Clarification on .meanP output of fastSTRUCTURE

[Hannah Patricia Chua]

Good day everyone!

The .meanP output lists the mean allele frequencies of each SNP location across k populations (k columns). But it doesn't explicitly say which allele is being referred to here? Is it the reference allele or the non-reference (mutant) allele? I'd like to know the answer so I know if my mutations/SNPs appear closer to the reference or further from the reference.

Example, if the allele being measured here is the reference allele, and I notice my SNP in a certain location for a certain population (e.g. Population 2) is significantly lower (0.02) compared to other populations (0.9x), this means that it appears to be further from the reference, because then the mean allele frequency of the non-reference allele for my SNP in Population 2 would be 0.98 (1-0.02). And vice versa, if the allele being referred to here is the non-reference allele. 

Not entirely sure if my understanding of the whole concept is accurate, please correct me if I am wrong. Thank you!