I have used PGDspider to convert a plink ped file to a Bayescan file. My ped file has just 5 SNPs for 2 populations in it. However, In the Bayescan formatted file outputted from PGDspider there are 7 loci and Index 1-7 in the first column. Can someone explain how the index relate back to the SNPs , why are there 7 loci there ? plink ped and map file checked multiple times and only 5 Snps. Many thanks for your time.
Bayescan output [loci]=7