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. 2022 Jun 6;113(6):624–631. doi: 10.1093/jhered/esac021

Table 2.

Sequencing and assembly statistics, and accession numbers

Bio projects and vouchers CCGP NCBI BioProject PRJNA720569
Genera NCBI BioProject PRJNA763234
Species NCBI BioProject PRJNA782591
NCBI BioSample SAMN21436765
Specimen identification Photo voucher MWFB Acc 2021-49
NCBI Genome accessions Primary Alternate
Assembly accession GCA_022086475.1 GCA_022086895.1
Genome sequences JAJLPC000000000 JAJLPC000000000
Genome sequence PacBio HiFi reads Run 3 PACBIO_SMRT (Sequel II) runs: 5.5M spots, 80.5G bases, 55.6Gb
Accession SRR17460090
Hi-C Illumina reads Run 2 Illumina HiSeq X Ten runs: 738.2M spots, 222.9G bases, 74.4Gb
Accession SRX13631283
Genome Assembly Quality Metrics Assembly identifier (quality codea) rActMar1 (6.C.Q66)
HiFi Read coverageb 30X
Primary Alternate
Number of contigs 198 4308
Contig N50 (bp) 75 081 387 2 165 034
Longest Contigs 223 757 816 15 093 301
Number of scaffolds 49 2508
Scaffold N50 (bp) 146 229 595 18 355 815
Largest scaffold 361 952 230 118 325 371
Size of final assembly (bp) 2 319 354 532 2 209 870 670
Gaps per Gbp 54 818
Indel QV (Frame shift) 46.59 46.59
Base pair QV 66.58 65.45
Full assembly = 66.00
k-mer completeness 92.881 88.25
Full assembly = 99.01
BUSCO completeness
(vertebrata) n = 3354
C S D F M
Pc 96.70% 95.80% 0.90% 0.90% 2.40%
Ac 91.20% 89.90% 1.30% 1.50% 7.30%
Organelles 1 Complete mitochondrial sequence CM039065.1

Assembly quality code x.y.Q-derived notation, from Rhie et al. (2020). x = log10[contig NG50]; y = log10[scaffold NG50]; Q = Phred base accuracy QV (quality value). C = chromosome level. BUSCO Scores. (C)omplete and (S)ingle; (C)omplete and (D)uplicated; (F)ragmented and (M)issing BUSCO genes. n, number of BUSCO genes in the set/data base. bp, base pairs.

Read coverage has been calculated based on a genome size of 2.6 Gb.

P(rimary) and (A)lternate assembly values.