Table 6 Type I error rates of five tests based on simulation set 2 for qualitative traits.

Model	Test	Alpha	Un-corrected	GC	PC-linear	BiasedPerm	PC-nonp
1	Single Variant	0.01	0.0384	0.0128	0.0409	0.02564	0.007
	Single Variant	0.001	0.0132	0.0022	0.0151	0.00652	0.0005
	Regional	0.01	0.0248	0.0095	0.0288	0.02752	0.0114
	Regional	0.001	0.0056	0.0009	0.005	0.00584	0.0008
2	Single Variant	0.01	0.0453	0.0174	0.0087	0.00514	0.0088
	Single Variant	0.001	0.0182	0.0048	0.0006	0.00032	0.001
	Regional	0.01	0.0366	0.0115	0.0121	0.00684	0.0093
	Regional	0.001	0.0078	0.0007	0.0016	0.00046	0.0012

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