Description
- Assembly Name: Mnor_HA_v2
- Assembly Type: Haploid
- Assembly Level: Scaffold
- Genome Representation: Full
- Accession: GCA_964058975.1
Assembly Statistics
| Statistic | Value |
|---|---|
| Assembly length (Mbp) | 19.73 |
| GC % | 29.92 |
| Contig # | 422377 |
| Contig N50 (Mbp) | 70524 |
| Contig L50 | 82325 |
| Contig N90 (Mbp) | 21391 |
| Contig L90 | 272177 |
| Scaffold # | 216567 |
| Scaffold N50 (Mbp) | 220856 |
| Scaffold L50 | 24545 |
| Scaffold N90 (Mbp) | 38152 |
| Scaffold L90 | 111071 |
| Scaffolds >= 10 kb | 192940 |
| BUSCO % (arthropoda_odb10) | C:99.7 [S:72, D:3.7], F:14, M:10, n:1013 |
Annotation Statistics
| Statistic | Value |
|---|---|
| Gene # | 42189 |
| Transcript # | 42189 |
| Avg exons per transcript | 5.7 |
| Avg gene length (bp) | 50276 |
| Avg transcript length (bp) | 50276 |
| Avg exon length (bp) | 282 |
| Avg intron length (bp) | 9804 |
Notes: Assembly statistics were calculated for the primary genome assembly GCA_964058975.1 (CAXKWB01.fasta.gz) using Quast (v5.2.0; Mikheenko et al. 2018). Busco statistics (Manni et al., 2021) were taken from Unneberg et al. (2024). Annotation statistics were calculated for GCA_964058975.1_Mnor_HA_v2_genomic.gff using AGAT (v1.4.1; Dainat, 2024).
BUSCO notation: C: Complete; S: Single-copy; D: Duplicated; F: Fragmented; M: Missing; n: Total BUSCO genes included in the dataset (here: arthropoda_odb10). See also the official BUSCO manual.
Publication(s)
The Meganyctiphanes norvegica data displayed in the genome portal comes from:
Unneberg, P., Larsson, M., Olsson, A., Wallerman, O., Petri, A., Bunikis, I., Vinnere Pettersson, O., Papetti, C., Gislason, A., Glenner, H., Cartes, J. E., Blanco-Bercial, L., Eriksen, E., Meyer, B., & Wallberg, A. (2024). Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins. Nature Communications, 15(1), 6297. https://doi.org/10.1038/s41467-024-50239-7The tools used by to calculate the statistics shown on top of this page are described in:
Dainat J. (2024). AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v1.4.1). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Molecular Biology and Evolution, 38(10), 4647–4654. https://doi.org/10.1093/molbev/msab199
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., & Gurevich, A. (2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics, 34(13), i142–i150. https://doi.org/10.1093/bioinformatics/bty266
Funding
The study in which the genome data was generated (Unneberg et al. 2024) was funded by:
Swedish Research Council Formas 2017-00413
U.S. National Science Foundation, Division Of Ocean Sciences (NSF OCE) grants 1316040 and 1948162
Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab, grant ID KAW 2017.0003.
Page last updated: 05/11/2024