Misassemblies
| Genome | H. influenzae | S. cerevisiae | D. melanogaster | Human 21 | Human 22 |
| Full Coverage (∼10-fold) | |||||
| Deletions | 2 | 5 | 102 | 13 | 26 |
| Mean length (bp) | 440 | 470 | 1660 | 360 | 430 |
| Insertions | — | 1 | 7 | — | 2 |
| Mean length (bp) | — | 350 | 990 | — | 400 |
| Hanging ends | — | — | 3 | — | 4 |
| Mean length (bp) | — | — | 190 | — | 800 |
| Other | — | — | 3 | 1 | — |
| Misassemblies | — | — | (note[ii]) | (note[iii]) | — |
| Half Coverage (∼5-fold) | |||||
| Deletions | 3 | 4 | 116 | 26 | 41 |
| Mean length (bp) | 290 | 3790 | 1600 | 220 | 340 |
| Insertions | 2 | — | 12 | 2 | 3 |
| Mean length (bp) | 380 | — | 670 | 90 | 390 |
| Hanging ends | 1 | 2 | 42 | 11 | 14 |
| Mean length (bp) | 78 | 450 | 460 | 1330 | 826 |
| Other | — | — | 5 | 4 | 5 |
| misassemblies | — | — | (note[iv]) | (note[v]) | (note[vi]) |
[i] See Figure 6A,B for an illustration of the various types of common misassemblies. Other misassemblies are as follows:
[ii] Two contigs of lengths 1 kb and 138 kb were exchanged in a supercontig. Two correct contigs of lengths 313 kb and 169 kb, which were separated in the genome by 60 bp, were glued along a 440-bp segment that appeared at the left end of the left contig, and also at the right end of the right contig, yielding a chimeric contig in the final assembly (which we call a slipped join). There was a standard misassembly (Fig. 6B), occurring in a 4.8-Mb supercontig.
[iii] At the end of a supercontig, there was a contig of length 10 kb, which aligned at a distant location in the genome relative to the rest of the supercontig.
[iv] A supercontig of 467 kb had a standard major misassembly. A supercontig of 1.4 Mb had two stray contigs of 5 kb and 2 kb. A contig had a deletion of 29 kb. Contigs of 27 kb and 37 kb were misassembled.
[v] A 3.4-Mb supercontig had a standard major misassembly. Contigs of 9 kb and 24 kb had slipped joins. A 12-kb contig at the end of a 2.6-Mb supercontig was misassembled.
[vi] A 4.5-Mb supercontig had a standard major misassembly. A 14-kb contig had a slipped join. A 303-kb supercontig was slightly misassembled near one of its ends. A supercontig had a spurious contig of length 5 kb. A 9-kb supercontig consisted of two incorrectly linked contigs.