Table 1.
Recall rates of breakpoint detection of iMGEins and novel insertions, popoolationTE, TEMP, RetroSeq and MELT in the simulation set 1
| Simulation type | MGE type | Ratio of SNVs | iMGEins | PoPoolationTE | TEMP | RetroSeq | MELT |
|---|---|---|---|---|---|---|---|
| Non variant (%) | LINE | 100.00 | 22.00 | 90.00 | 2.00 | 98.00 | |
| SINE | 94.00 | 84.00 | 96.00 | 24.00 | 98.00 | ||
| LTR | 96.00 | 86.00 | 100.00 | 62.00 | 100.00 | ||
| DNA | 98.00 | 86.00 | 98.00 | 26.00 | 98.00 | ||
| SNV (%) | LINE | 10% | 100.00 | 10.00 | 0.00 | 0.00 | 40.00 |
| 20% | 100.00 | 0.00 | 0.00 | 20.00 | 0.00 | ||
| 30% | 100.00 | 0.00 | 0.00 | 0.00 | 0.00 | ||
| 40% | 100.00 | 0.00 | 0.00 | 10.00 | 0.00 | ||
| 50% | 90.00 | 0.00 | 0.00 | 25.00 | 0.00 | ||
| SINE | 10% | 95.00 | 60.00 | 0.00 | 25.00 | 10.00 | |
| 20% | 100.00 | 0.00 | 0.00 | 40.00 | 0.00 | ||
| 30% | 100.00 | 0.00 | 0.00 | 25.00 | 0.00 | ||
| 40% | 95.00 | 5.00 | 0.00 | 35.00 | 0.00 | ||
| 50% | 100.00 | 0.00 | 0.00 | 50.00 | 0.00 | ||
| LTR | 10% | 90.00 | 70.00 | 0.00 | 45.00 | 55.00 | |
| 20% | 100.00 | 0.00 | 0.00 | 55.00 | 0.00 | ||
| 30% | 85.00 | 0.00 | 0.00 | 50.00 | 0.00 | ||
| 40% | 95.00 | 0.00 | 0.00 | 40.00 | 0.00 | ||
| 50% | 95.00 | 0.00 | 0.00 | 60.00 | 0.00 | ||
| Random (%) | LINE | 98.00 | 3.33 | 0.00 | 34.67 | 0.00 | |
| SINE | 98.67 | 6.00 | 0.00 | 36.00 | 0.00 | ||
| LTR | 98.00 | 0.67 | 0.00 | 34.00 | 0.00 | ||
| DNA | 100.00 | 0.00 | 0.00 | 36.00 | 0.00 | ||
| True Positives | 975 | 183 | 192 | 328 | 218 | ||
| False Positives | 21 | 16,109 | 22 | 663 | 9 | ||