Table 4.
True CNVs detected in the Dd2 bulk genome
| Name | Chr. | Start Pos. | Size (bp) | Type | Support read* | Start Pos. | Size (bp) | Copy number detected by Ginkgo** in different bin sizes | Mappability^ | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Discordant read | Split read | 1 kb | 5 kb | 8 kb | 10 kb | ||||||||
| Pfmdr1 | 5 | 888316 | 81,935 | DUP | 53 | 0 | 888000 | 82,000 | 2 | 2 | Nd | Nd | 1 |
| Pf11-1 | 10 | 1524527 | 18,472 | DUP | 29 | 1 | 1520000 | 28,000 | 4 | 5 | N/A | N/A | 0.86 |
| Pf332 | 11 | 1956623 | 8719 | DUP | 0 | 8 | 1953000 | 13,000 | 4 | N/A | N/A | N/A | 0.92 |
*Detected by LUMPY based on discordant/split read detection, minimum number of supporting reads is 2
**For Ginkgo analysis, the minimum bin number of segmentation is 5
^For comparison, the mean mappability of the core genome is 0.99 and the mean mappability telomere/subtelomere regions including var gene clusters is 0.65
DUP duplication, N/A not applicable because the target CNVs will not be detected as the bin size (≥ 5× bin size) is larger than the size of the target CNVs, Nd not detected in the specified bin size