Table 1 PREP-Mt performance results subdivided by gene
From: PREP-Mt: predictive RNA editor for plant mitochondrial genes
Gene | No. of Species | TP | TN | FP | FN | Specificity | Sensitivity | Accuracy | Balanced Accuracy |
|---|---|---|---|---|---|---|---|---|---|
Complex I | |||||||||
   nad1 | 10 | 135 | 1632 | 14 | 33 (2) | 99.1 | 80.4 (98.5) | 97.4 (99.1) | 89.8 (98.8) |
   nad2 | 9 | 140 | 2337 | 22 | 42 (9) | 99.1 | 76.9 (94.0) | 97.5 (98.8) | 88.0 (96.5) |
   nad3 | 22 | 274 | 1217 | 8 | 47 (4) | 99.3 | 85.4 (98.6) | 96.4 (99.2) | 92.4 (99.0) |
   nad4 | 9 | 133 | 2358 | 19 | 12 (1) | 99.2 | 91.7 (99.3) | 98.8 (99.2) | 95.5 (99.2) |
   nad4L | 8 | 49 | 303 | 5 | 0 (0) | 98.4 | 100.0 (100.0) | 98.6 (98.6) | 99.2 (99.2) |
   nad5 | 10 | 122 | 3647 | 29 | 10 (4) | 99.2 | 92.4 (96.8) | 99.0 (99.1) | 95.8 (98.0) |
   nad6 | 10 | 70 | 995 | 16 | 15 (3) | 98.4 | 82.4 (95.9) | 97.2 (98.2) | 90.4 (97.2) |
   nad7 | 8 | 117 | 1655 | 5 | 22 (1) | 99.7 | 84.2 (99.2) | 98.5 (99.7) | 91.9 (99.4) |
   nad9 | 12 | 75 | 1236 | 7 | 5 (3) | 99.4 | 93.8 (96.2) | 99.1 (99.2) | 96.6 (97.8) |
Complex II | |||||||||
   sdh3 | 7 | 6 | 391 | 12 | 11 (2) | 97.0 | 35.3 (75.0) | 94.5 (96.6) | 66.2 (86.0) |
   sdh4 | 8 | 10 | 361 | 14 | 16 (3) | 96.3 | 38.5 (76.9) | 92.5 (95.6) | 67.4 (86.6) |
Complex III | |||||||||
   cob | 13 | 117 | 2834 | 19 | 25 (8) | 99.3 | 82.4 (93.6) | 98.5 (99.1) | 90.9 (96.5) |
Complex IV | |||||||||
   cox1 | 9 | 38 | 2936 | 7 | 7 (5) | 99.8 | 84.4 (88.4) | 99.5 (99.6) | 92.1 (94.1) |
   cox2 | 19 | 193 | 2644 | 22 | 33 (11) | 99.2 | 85.4 (94.6) | 98.1 (98.9) | 92.3 (96.9) |
   cox3 | 12 | 80 | 1793 | 21 | 11 (2) | 98.8 | 87.9 (97.6) | 98.3 (98.8) | 93.4 (98.2) |
Complex V | |||||||||
   atp1 | 10 | 21 | 2926 | 10 | 8 (1) | 99.7 | 72.4 (95.5) | 99.4 (99.6) | 86.0 (97.6) |
   atp4 | 7 | 51 | 730 | 21 | 18 (8) | 97.2 | 73.9 (86.4) | 95.2 (96.4) | 85.6 (91.8) |
   atp6 | 12 | 88 | 1893 | 11 | 10 (2) | 99.4 | 89.8 (97.8) | 99.0 (99.3) | 94.6 (98.6) |
   atp8 | 8 | 16 | 757 | 10 | 10 (2) | 98.7 | 61.5 (88.9) | 97.5 (98.5) | 80.1 (93.8) |
