Methods correlated more for rare than for common 1KG SAVs. Each plot shows the correlation of functional effect scores between one pair of prediction methods for two samples of 1,000 rare and 1,000 common SAVs from 1KG. Results for common SAVs are shown above diagonal, those for rare SAVs are given below the diagonal. With the order of the plots being 1 = SNAP2, 2 = CADD, 3 = PolyPhen-2, and 4 = SIFT, this implied that the plot corresponding to matrix element Pmn compared common SAVs between methods m and n (above diagonal), and the element Pnm rare SAVs between those two (below diagonal). For instance, row = 1/column = 2 gave the correlation between SNAP2 and CADD for common SAVs, while the transposed element row = 2/column = 1 correlated rare SAVs for SNAP2 and CADD. Each point represents a pair of scores for a single SAV, e.g. from SNAP2 and CADD. The predicted score for SIFT has been inverted (1-SIFT) to ease the comparisons. The shape and color reflect the overall method agreement. We use the following code: black squares mark SAVs for which all four methods agree on the binary classification. Blue circles mark SAVs for which all methods but SNAP2 agree; orange triangles mark all other points. The Pearson Correlation Coefficient for all 1,000 SAVs was added above each plot, along with the corresponding value for the full set of all SAVs (in brackets, as in Table 2).