Table 1.
A summary of REAPR results on a range of genome sequences.
| Scaffold errorsa | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Genome assembly | Total length (Mb) | Gaps (n) |
Total gap length (bp) |
Original N50 (Mb) | Corrected N50b (Mb) |
Called by REAPR | False +ve | False -ve |
Error-free bases (%) |
| S. aureus TW20 k71 | 3.0 | 31 | 249 | 0.2 | 0.2 | 18 | 2 | 0 | 98.2 |
| S. aureus, GAGE Velvet | 2.9 | 128 | 17,688 | 0.8 | 0.2 | 24 | 0 | 1 | 89.5 |
| P. falciparum de novo k55 | 23.8 | 11,636 | 2,638,349 | 0.4 | 0.3 | 56 | 1 | 8 | 81.2 |
| P. falciparum v2.1.4 | 23.3 | 160 | 947 | 1.7 | 1.7 | 4 | 1 | 0 | 94.5 |
| P. falciparum v3 | 23.3 | 0 | 0 | 1.7 | 1.7 | NA | NA | NA | 94.9 |
| C. elegans WS228 | 100.3 | 0 | 0 | 17.5 | 17.5 | NA | NA | NA | 90.3 |
| M. musculus GRCm38 | 2725.5 | 522 | 77,999,939 | 130.7 | 100.2 | 41 | ND | ND | 80.1 |
| H. sapiens GRCh37 | 3095.7 | 360 | 234,350,278 | 155.3 | 146.4 | 6 | ND | ND | 79.1 |
aScaffold errors are not applicable (NA) when the assembly contains no gaps. Where a second genome sequence was unavailable for comparison, false-positives and false-negatives were not determined (ND).
bCorrected N50 refers to the N50 of the assembly after breaking the original assembly at breakpoints called by REAPR.