Table 1. SVC count and percentage of total by variant types from combined-set across all studies.
The most common variant type was deletion followed by CNV. All CNV types combined (rows 1, 7, and 8 in Table 1) total 972,335. We also generated SVC for each variant type (ie. CNV, in/del, etc.) and by individual studies (study-set) for QA/QC and analysis between types and studies of interest. The study-set generated a total of 2.5 million SVCs versus 3.4 million SVCs from the combined-set.
| Variant Type | Percent
Total (%) |
SVC Count |
|---|---|---|
| deletion | 35% | 1194270 |
| copy number loss | 18% | 633268 |
| mobile element insertion | 15% | 517506 |
| duplication | 9% | 303790 |
| insertion | 7% | 232552 |
| indel | 5% | 186658 |
| copy number gain | 5% | 169876 |
| copy number variation | 5% | 169191 |
| Others | 1% | 17810 |
| Total | 100% | 3424921 |