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?
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?