Table 1 Comparison of various metrics T.P., F.P., F.N., Precision, Recall and F-Measure in SNP calling between different tools
From: Better quality score compression through sequence-based quality smoothing
Smoothing algorithm | T.P. | F.P. | F.N. | Precision | Recall | F-Measure |
|---|---|---|---|---|---|---|
None (original files) | 2588159 | 219803 | 1493731 | 0.9217 | 0.6341 | 0.7513 |
YALFF | 2603620 | 221368 | 1478264 | 0.9216 | 0.6378 | 0.7539 |
Quartz | 2661218 | 237820 | 1420672 | 0.9180 | 0.6520 | 0.7624 |
Leon | 2278517 | 204803 | 1803366 | 0.9175 | 0.5582 | 0.6941 |
Illumina 8bin | 2546518 | 216128 | 1535370 | 0.9218 | 0.6239 | 0.7441 |
Pblock p =2 | 2574111 | 218405 | 1507773 | 0.9218 | 0.6306 | 0.7489 |
Pblock p =4 | 2558612 | 216995 | 1523273 | 0.9218 | 0.6268 | 0.7462 |
Rblock t =1.1 | 2550179 | 216738 | 1531706 | 0.9217 | 0.6248 | 0.7447 |
Rblock t =1.15 | 2526704 | 215721 | 1555181 | 0.9213 | 0.6190 | 0.7405 |
QVZ 0.6 | 2588704 | 225730 | 1493180 | 0.9198 | 0.6342 | 0.7507 |
QVZ 0.8 | 2588773 | 223210 | 1493112 | 0.9206 | 0.6342 | 0.7510 |