Table 1 Performance of the Altools platform (detection of polymorphisms). Statistical analysis of Altools polymorphism calling was carried out at five simulated coverage levels
Coverage | 4x | 10x | 20x | 40x | 100x |
|---|---|---|---|---|---|
dgwsim generated polymorphisms | 121,388 | 122,074 | 121,368 | 121,540 | 121,638 |
dgwsim generated SNPs | 107,054 | 107,411 | 106,766 | 107,372 | 107,277 |
dgwsim generated indels | 14,334 | 14,663 | 14,602 | 14,168 | 14,361 |
Altools total called SNPs | 35,714 | 81,647 | 102,493 | 105,164 | 105,580 |
Altools correctly called SNPs | 35,650 | 81,482 | 102,274 | 104,910 | 105,243 |
Altools false positive SNPs | 64 | 165 | 219 | 254 | 337 |
Altools total called indels | 3049 | 8307 | 11,134 | 11,542 | 11,657 |
Altools correctly called indels | 3040 | 8280 | 11,112 | 11,503 | 11,621 |
Altools false positive indels | 9 | 27 | 22 | 39 | 36 |
PPV | |||||
SNPs | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
Indels | 0.33 | 0.76 | 0.96 | 0.98 | 0.98 |
Sensitivity | |||||
SNPs | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
Indels | 0.21 | 0.56 | 0.76 | 0.81 | 0.81 |