why A/T or C/G are ambiguous SNPs?

Question

[seta]

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

[Carambakaracho]

Hi seta, I'm afraid your question is not exactly clear and hence might make it difficult to give you the best answer.

This is what I think: Afaik, ambiguous nucleotides are single letters other than A/T/G/C, see for example IUPAC codes at bioinformatics.org. Any ambiguity in one strand necessarily results in an ambiguity on the opposite strand - a W in one means a W in the other. However, such ambiguities are rarely used, only few programs can deal with characters other than A/T/C/G and N

[seta]

Sorry if it isn't clear.

My mean is: for strand unambiguous SNPs, genotypes called on different strands are readily identifiable (e.g., A/G alleles on one strand are T/C alleles on the opposite strand). But it isn't true for ambiguous SNPs (A/T or C/G); if such a SNP, say A/T, locate on one strand, we cannot say that T/A is on the opposite strand, I would like to know the reason of it?

Thank you for any help and explanation

Answer 1

[Emily]

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.