Hi all,

Sorry, if you find the question is basic. Could you please let me know why "A/T" and "C/G" called ambiguous SNP? why if such a SNP, say A/T, locate on one strand, we cannot T/A is on the opposite strand? 


Thank you
So if you know that a SNP is A/T on the forward strand it is T/A on the reverse strand. That's fine. You can check the reference genome and it's clear which is the reference allele and which is the alternative.

The ambiguity is when someone says something like "A is the minor allele" or "A is associated with this phenotype" or "A is the ancestral allele" and they are not clear about which strand they are talking about. Then you don't know if they mean forward A and T is the minor/phenotype-associated/ancestral, or if forward T reverse A is the minor/phenotype-associated/ancestral.