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.