Table 3.

Simulation results with MA data using GCTA model with the true heritability $h^2=0.5$

	100 causal SNPs	5000 causal SNPs	100 causal SNPs from 3 genes
GCTA	0.3176 (.0268)	0.2890 (.0358)	0.3614 (.0395)
Enet	0.4014 (.0393)	0.4018 (.0538)	0.3965 (.0474)
HERRA	0.5248 (.0342)	0.5142 (.0586)	0.5246 (.0427)
B_herra	0.5217 (.0260)	0.5150 (.0447)	0.5192 (.0339)
Enet (remove 60% covariates)	0.4541 (.0364)	0.4614 (.0371)	0.4408 (.0403)
HERRA (remove 60% covariates)	0.4988 (.0356)	0.4941 (.0469)	0.4966 (.0338)
B_herra (remove 60% covariates)	0.5015 (.0260)	0.4892 (.0426)	0.4965 (.0306)

The mean and the standard deviation (in parentheses) of the estimated heritabilities between the simulation replicates are presented