I used vcftools for calculation the Fst value between two populations (pop1 and pop2) using the below command:
./vcftools --vcf file.vcf --weir-fst-pop population_1.txt --weir-fst-pop population_2.txt --out pop1_vs_pop2
However, some Fst value sounds strange to me. For example, please consider the allele frequency of some variants in two pops and the obtained Fst value:
SNP AF_pop1 AF_pop2 Fst value snp1 0.74 0.43 0.037 snp2 0.33 0.79 0.423 snp3 0.69 0.03 0.42
As you see, the frequency of snp1 and snp2 is similar between the two populations, but there is a huge difference in the related Fst values. Similarly, while the allele frequency of snp2 and snp3 is very different between populations, the related Fst values are similar. I'm confused with such an output. Could you please let me know your idea about it, is it reasonable to you?
Thank in advance