Table 2:
Assembly quality assessment of Cassava TME204 haplotigs generated by hifiasm v0.15.3
| Quality Category | Quality Metric | Haplotype 1 | Haplotype 2 |
|---|---|---|---|
| General | Contig Size (Mb) | 762 | 706 |
| Continuity | Contig N50 (Mb) | 18 | 26 |
| Contig NG50 (Mb) | 18 | 22 | |
| Largest contig (Mb) | 41 | 44 | |
| Base accuracy | QV a | 45.23 | 48.94 |
| k-mer completeness (%)a | 79.6 | 79.1 | |
| Structural accuracy | k-mer false duplications (%)a | 3.0 | 2.4 |
| BUSCO duplicate (%) | 4.9 | 4.2 | |
| Reference asmgene duplicate (%) | 1.6 | 0.8 | |
| Reference gene transfer duplicate (%)b | 3.8 | 3.2 | |
| Reliable blocks (%) | 97.2 | 97.5 | |
| Congruent genetic markers (%) | 99.8 | 99.9 | |
| Functional completeness | BUSCO complete (%) | 99.0 | 98.8 |
| Reference asmgene complete (%) | 95.2 | 95.4 | |
| Reference gene transfer rate (%)b | 96.3 | 96.5 | |
| Transcript alignment rate (%) | 99.3 | 99.4 |
a
QV and k-mer completeness for the combined assembly is 46.63 and 98.4%, respectively. The k-mer false duplication rate for the combined assembly is 3.5%.
b
Calculated on the basis of the number of lifted genes regardless of completeness.