Table 2.
Identified candidate CNV and SVs in the F1 progenies.
| Variants | P59 | P6 | P97 | P8 | P9 |
|---|---|---|---|---|---|
| CNV | |||||
| Called by CNVcaller | 1426 | 1016 | 2835 | 418 | 307 |
| Filtering by genotype and effective window | 6 | 8 | 15 | 5 | 2 |
| Candidate de novo CNVs | 1 | 1 | 2 | 0 | 0 |
| SVs | |||||
| (1) Called by BreakDancer, and specific in F1 animals | 1570 | 1411 | 1633 | 2058 | 2107 |
| After removal of common SVs in every two animals, and the read depth <50%, manual check | 3 | 9 | 13 | 12 | 13 |
| (2) Called by Lumpy | 3609 | 3116 | 3406 | 2697 | 3082 |
| After removal of common SVs in every two animals, and the read depth <50%, manual check | 3 | 2 | 0 | 3 | 1 |