Fig. 3.

Q-Q plots of p values from the single-variant tests under the null hypothesis. The p values from the standard likelihood ratio test (LRT), penalized likelihood ratio test (PLRT), standard score test (Score) and small-sample-adjusted score tests (Score-Var-Adj and Score-Var-Kurt-Adj) are indicated by yellow squares, black circles, red point-down triangles, purple diamonds, and green point-up triangles, respectively. Panels (a), (b), and (c) show a rare, a low-frequency, and a common variant with $\widetilde{MAC}$ = 1, 87, and 1065 observations with genotype dosage G > 0. The results are based on 200 replicates of the null binary phenotypes Q ₂