Given genotype information (SNP allele frequencies) from different pooled populations, how can I calculate the probability (or significance, or some confidence value) of the populations having different allele frequencies? I'm not terribly interested (and it's easy to do anyway) in estimating the actual allele frequencies, just the probability of it differing.
E.g. if I have alleles A and C, with observed frequencies of 9/3 and 6/1, I can estimate minor allele frequency to 0.33 and 0.17, respectively, but is the difference significant - and what is the p-value?
Or more generally: given two set of samples from binomial distributions with success probabilities p1 and p2, how can I calculate the probability of p1=p2?
It seems this would be a rather fundamental task, but I haven't found any good source on how to do this, and my statistics-fu seems to have rusted...