To empirically evaluate the relationship between the reduction in the over-dispersion factor and the number of structure inference SNPs used in the correction of PS, we focused on the reconstructed study PLCOca-NHSco, where the most extensive confounding by PS was observed (λ = 1.090). We conducted PCA using nested sets of 1,500, 3,000, 6,000, 9,000 and 12,898 population structure inference SNPs (Table 7).
