I have taken two groups high fertile and low fertile having 5 bulls in each group. Semen samples were collected from each bull and genomic DNA isolation was done for all animals of both groups and amplification was done of the desired gene. 200 clones have taken from both groups (40 clones from a single bull) and subsequently, sequencing was done of all clones and I got two SNPs. Both groups have both SNPs (at the same positions) but the percentage (%) varies about 35-40% between both groups. Scientists have arisen the question that How I can say SNPs only on such a small sample size? It might be due to minor allele frequency. So, how I can relate this data to minor alleles or SNPs? please suggest to me....thank you in advance.

and one question is that can I consider semen as a population because of the single dose of semen has millions of sperm cells