| program | total | TP | TN | FP | FN | NPV | PPV | sensitivity | specificity | accuracy |
| PPH2-var | 2600 | 1108 | 1159 | 141 | 192 | 85.8% | 88.7% | 85.2% | 89.2% | 87.2% |
| PPH2-div | 2600 | 1175 | 1076 | 224 | 125 | 89.6% | 84.0% | 90.4% | 82.8% | 86.6% |
| PROVEAN | 2600 | 1096 | 1146 | 154 | 204 | 84.9% | 87.7% | 84.3% | 88.2% | 86.2% |
| SIFT | 2600 | 1136 | 1123 | 177 | 164 | 87.3% | 86.5% | 87.4% | 86.4% | 86.9% |
| MT | 2600 | 1213 | 1132 | 168 | 87 | 92.9% | 87.8% | 93.3% | 87.1% | 90.2% |
MutationTaster displays automatic predictions for known harmless polymorphisms from the 1000 Genomes Project
and known disease mutations from NCBI ClinVar. For the comparison of MutationTaster with the other tools, we did not
consider the automatically displayed prediction (which is per se correct - or at least the same as our prior) but the actual
prediction made by the classifier, which is reflected by the probability-value.
(An automatic prediction with a probability below 0.5 means that MutationTaster would predict the other case
if it would not consider the known outcome of this variant.) The performance of MutationTaster on real life data, where known polymorphisms / disease mutations are
recognised, is hence even better than the
accuracy shown here.