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.
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.
Is "user5054" the same as "user5504"? No? Exactly. Not only does order matter, it's incredibly vitally important.
GA are completely and totally different from each other. If this is in a coding region, then the resulting amino acid is undoubtedly changed (fun fact, the only exception is
TGA). If it's at a splice site then splicing is likely altered (AG is part of a splice acceptor site). If it's at the binding site of something then it wouldn't be surprised if it didn't bind any more.
Most association analyses are carried out at a single SNP level, so AG and GA are likely to indicate a heterozygous genotype at a particular location. However, the precise notation matters.
As @Emily_Ensembl has alluded to, for VCF files, A/G indicates unphased SNPs (order unknown, and shouldn't be considered in analyses), whereas A|G indicates phased SNPs (order matters).
It is possible to carry out association analyses by combining multiple variants into a single haplotype, in which case the order would also matter. It's unlikely that this is the case, because such haplotype variant analyses are substantially more complicated to carry out, and will typically be paired with information about SNP linkage (statistic D´ or r²).