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mLutLut1.1 alternate haplotype

Organism name:
Lutra lutra (Eurasian river otter)
BioSample:
SAMEA994731
BioProject:
PRJEB35338
Submitter:
SC
Date:
2019/12/09
Assembly type:
alternate-pseudohaplotype
Assembly level:
Contig
Genome representation:
full
GenBank assembly accession:
GCA_902653095.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CACRWF01
Genome coverage:
63x
Linked assembly:
GCA_902655055.1 (principal pseudohaplotype of diploid)

IDs: 5386191 [UID] 15609768 [GenBank]

See Genome Information for Lutra lutra

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly mLutLut1.1 is based on 63x PacBio data, 58x 10X Genomics Chromium data, BioNano data and 17x Hi-C data generated at the Baylor College of Medicine. The assembly process included the following sequence of steps: initial PacBio assembly ... generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, Hi-C based scaffolding and improvement by the Aiden lab as part of a collaboration with DNA Zoo using 3D-DNA and Juicebox, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length1,081,484,062
Total ungapped length1,081,484,062
Number of contigs8,506
Contig N50174,900
Contig L501,412
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)8,506

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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
unplaced1,081,484,0628,5061,081,484,062174,90000
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