Table 1.
Summary of detected SVs across 15 different data sets. SVs were reported with a min. size of 50bp using SURVIVOR based on Delly, Lumpy and Manta for Illumina or Sniffles for PacBio (min 10 reads) or Oxford Nanopore (min 5 reads) due to the lower coverage. Supplementary Table 5 has the full details of all the data sets used.
| Data Set | Tech. | Cov. | Avg. read length(bp) | Total SVs | DEL | DUP | INS | INV | TRA |
|---|---|---|---|---|---|---|---|---|---|
| Arabidopsis Col-0 | PacBio | 127× | 6,482 | 355 | 67 | 63 | 106 | 68 | 51 |
| Arabidopsis CVI | PacBio | 123× | 6,073 | 9,652 | 3,822 | 904 | 1,823 | 478 | 2,625 |
| Arabidopsis Col-0 x CVI F1 | PacBio | 155× | 11,206 | 11,935 | 4,974 | 582 | 4,049 | 567 | 1,763 |
| Arabidopsis Col-0 X CVI F1 | Illumina | 40× | 250 | 10,950 | 4,324 | 643 | 0 | 671 | 5,312 |
| GiaB HG002 (son) | PacBio | 69× | 8,540 | 19,131 | 7,957 | 1,084 | 9,656 | 232 | 202 |
| GiaB HG002 (son) | Illumina | 80× | 148 | 10,822 | 5,018 | 863 | 0 | 823 | 4,118 |
| GiaB HG003 (father) | PacBio | 32× | 6,284 | 11,964 | 5,296 | 408 | 6,048 | 99 | 113 |
| GiaB HG003 (father) | Illumina | 80× | 148 | 11,395 | 5,553 | 869 | 0 | 818 | 4,155 |
| GiaB HG004 (mother) | PacBio | 30× | 7,285 | 10,463 | 4,590 | 276 | 5,436 | 93 | 68 |
| GiaB HG004 (mother) | Illumina | 80× | 148 | 8,901 | 5,000 | 868 | 0 | 829 | 2,204 |
| NA12878 (healthy female) | PacBio | 55× | 4,334 | 15,499 | 6,734 | 606 | 7,880 | 160 | 119 |
| NA12878 (healthy female) | Oxford Nanopore | 28× | 6,432 | 26,657 | 19,074 | 761 | 6,376 | 334 | 112 |
| NA12878 (healthy female) | Illumina | 50× | 101 | 7,275 | 3,744 | 553 | 0 | 731 | 2,247 |
| SKBR3 (Breast Cancer) | PacBio | 69× | 9,872 | 19,165 | 7,268 | 1,019 | 10,391 | 328 | 159 |
| SKBR3 (Breast Cancer) | Illumina | 25× | 101 | 5,046 | 2,776 | 483 | 0 | 627 | 1,160 |