Why most of alternative alleles are the alleles with major frequency?

Question

[star]

I find set of SNPs that in 4 different population have same minor allele frequency and also same alleles. but I find that most of my alternative alleles are the alleles with major frequency! how can I genetically explain it?

Answer 1

[Adrian Pelin]

Well... if it's something you expect to be heterozygous, 50/50, than major and minor make no difference, in one population you can see it as 45/55 and in another 51/49, so major and minor change places but that has no biological impact. Need more info on what it is you are actually doing, is this for human genome?

[star]

Yes, it is for human genome. I find alternative allele for my data according to reference allele and I expect most of alternative alleles be minor allele but they are major allele?

[Adrian Pelin]

In human genomes you would just be looking at heterozygous or homozygous SNPs, not major/minor. If you alternate allele is 0.9-1.0 in frequency, I would call this as a homozygous SNP. If it is 0.35-0.65, I would call it a heterozygous SNP.

This is assuming each of your datasets represents one individuals sequencing, rather then populations as you previously mentioned.