FIGURE 3.

Empirical type I error rate of T _LMM based on the linear mixed-effect model (Eq. 4) against δ _causal . (A) When G _tested of tested SNPs is in HWD with δ _tested = 0.06. (B) When G _tested of tested SNPs is in HWE with δ _tested = 0. The true heritability of the phenotype is h ² = 0.5, the minor allele frequencies p _causal = p _tested = 0.2, and 10,000 independent replicates of phenotypes and genotypes for 65 sibling pairs were simulated for each δ _causal value. The blue circles are for T _LMM using the true heritability h ² = 0.5, and the black squares are for T _LMM while estimating h ² (results of ${\widehat{h}}^2$ are shown in Figure 1).