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mOrcOrc1.1 alternate haplotype

Organism name:
Orcinus orca (killer whale)
BioSample:
SAMEA8800229
BioProject:
PRJEB52132
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2022/05/01
Assembly type:
alternate-pseudohaplotype
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_937001455.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CAKZJS01
Genome coverage:
34x
Linked assembly:
GCA_937001465.1 (principal pseudohaplotype of diploid)

IDs: 12880921 [UID] 33642768 [GenBank]

See Genome Information for Orcinus orca

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The assembly mOrcOrc1.1 is based on 34x PacBio data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/) and Hi-C data made publicly available by DNA Zoo (https://dnazoo.org); PMID:28336562. The assembly process included the following sequence of steps: initial ... PacBio assembly generation with Hifiasm, retained haplotig separation with purge_dups, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi. Finally, the assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Order and orientation of scaffolds in a repetitive region of chromosome 17 (
33.6Mb) is uncertain.  more

Global statistics

Total sequence length1,882,900,201
Total ungapped length1,882,900,201
Number of contigs12,410
Contig N50374,481
Contig L501,338
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)12,410

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Contig
Count
Ungapped
Length
Contig
N50
Spanned
Gaps
Unspanned
Gaps
unplaced1,882,900,20112,4101,882,900,201374,48100