Table 2.
Quality assessment of the channel catfish genome assembly Coco_2.0 and blue catfish genome assembly Billie_1.0 using International Genome 10 K (G10K) Consortium metrics [30]
| Assemblies | Assembly metrics | Blue catfish Billie 1.0 | Channel catfish Coco 2.0 |
|---|---|---|---|
| Overall quality | x.y.P.Q.C | > 6. > 30.–.39.99 | > 12. > 29.–.37.97 |
| 1. Continuity | 1.1. Contig NG50 (x) | 6.7 Mb | 12.8 Mb |
| 1.2. Scaffolds NG50 (y) | 30.4 Mb | 29.2 Mb | |
| 1.3. Gaps per Gb | 170 | 82 | |
| 2. Structural accuracy | 2.1. Reliable blocks | 2.8–33.9 Mb | 7.2–33.6 Mb |
| 2.2. False duplications | - | - | |
| 2.3. Curation | Manual | Manual | |
| 3. Base accuracy | 1.1 Base pair QV (Q) | 39.17 | 37.15 |
| 3.2. k-mer completeness | 98.65% | 98.05% | |
| 4. Haplotype phasing | 1.2 Phase block NG50 (P) | - | - |
| 5. Functional completeness | 1.3 Genes | 26,575 | 27,504 |
| 5.2. Transcript mappability | - | - | |
| 6. Chromosome status | 1.4 Assigned (C) | 99% | 97% |
| 1.5 Sex chromosome | X | X and Ya | |
| 1.6 Mitochondrial genome | One complete allele, KM576102.1 | One complete allele, NC_003489.1 | |
| Additional assurances | Bionano optical mapping | 306X genome coverage | 233X genome coverage |
| Additional assurances | Genetic linkage mapping | 690 K SNP arrays | 690 K SNP arrays |
aY chromosome available in GenBank from prior research