SNP FST file

This is the pairwise fst output for individual snps. The non-informative sites have been suppressed, so all the rows are the SNPs that meet the coverage criteria.

the columns are:

col1: scaffold number
col2: SNP position on scaffold
col3: number of snps in window (because the window size was set to 1 to get individual SNP estimates, all values should be 1)
col4: fraction of the window covered (more relevant for sliding window analyses)
col5: mean coverage at SNP over all four populations
col6: pairwise Fst for Tac-C:Tac-S
col7: pairwise Fst for Tac-C:Puy-C
col8: pairwise Fst for Tac-C:Puy-S
col9: pairwise Fst for Tac-S:Puy-C
col10: pairwise Fst for Tac-S:Puy-S
col11: pairwise Fst for Puy-C:Puy-S

population codes: 1=Tac-C, 2=Tac-S, 3=Puy-C, 4=Puy-S

Note that the Fst values that are 0.000000000 are not polymorphic SNPs for a given pairwise comparison. For example, snp 'NW_006799939.1 19911'
has an Fst of 0.00000000 in the Tac-C:Tac-S comparison because it is not polymorphic between Tac-C and Tac-S. From the sync file:

NW_006799939.1 19911 A 21:0:0:0:0:0 21:0:0:0:0:0 39:0:0:2:0:0 37:0:0:5:0:0

you can see that Tac-C and Tac-S are fixed for the A allele (21 counts in each). The only reason it is included as a SNP in the .fst file is because
it is polymorphic in the Puy-C & Puy-S populations (and polmorhic in the comparison across Tac & Puy).