Table 1.
Improvement in mappability of reads using DuploMap on multiple SMS whole-genome sequence datasets
| Genome | Sequencing | Median | Reads | Read | MM2 (%) | ΔMM2 + DuploMap (%) | ||
|---|---|---|---|---|---|---|---|---|
| technology | coverage | analyzed | length (N50) | MQ ≥ 10 | MQ ≥ 20 | MQ ≥ 10 | MQ ≥ 20 | |
| HG002 | PacBio CLR | 45 | 878k | 11 318 | 59.4 | 52.9 | +8.4 | +10.7 |
| HG003 | PacBio CLR | 20 | 416k | 10 999 | 59.9 | 53.5 | +9.8 | +11.3 |
| HG004 | PacBio CLR | 19 | 362k | 10 946 | 65.1 | 58.3 | +8.7 | +10.5 |
| HG002 | PacBio CCS | 29 | 300k | 13 480 | 65.7 | 58.9 | +14.9 | +19.5 |
| HG005 | PacBio CCS | 32 | 454k | 10 436 | 64.2 | 56.6 | +15.8 | +20.7 |
| HG001 | PacBio CCS | 29 | 381k | 10 004 | 71.6 | 63.7 | +15.0 | +21.2 |
| HG001 | ONT | 36 | 535k | 13 788 | 63.5 | 55.7 | +3.9 | +7.8 |
| HG002 | ONT | 58 | 464k | 54 352 | 64.5 | 58.0 | −1.5 | +1.7 |
The last four columns show the percentage of reads with high mapping quality (≥10 and ≥20) that overlap Long-SegDups regions in the Minimap2 alignments and the difference between Minimap2 + DuploMap alignments and Minimap2 alignments. MM2 = Minimap2.