Table 5.
Phasing information and accuracy for each library from Aquila versus Longranger.
| Method | W (kb) | PB N50 (Mb) | Max. PB (Mb) | Long errors | Mismatch errors | Phased in GiaB | Long error (%) | Mismatch error (%) | |
|---|---|---|---|---|---|---|---|---|---|
| L1 | Aquila | 304.3 | 25.1 | 104.5 | 453 | 1492 | 1,613,542 | 0.02 | 0.16 |
| Longranger | 12.7 | 49.3 | 1092 | 2860 | 1,862,855 | 0.04 | 0.19 | ||
| HapCUT2 | 58.1 | 131.6 | 565 | 2336 | 1,748,918 | 0.02 | 0.19 | ||
| L2 | Aquila | 41.1 | 0.6 | 4.9 | 486 | 1532 | 1,697,703 | 0.02 | 0.15 |
| Longranger | N/A | N/A | N/A | N/A | N/A | N/A | N/A | ||
| HapCUT2 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | ||
| L3 | Aquila | 214.5 | 12.7 | 57.5 | 499 | 1481 | 1,323,959 | 0.03 | 0.18 |
| Longranger | 12.5 | 57.7 | 1124 | 2679 | 1,868,719 | 0.04 | 0.20 | ||
| HapCUT2 | 55.4 | 121.5 | 451 | 2216 | 1,763,129 | 0.02 | 0.18 | ||
| L4 | Aquila | 267.4 | 22.1 | 104.5 | 608 | 2182 | 1,313,659 | 0.03 | 0.23 |
| Longranger | 17.2 | 61.3 | 1638 | 5345 | 1,583,816 | 0.06 | 0.37 | ||
| HapCUT2 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | ||
| L5 | Aquila | 151.7 | 15.8 | 62.4 | 719 | 2388 | 1,342,247 | 0.04 | 0.24 |
| Longranger | 13.4 | 46.8 | 1682 | 5171 | 1,586,187 | 0.06 | 0.37 | ||
| HapCUT2 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | ||
| L6 | Aquila | 216.9 | 10.6 | 63.6 | 641 | 2218 | 1,147,993 | 0.04 | 0.26 |
| Longranger | N/A | N/A | N/A | N/A | N/A | N/A | N/A | ||
| HapCUT2 | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
W weighted fragment length of the library, PB N50 phase blocks length N50, Max. PB maximum phase block length, Phased in GiaB number of phased SNPs overlapping with callset v3.3.2, N/A not applicable because Longranger could not complete runs in wgs mode.