Table 2 Summary of assembly metric of the Clarias gariepinus genome, including the primary (Prim), haplotype-1 (Hap1) and haplotype-2 (Hap2).
From: Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus)
Category | Quality Metrics | Primary | Haplotype-1 | Haplotype-2 |
|---|---|---|---|---|
General | Total assembly size (Mb) | 969.67 | 968.90 | 954.25 |
GC content | 39.0 | 38.98 | 38.93 | |
Repeat content (%) | 43.94 | 44.07 | 43.29 | |
Continuity | No. Contigs | 47 | 142 | 212 |
Contig N50 (Mb) | 33.71 | 32.12 | 19.53 | |
No. Scaffolds | 47 | 135 | 175 | |
Scaffolds N50 (Mb) | 33.71 | 34.0 | 33.18 | |
Scaffold L50 | 12 | 12 | 12 | |
Number of gaps | 0 | 180 | 115 | |
% Unplaced sequences (Mbp) | 1.01 (12.69) | 1.70 (16.5) | 2.63 (25.12) | |
% Gapless length | 100 | 99.99 | 98.54 | |
Base accuracy | QV | 41.86 | 38.14 | 39.39 |
Structural accuracy | k-mer completeness (%) | 98.32 | 83.61 | 81.93 |
Concondantly mapped PE reads (%) | 96.75 | 96.69 | 97.81 | |
BUSCO duplicate (%) | 0.55 | 0.58 | 1.26 | |
BUSCO missing (%) | 0.70 | 0.58 | 0.99 | |
Reliably phased blocks (%) | — | 96.87 | 94.00 | |
Functional completeness | Protein coding genes | 25,655 | 23,577 | 24,223 |
BUSCO complete (%) | 99.18 | 99.32 | 98.84 | |
BUSCO fragmented (%) | 0.12 | 0.11 | 0.16 | |
NR annotation (%) | 87.80 | 86.17 | 87.00 | |
Swissprot/Uniprot annotation (%) | 68.23 | 63.12 | 64.45 | |
Transcripts alignment rate (%) | 95.52 | 94.61 | 94.09 |
