Table 2.
Comparison of deleterious SNPs across programs
| Program | Number of variants classified | Deleterious | Conditional probability of pairwise prediction | ||||
|---|---|---|---|---|---|---|---|
| Number | % | MAPP (%) | SIFT (%) | VarioWatch (%) | PolyPhen-2 (%) | ||
| MAPP | 3,199 | 1,472 | 46.0 | 100 | 58 | 65 | 78 |
| SIFT | 3,562 | 1,603 | 45.0 | 62 | 100 | 71 | 69 |
| VarioWatch | 3,429 | 1,882 | 54.9 | 55 | 58 | 100 | 64 |
| PolyPhen-2 | 3,333 | 1,757 | 52.7 | 65 | 58 | 67 | 100 |
Each program characterizes a different number of deleterious alleles. The pairwise prediction is calculated by conditioning on the probability of a program predicting a variant as deleterious, given that the comparison program already has predicted it as deleterious. For example, in the first row, among those 1,472 variants that MAPP classifies as deleterious, only 58% are also classified as deleterious by SIFT.