Table 1.
Comparison of assembly metrics between v6 assemblies, previous reference genome versions, and the CC-1690 assembly
| Assembly strain/version | CC-503 v4 | CC-503 v5 | CC-503 v6 | CC-4532 v6 | CC-1690 |
|---|---|---|---|---|---|
| Year | 2008 | 2012 | 2022 | 2022 | 2020 |
| Technology | Sanger | Sanger + 454 | PacBio + Illumina | PacBio + Illumina | Nanopore + Illumina |
| Total length (Mb) | 112.3 | 111.1 | 111.5 | 114.0 | 111.1 |
| Unplaced scaffolds/contigs | 71 | 37 | 42 | 40 | 1 |
| Unplaced length (Mb) | 9.68 | 2.20 | 1.45 | 1.72 | 1.65 |
| Total contigs | 2,739 | 1,495 | 145 | 120 | 21 |
| Contig N50 (Mb) | 0.09 | 0.22 | 2.92 | 2.65 | 3.58 |
| GC (%) | 64.1 | 64.1 | 64.1 | 64.1 | 64.1 |
| Gaps/Ns (%) | 7.54 | 3.65 | 1.66 | 0.81 | <0.01 |
| Transposable elements (%) | 9.84 | 10.61 | 10.80 | 12.42 | 11.24 |
| Microsatellites (%) | 1.32 | 1.43 | 1.72 | 1.76 | 1.65 |
| Satellite DNA (%) | 3.33 | 3.68 | 4.79 | 5.25 | 5.09 |
Unplaced sequence was assembled as scaffolds in v4 and v5, and contigs in all other assemblies. The single unplaced contig in the released version of the CC-1690 assembly was later assembled to the right arm of chromosome 15 (Chaux-Jukic et al. 2021).