I used vcftools to get counts of alleles (using --counts) and the output was written to a .frq.count file. The header column and first few lines of this file are as follows:
CHROM || POS || N_ALLELES || N_CHR || {ALLELE:COUNT}
1 || 232603151 || 2 || 44 || 3:42 4:2
1 || 232604178 || 2 || 42 || 3:36 1:6
1 || 232606161 || 1 || 22 || 4:22
1 || 232606219 || 1 || 28 || 2:28
My interpretation of the above for each column:
CHROM = chromosome, POS = position, N_ALLELES = number of different alleles at this site, N_CHR = total number of alleles that we have information for at this site (from all individuals), ALLELE:COUNT = allele identity : number of alleles of this identity (and listed again if the site is biallelic).
My question is: How do I interpret the allele identity, or does it mean something different? Do the numbers refer to different nucleotides?
