Table 2.
Summary of SVs validated from Delly predictions
| Delly call type | Illumina calls
|
PacBio calls
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Illumina library with call
|
Deletions
|
Insertions
|
Unsupported
|
|||||||||
| Long | Short | Both | Pdel | Simple | Pdup | Tandem duplication | Simple | Inversions | Reference only | Cov | Complex | |
| Tandem duplication | 22 | 19 | 7 | 0 | 1 | 2 | 29 | 0 | 0 | 5 | 7 | 4 |
| Inversion | 21 | 31 | 13 | 0 | 3 | 18 | 1 | 0 | 23 | 1 | 2 | 17 |
| Deletion | 22 | 691 | 24 | 9 | 701 | 1 | 0 | 2 | 0 | 5 | 11 | 8 |
Two separate paired-end Illumina libraries of different sizes were constructed and sequenced from NA12878 and were subjected to the Delly structural variation finder. Events that were confirmed by both the long and short libraries are enumerated under ‘Both’. PacBio Calls include the number of Delly predictions that were confirmed using manual examination of dot plots. The unsupported column includes any Delly events for which we found either no evidence for the indicated SV despite reasonable coverage (reference only) or for which we had insufficient coverage to reliably confirm the corresponding Delly call. Cov, coverage; PDel, proximal deleted substring; PDup, proximal duplicated substring.