From: SNVHMM: predicting single nucleotide variants from next generation sequencing
Model | MQ | BQ | TP | FP | TN | FN | Sensitivity(%) | Specificity(%) | Accuracy(%) | F-score |
---|---|---|---|---|---|---|---|---|---|---|
SNVHMM | 50 | 20 | 281 | 77 | 115 | 24 | 92.13 | 59.89 | 79.68(MVC = 7) | 0.8477 |
40 | 20 | 283 | 83 | 109 | 22 | 92.78 | 56.77 | 78.87(MVC = 6) | 0.8435 | |
30 | 20 | 273 | 77 | 115 | 32 | 89.51 | 59.89 | 78.07(MVC = 9) | 0.8336 | |
30 | 10 | 289 | 79 | 113 | 16 | 94.75 | 58.85 | 80.88(MVC = 9) | 0.8588 | |
20 | 10 | 279 | 86 | 106 | 26 | 91.47 | 55.21 | 77.46(MVC = 8) | 0.8328 | |
10 | 5 | 281 | 87 | 105 | 24 | 92.13 | 54.69 | 77.67(MVC = 7) | 0.8351 | |
SNVMix2_TI | 50 | 20 | 291 | 109 | 83 | 14 | 95.40 | 43.23 | 75.25 | 0.8255 |
40 | 20 | 294 | 113 | 79 | 11 | 96.39 | 41.14 | 75.05 | 0.8258 | |
30 | 20 | 294 | 115 | 77 | 11 | 96.39 | 40.10 | 74.65 | 0.8235 | |
30 | 10 | 295 | 113 | 79 | 10 | 96.72 | 41.15 | 75.25 | 0.8275 | |
20 | 10 | 294 | 117 | 75 | 11 | 96.39 | 39.06 | 74.25 | 0.8212 | |
10 | 5 | 295 | 118 | 74 | 10 | 96.72 | 38.54 | 74.25 | 0.8217 | |
SNVMix2_TO | 50 | 20 | 283 | 86 | 106 | 22 | 92.79 | 55.21 | 78.27 | 0.8398 |
40 | 20 | 287 | 93 | 99 | 18 | 94.10 | 51.56 | 77.67 | 0.8380 | |
30 | 20 | 287 | 96 | 96 | 18 | 94.10 | 50.00 | 77.06 | 0.8343 | |
30 | 10 | 284 | 105 | 87 | 21 | 93.11 | 45.31 | 74.65 | 0.8184 | |
20 | 10 | 291 | 105 | 87 | 14 | 95.40 | 45.31 | 76.06 | 0.8302 | |
 | 10 | 5 | 291 | 104 | 88 | 14 | 95.41 | 45.83 | 76.26 | 0.8314 |