AC=37 is being calculated.

Chr1 pos=565286, REF=C, ALT=T, Info AC=37; AF=1.0 Format GT:AC:AF:NC Child=1:11:1.0:+T=4,-T=7 mother=1:26:1.0:+T=8,-T=18,

Cheers, Ambi.

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  • $\begingroup$ Please let us know a bit more about your .vcf file. Spontaneously, I would say that all individuals in that file have a different allele (ALT) than the human reference (REF). It"s impossible to give an interpretation based on these information though. Allele count is defined as: "AC : allele count in genotypes, for each ALT allele, in the same order as listed" in the .vcf specification file. It is not really calculated, it is counted. $\endgroup$ – AlexDeLarge Sep 12 '16 at 14:56

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