Fig. 5.

Q-Q plots of the p values from the single-variant tests and variant-collapsing tests of markers in subregion 4 (see Table 1 and Fig. 2a). Panels (a) to (c) show the p values from the single-variant tests for a rare, low-frequency, and common functional variant, respectively; the tests are 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), which are indicated by yellow squares, black circles, red point-down triangles, purple diamonds, and green point-up triangles, respectively. Panels (d) to (f) show the results from the variant-collapsing tests when they include the rare variants, rare and low-frequency variants, and all the variants within the region. The p values from the weighted burden tests, SKAT, and SKAT-O are, respectively, represented by pink circles, blue cross marks, and green diamonds. The calculations are based on 200 simulated data sets in SIMPHEN