PMC full text:
Published online 2011 Jan 6. doi: 10.1371/journal.pone.0015925
Table 2
Comparison of mapping strategies.
| seed | No | No | No | No | Yes | No |
| Max. # gap openings | 0 | 0 | 1 | 2 | 1 | 2 |
| Max. # mismatches | 5 | 4 | 5 | 5 | 5 | 5 |
| PE-SW-remap | No | No | No | No | No | Yes |
| Mapped | 94.83 | 93.78 | 97.79 | 97.59 | 96.45 | 99.25 |
| Proper pair | 89.66 | 87.81 | 95.10 | 94.75 | 92.57 | 98.28 |
| Mate not mapped | 4.30 | 5.16 | 1.71 | 1.90 | 2.94 | 0.24 |
| Mate mapped to wrong chromosome | 0.53 | 0.50 | 0.59 | 0.58 | 0.57 | 0.46 |
30×106 paired-end reads were used for mapping. Long insertions and deletions with 12 bp were allowed for mapping strategies including gaps. If seeding was used, the seed length was 32 bp.