   atp9 | 19 | 91 | 792 | 1 | 17 (0) | 99.9 | 84.3 (100.0) | 98.0 (99.9) | 92.1 (99.9) |
Cytochrome c biogenesis | |||||||||
   ccmB | 9 | 216 | 1013 | 14 | 63 (6) | 98.6 | 77.4 (97.3) | 94.1 (98.4) | 88.0 (98.0) |
   ccmC | 9 | 187 | 1212 | 24 | 26 (1) | 98.1 | 87.8 (99.5) | 96.5 (98.2) | 92.9 (98.8) |
   ccmFc | 6 | 84 | 1631 | 23 | 30 (10) | 98.6 | 73.7 (89.4) | 97.0 (98.1) | 86.1 (94.0) |
   ccmFn | 6 | 155 | 2249 | 39 | 38 (21) | 98.3 | 80.3 (88.1) | 96.9 (97.6) | 89.3 (93.2) |
Ribosomal proteins | |||||||||
   rpl2 | 4 | 2 | 1057 | 14 | 6 (4) | 98.7 | 25.0 (33.3) | 98.1 (98.3) | 61.8 (66.0) |
   rpl5 | 9 | 45 | 919 | 14 | 5 (3) | 98.5 | 90.0 | 98.1 (98.3) | 94.2 (96.1) |
   rpl6 | 3 | 0 | 138 | 3 | 0 (0) | 97.9 | - | 97.9 (97.9) | - |
   rpl16 | 9 | 33 | 692 | 6 | 13 (2) | 99.1 | 71.7 (94.3) | 97.4 (98.9) | 85.4 (96.7) |
   rps1 | 3 | 2 | 295 | 4 | 5 (5) | 98.7 | 28.6 (28.6) | 97.1 (97.1) | 63.6 (63.6) |
   rps2 | 7 | 25 | 1489 | 15 | 7 (5) | 99.0 | 78.1 (83.3) | 98.6 (98.7) | 88.6 (91.2) |
   rps3 | 7 | 54 | 2183 | 19 | 33 (11) | 99.1 | 62.1 (83.1) | 97.7 (98.7) | 80.6 (91.1) |
   rps4 | 6 | 83 | 1116 | 22 | 18 (6) | 98.1 | 82.2 (93.3) | 96.8 (97.7) | 90.1 (95.7) |
   rps7 | 8 | 6 | 664 | 19 | 2 (1) | 97.2 | 75.0 (85.7) | 97.0 (97.1) | 86.1 (91.5) |
   rps10 | 5 | 8 | 266 | 9 | 0 (0) | 96.7 | 100.0 (100.0) | 96.8 (96.8) | 98.4 (98.4) |
   rps11 | 3 | 0 | 222 | 1 | 0 (0) | 99.6 | - | 99.6 (99.6) | - |
   rps12 | 17 | 87 | 1142 | 13 | 5 (1) | 98.9 | 94.6 (98.9) | 98.6 (98.9) | 96.7 (98.9) |
   rps13 | 10 | 34 | 554 | 8 | 5 (2) | 98.6 | 87.2 (94.4) | 97.8 (98.3) | 92.9 (96.5) |
   rps14 | 5 | 2 | 239 | 7 | 0 (0) | 97.2 | 100.0 (100.0) | (97.2) (97.2) | 98.6 (98.6) |
   rps19 | 6 | 16 | 242 | 11 | 9 (3) | 95.7 | 64.0 (84.2) | 92.8 (94.9) | 79.8 (89.9) |
Other | |||||||||
   matR | 8 | 73 | 4109 | 30 | 20 (7) | 99.3 | 78.5 (91.3) | 98.8 (99.1) | 88.9 (95.3) |
   mttB | 8 | 100 | 1087 | 41 | 23 (12) | 96.4 | 81.3 (89.3) | 94.9 (95.7) | 88.8 (92.8) |
Overall | 370 | 3,038 | 55,956 | 609 | 660 (171) | 98.9 | 82.2 (94.7) | 97.9 (98.7) | 90.5 (96.8) |