Table 1.

Simulated Type I Error Rate for Dichotomous Traits over 1,000 Replicates

Method	α = 0.05					α = 0.01
No. of Neutral Rare Variants					No. of Neutral Rare Variants
0	4	8	16	32	0	4	8	16	32
Without Covariates
SKAT+	0.046	0.040	0.047	0.043	0.040	0.007	0.005	0.013	0.005	0.006
SKAT+ (rs)	0.063	0.046	0.059	0.062	0.049	0.017	0.012	0.017	0.014	0.013
SKAT	0.050	0.036	0.049	0.049	0.040	0.007	0.006	0.011	0.004	0.006
SKAT-O	0.041	0.041	0.052	0.052	0.045	0.009	0.008	0.010	0.004	0.005
aSPU	0.037	0.037	0.047	0.048	0.041	0.005	0.007	0.009	0.005	0.005
With Covariates
SKAT+	0.050	0.042	0.038	0.051	0.039	0.004	0.011	0.002	0.012	0.004
SKAT+ (rs)	0.062	0.047	0.049	0.066	0.050	0.012	0.016	0.010	0.017	0.008
SKAT	0.042	0.039	0.044	0.049	0.045	0.006	0.008	0.003	0.013	0.008
SKAT-O	0.055	0.046	0.054	0.057	0.051	0.006	0.013	0.005	0.012	0.008
aSPU	0.045	0.046	0.049	0.053	0.051	0.005	0.011	0.007	0.016	0.011

SKAT+ (rs) represents the SKAT+ method based on resampling p values.