Table 5.
Errors in CABOG assemblies
| Genome | Dataset | Chimeric | Chimeric | Bad | Bad | Collapsed |
|---|---|---|---|---|---|---|
| join | end | end | contig | tandem | ||
| P.gingivalis | F1 | 0 | 0 | 0 | 0 | 4 |
| P.gingivalis | F1+M2 | 3 | 8 | 1 | 1 | 11 |
| P.gingivalis | F1+S1 | 0 | 0 | 1 | 0 | 7 |
| P.gingivalis | M2+S1 | 0 | 1 | 2 | 0 | 9 |
| P.sp CNPT3 | F1 | 0 | 1 | 0 | 0 | 1 |
| P.sp CNPT3 | F2 | 0 | 2 | 0 | 0 | 4 |
| P.sp CNPT3 | F1+S1 | 0 | 0 | 0 | 0 | 1 |
| P.sp CNPT3 | F2+S1 | 0 | 0 | 0 | 0 | 0 |
The analysis included contigs at least 2 kb long. Chimeric join, a concatenation of unrelated sequences of at least 1 kb. Chimeric End, concatenation of less than 1 kb to a contig end. Bad end, less than 1 kb of unaligned sequence at a contig end. Bad Contig, unaligned contig. Collapsed Tandem, multiple alignments between a contig and the reference, partially overlapping in either sequence. Errors were estimated by analysis of alignments to reference sequences. Estimates were confirmed by two other alignment-based methods.