Table 2.
Sequencing and assembly statistics, and accession numbers.
| BioProjects and Vouchers | CCGP NCBI BioProject | PRJNA720569 | ||||
| Genera NCBI BioProject | PRJNA766285 | |||||
| Species NCBI BioProject | PRJNA777152 | |||||
| NCBI BioSample | SAMN25872352 | |||||
| Specimen identification | CVI_PGR_0920_01 | |||||
| NCBI Genome accessions | Primary | Alternate | ||||
| Assembly accession | JAKSXS000000000 | JAKSXT000000000 | ||||
| Genome sequences | GCA_023349555.1 | GCA_023349535.1 | ||||
| Genome Sequence | PacBio HiFi reads | Run | 1 PACBIO_SMRT (Sequel II) run: 1.2M spots, 21.7G bases, 15.6 Gb | |||
| Accession | SRX15703629 | |||||
| Omni-C Illumina reads | Run | 1 ILLUMINA (Illumina NovaSeq 6000) run: 48.8M spots, 14.7G bases, 4.7 Gb | ||||
| Accession | SRX15703630 | |||||
| Genome Assembly Quality Metrics | Assembly identifier (quality codea) | fCebVio1(6.7.Q35.C68) | ||||
| HiFi read coverageb | 43.95× | |||||
| Primary | Alternate | |||||
| Number of contigs | 1,661 | 1,413 | ||||
| Contig N50 (bp) | 1,006,396 | 1,119,041 | ||||
| Contig NG50 (bp)b | 1,215,027 | 1,642,841 | ||||
| Longest contigs | 8,638,030 | 10,494,032 | ||||
| Number of scaffolds | 725 | 486 | ||||
| Scaffold N50 (bp) | 16,359,613 | 12,913,723 | ||||
| Scaffold NG50 (bp)b | 16,819,117 | 14,679,334 | ||||
| Largest scaffold | 25,343,235 | 27,304,300 | ||||
| Size of final assembly (bp) | 575,660,146 | 606,177,218 | ||||
| Gaps per Gbp (#Gaps) | 1,625 (936) | 1,529 (927) | ||||
| Indel QV (frameshift) | 46.5463 | 46.1586 | ||||
| Base pair QV | 35.7735 | 35.6002 | ||||
| Full assembly = 35.6837 | ||||||
| K-mer completeness | 94.1174 | 98.4403 | ||||
| Full assembly = 99.5766 | ||||||
| BUSCO completeness (actinopterygii ), n = 3640 | C | S | D | F | M | |
| Pc | 93.20% | 92.50% | 0.70% | 0.80% | 6.00% | |
| Ac | 97.40% | 96.50% | 0.90% | 0.70% | 1.90% | |
| Organelles | 1 partial mitochondrial sequence | JAKSXS010000725.1 | ||||
aAssembly quality code x·y·Q·C derived notation, from Rhie et al. (2020b). x = log10[contig NG50]; y = log10[scaffold NG50]; Q = Phred base accuracy QV (quality value); C = % genome represented by the first “n” scaffolds, following a known karyotype of 2n. In this case, 2n = 48 inferred from ancestral taxa. Quality code for all the assembly denoted by primary assembly (fCebVio1.0.p). BUSCO scores.
bRead coverage and NGx statistics have been calculated based on the estimated genome size of 494.2 Mb.
cP(rimary) and (A)lternate assembly values.