Table 7 shows that, as expected, using a larger number of SNPs in the correction of PS results in the detection of more subtle population structure. For example, with 12,898 SNPs, we can detect four significant PCs (P-value <0.05 based on the Tracy-Widom test). With 6,000 or fewer population structure inference SNPs, only two significant PCs can be identified. Also, the over-dispersion factor of the test with the adjustment of PCs chosen by the proposed permutation procedure decreases as the number of SNPs used in the PCA increases. When 12,898 SNPs are used in the correction of PS, we can reduce the over-dispersion factor to an acceptable level (λ = 1.032) with the adjustment of 3 PCs.
