Table 2. Type I error rates of four tests in a homogenous population and in the case of no population stratification for qualitative traits.

Population Structures	Test	Alpha	Un-corrected	GC	PC-linear	PC-nonp
A Homogenous Population	SingleVariant	0.01	0.0131	0.0076	0.0129	0.01178
		0.001	0.00168	0.00112	0.00182	0.00172
	Regional	0.01	0.00992	0.00958	0.00992	0.0121
		0.001	0.00124	0.00116	0.00122	0.00162
No Population Stratification	SingleVariant	0.01	0.01082	0.0053	0.01	0.0079
		0.001	0.00169	0.0007	0.00162	0.0014
	Regional	0.01	0.0113	0.00904	0.01176	0.00926
		0.001	0.00178	0.00138	0.00166	0.00134

Note: “A homogenous population” means k₀ = 1 in simulation set 1; “no population stratification” means model 0 in simulation set 2.