How To Interpret Snps

Question

[Ankur]

a.) If I have a SNP like A/C/G/T does that mean the position can either be A/C or G or T. eq (rs762551). Does the order matter?

b.) By looking at a SNP how would I know if its a common allele or a rare allele.

c.) If I have a SNP saying -/A how would I interpret its an insertion or a deletion (eg rs72558196). Can I write it other way around i.e A/-.

d.) What does a SNP like this indicate (rs4646281) -/AAGTTGGT/TGGTAAGT. I thought SNP's were single nucleotides.

Answer 1

[Wen.Huang]

a) no b) you would need population genotype data c) yes, reference is arbitrary d) it indicates it is an indel, its just that some non-SNPs get into dbSNP, dbSNP is really a variant database now, though SNP is the great majority.

[Ankur]

If I have a SNP saying -/A how would I interpret its an insertion or a deletion (eg rs72558196)

[Ankur]

Thanks for your answers. If I have a SNP saying -/A how would I interpret its an insertion or a deletion (eg rs72558196)

[Maxime Lamontagne]

I think it's a deletion because the ancestral allele is A. (dbSBP)

[Ankur]

If the ancestral allele is 'A' then why is it deletion?