Computing the fixation index

In the section Genome Diversity and subsection FST and Selective Sweeps, click on the Per-SNP FSTs tool. This will add a score for each SNP indicating how fixed on different alleles the SNP is. The autosome SNP dataset should be chosen by default, as well as the population E2-5. Select the dataset F2-5 for the second population. Use the estimated genotype again for the Data source. To filter for more reliable SNPs enter the minimum total read count of twenty for a population. This is the five we used per-individual earlier times the four individuals in the populations. Leave the rest of the options as the default. Then click the Execute button.