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 | 247 | 59 | 133 | 58 | 80.98 | 69.27 | 76.46(MVC = 4) | 0.8085 |
40 | 20 | 254 | 66 | 126 | 51 | 83.28 | 65.63 | 76.46(MVC = 4) | 0.8128 | |
30 | 20 | 256 | 70 | 112 | 49 | 83.93 | 65.54 | 76.05(MVC = 4) | 0.8114 | |
30 | 10 | 236 | 63 | 129 | 69 | 77.38 | 67.19 | 73.44(MVC = 5) | 0.7815 | |
20 | 10 | 273 | 111 | 81 | 32 | 89.51 | 42.19 | 71.23(MVC = 3) | 0.7925 | |
10 | 5 | 273 | 110 | 82 | 32 | 89.51 | 42.71 | 71.43(MVC = 2) | 0.7936 | |
SNVMix2_TI | 50 | 20 | 303 | 160 | 32 | 2 | 99.34 | 16.67 | 67.40 | 0.7891 |
40 | 20 | 305 | 174 | 18 | 0 | 100 | 9.38 | 64.99 | 0.7781 | |
30 | 20 | 305 | 174 | 18 | 0 | 100 | 9.38 | 64.99 | 0.7781 | |
30 | 10 | 305 | 173 | 19 | 0 | 100 | 9.89 | 65.19 | 0.7791 | |
20 | 10 | 305 | 191 | 1 | 0 | 100 | 0.52 | 61.56 | 0.7615 | |
10 | 5 | 305 | 192 | 0 | 0 | 100 | 0 | 61.37 | 0.7606 | |
SNVMix2_TO | 50 | 20 | 245 | 75 | 117 | 60 | 80.32 | 60.94 | 72.84 | 0.7840 |
40 | 20 | 261 | 88 | 104 | 44 | 85.57 | 54.17 | 73.44 | 0.7982 | |
30 | 20 | 266 | 90 | 102 | 39 | 87.21 | 53.13 | 74.04 | 0.8048 | |
30 | 10 | 274 | 92 | 100 | 31 | 89.83 | 52.08 | 75.25 | 0.8167 | |
20 | 10 | 283 | 125 | 67 | 22 | 92.78 | 34.90 | 70.42 | 0.7938 | |
 | 10 | 5 | 290 | 134 | 58 | 15 | 95.08 | 30.21 | 70.02 | 0.7956 |