Population stratification and average genome heterozygosity
Principal Component Analysis (PCA) was performed using PCAngsd after obtaining genotype likelihoods with ANGSD including all individuals and plotted with R. To assess global levels of heterozygosity, the unfolded SFS was calculated for each sample separately using ANGSD and realSFS with the following quality filter parameters: -uniqueOnly 1 - remove_bads 1 -only_proper_pairs 1 -trim 10 -C 50 -baq 1 -minMapQ 30 -minQ 30 -setMaxDepth 200 - doCounts 1 -GL 2 -doSaf 1.