I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, for 6 out of 49 samples, the nucleotides are 'GA', and for the rest, they are 'AG', so only the order is different. I am not a biologist, but my basic genetics knowledge says that those two are semantically the same. However, obviously, plink does not agree with me and it associates this SNP with a small p-value since 'GA' samples have a higher value for the phenotype than 'AG' samples. I am very new to SNP analysis, any help is appreciated.
Is there any difference between SNPs 'AG' and 'GA' in association analyses?
snp;gwas
Could you please show us the context in which this appears, as you seem to be interpreting this differently to Devon.If it's appearing as you say, GA and AG, then Devon is right, this usually means that the sequence goes ###AG### or ###GA###, which are two very different sequences.If, however, as you're implying, the sequences are actually ###G### or ###A###, then semantically, the two ways of writing it have the same outcome. Normally, however, this is written as A/G or G/A.Alternatively, you're looking at genotypes, which would usually appear as A|G and G|A. In this case, both individuals are heterozygotes, and in terms of the individual SNP they are the same. However the side of the pipe is relevant as this tells you which homologous chromosome it is on. This allows you to calculate LD with respect to neighbouring SNPs, and to determine the actual sequences of the proteins in that individual.