Table 1 Method performance on PMD *
From: Better prediction of functional effects for sequence variants
| Â | Method | F effect (Eqn. 3) | F neutral (Eqn. 3) | Q2 (Eqn. 4) | MCC (Eqn. 5) |
|---|---|---|---|---|---|
human | SNAP2 | 78.0% ± 0.6 | 46.3% ± 1.3 | 68.8% ± 0.7 | 0.24 ± 0.01 |
|  | PolyPhen-2 | 78.4% ± 0.4 ** | 45.1% ± 1.1 ** | 68.9% ± 0.5 ** | 0.23 ± 0.01 ** |
|  | SNAP | 74.9% ± 0.5 | 46.7% ± 1.1 | 65.8% ± 0.6 | 0.22 ± 0.01 |
|  | SIFT | 72.2% ± 0.6 | 49.0% ± 1.0 | 63.6% ± 0.6 | 0.23 ± 0.01 |
non-human | SNAP2 | 79.9% ± 0.3 | 45.8% ± 0.8 | 70.7% ± 0.4 | 0.26 ± 0.01 |
|  | PolyPhen-2 | 77.1% ± 0.4 | 44.7% ± 0.8 | 67.6% ± 0.5 | 0.22 ± 0.01 |
|  | SNAP | 77.2% ± 0.3 | 45.5% ± 0.9 | 67.9% ± 0.5 | 0.23 ± 0.01 |
|  | SIFT | 77.0% ± 0.3 | 45.8% ± 0.8 | 67.7% ± 0.4 | 0.23 ± 0.01 |