Table 1. Genome data for Spisula subtruncata, xbSpiSubt1.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | xbSpiSubt1.1 | |
| Species | Spisula subtruncata | |
| Specimen | xbSpiSubt1 | |
| NCBI taxonomy ID | 31202 | |
| BioProject | PRJEB61702 | |
| BioSample ID | SAMEA110450095 | |
| Isolate information | xbSpiSubt1 (PacBio DNA sequencing)
xbSpiSubt5 (Illumina Hi-C sequencing) xbSpiSubt10 (Illumina RNA sequencing) |
|
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 67.8 | ≥ 50 |
| k-mer completeness | 100.0% | ≥ 95% |
| BUSCO ** | C:80.0%[S:78.5%,D:1.5%],
F:4.3%,M:15.7%,n:5,295 |
C ≥ 95% |
| Percentage of assembly
mapped to chromosomes |
99.25% | ≥ 95% |
| Sex chromosomes | None |
localised
homologous pairs |
| Organelles | Mitochondrial genome: 19.64 kb |
complete single
alleles |
| Raw data accessions | ||
| PacificBiosciences Sequel IIe | ERR11279106 | |
| Hi-C Illumina | ERR11439628 | |
| PolyA RNA-Seq Illumina | ERR11439629 | |
| Genome assembly | ||
| Assembly accession | GCA_963678985.1 | |
| Accession of alternate haplotype | GCA_963678955.1 | |
| Span (Mb) | 930.8 | |
| Number of contigs | 590 | |
| Contig N50 length (Mb) | 4.0 | |
| Number of scaffolds | 151 | |
| Scaffold N50 length (Mb) | 48.3 | |
| Longest scaffold (Mb) | 75.87 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).
** BUSCO scores based on the mollusca_odb10 BUSCO set using version v5.4.3. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Spisula_subtruncata/dataset/GCA_963678985.1/busco.