I'm running lositan on GBS data in two populations. Overall Fst is high between the populations, close to 0.6. I have several loci that are fixed between the two populations - so they have an Fst of 1 and heterozygosity of 1. However, they do not come out as outliers in the analysis. Is there a reason why Fst = 1 loci are not considered outliers? Some other High Fst loci do come out as outliers.
I have not used lositan, but is it possible those sites have many missing genotypes?