Table 2.
Measuring the Accuracy of CNV Break Points by Base Pairs Under Different Sequencing Depth and Mutation Rates Between Duplicated Segments
| Mutation rate between duplicated segments | Depth of coverage | Length of predicted CNVs (bp) | Length of overlap (bp) | False discovery rate | False negative rate |
|---|---|---|---|---|---|
| 1% (504000 bp) | 30X | 506755 | 502183 | 0.9% | 0.3% |
| 15X | 506162 | 501291 | 1.0% | 0.5% | |
| 5X | 507703 | 495074 | 1.8% | 2.5% | |
| 0.5% (493000 bp) | 30X | 492271 | 488114 | 0.9% | 1.0% |
| 15X | 500460 | 488387 | 2.4% | 0.9% | |
| 5X | 501139 | 483830 | 3.5% | 1.9% | |
| 0.1% (492000 bp) | 30X | 469821 | 452120 | 3.8% | 9.1% |
| 15X | 465518 | 433495 | 6.9% | 11.9% | |
| 5X | 462193 | 417340 | 9.7% | 15.2% |
False discovery rate is the ratio between length of false positive regions and total length of predicted CNVs, while false negative rate is the ratio between length of false negative regions and total length of true CNVs.