Figure 1

SIFT scores versus PolyPhen-2 scores. (a) (1 − SIFT score) plotted against PolyPhen-2 score. The red dashed lines correspond to the thresholds for predicting deleterious variants: 0.95 for SIFT and 0.2 for PolyPhen-2. The blue solid line corresponds to the LOESS curve (locally weighted scatterplot smoothing). (b) SIFT-based VT test p-values plotted against PolyPhen-2-based VT test p-values. Red plus signs correspond to genes that had tied rank 1 (posterior probabilities of association equal to 1) by the mixture model combining both tests. (c) Enlarged section of part b. (d) SIFT-based VT test z-values plotted against PolyPhen-2-based VT test z-values. Red plus signs correspond to genes that had tied rank 1 by the mixture model combining both tests. (e) Raw versus recalibrated PolyPhen-2 scores; solid line is the identical line. (f) Raw versus recalibrated PolyPhen-2 score-based VT test p-values.