Table 2.

Type I Error under Substantial and Moderate Stratification

Marker Type and Test Locus MAF	No Adjustment	Known Strata	StratScore with 100 SNPs	StratScore with 200 SNPs	StratScore with 500 SNPs	StratScore with 800 SNPs
Highly Ancestry Informative
0.1	0.155 (0.079)	0.051 (0.047)	0.049 (0.046)	0.049 (0.047)	0.042 (0.046)	0.057 (0.058)
0.25	0.220 (0.097)	0.051 (0.047)	0.051 (0.041)	0.048 (0.039)	0.046 (0.041)	0.056 (0.057)
0.4	0.178 (0.090)	0.053 (0.053)	0.046 (0.049)	0.049 (0.048)	0.048 (0.045)	0.054 (0.057)
Random
0.1	0.160 (0.085)	0.049 (0.055)	0.050 (0.057)	0.048 (0.055)	0.041 (0.046)	0.054 (0.052)
0.25	0.223 (0.097)	0.047 (0.045)	0.059 (0.048)	0.049 (0.043)	0.049 (0.040)	0.059 (0.049)
0.4	0.166 (0.089)	0.054 (0.047)	0.059 (0.053)	0.047 (0.045)	0.044 (0.044)	0.047 (0.049)

Type I error results at nominal α = 0.05 for 500 cases and 500 controls, when a test locus with F_st = 0.03 is used. Each entry shows the type I error under substantial stratification, followed by the type I error under moderate stratification in parentheses. Simulation conditions are described in the text.