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mLutLut1.2

Organism name:
Lutra lutra (Eurasian river otter)
BioSample:
SAMEA994731
BioProject:
PRJEB35339
Submitter:
SC
Date:
2020/07/31
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_902655055.2 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CACRWI02
Genome coverage:
63x

IDs: 7920831 [UID] 21712228 [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 mLutLut1.2 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. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. 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 length2,438,458,878
Total ungapped length2,438,368,607
Gaps between scaffolds0
Number of scaffolds44
Scaffold N50149,004,807
Scaffold L507
Number of contigs229
Contig N5030,403,456
Contig L5023
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)44

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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
non-nuclear
Assembly Unit: Primary Assembly (GCA_902655054.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR738403.1n/an/a0
Chromosome 2LR738404.1n/an/a0
Chromosome 3LR738405.1n/an/a0
Chromosome 4LR738406.1n/an/a0
Chromosome 5LR738407.1n/an/a0
Chromosome 6LR738408.1n/an/a0
Chromosome 7LR738409.1n/an/a0
Chromosome 8LR738410.1n/an/a0
Chromosome 9LR738411.1n/an/a0
Chromosome 10LR738412.1n/an/a0
Chromosome 11LR738413.1n/an/a0
Chromosome 12LR738414.1n/an/a0
Chromosome 13LR738415.1n/an/a0
Chromosome 14LR738416.1n/an/a0
Chromosome 15LR738417.1n/an/a0
Chromosome 16LR738418.1n/an/a0
Chromosome 17LR738419.1n/an/a0
Chromosome 18LR738420.1n/an/a0
Chromosome XLR738421.1n/an/a0
Chromosome YLR738422.1n/an/a0
unplacedn/an/an/a23

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All2,438,442,342432,438,352,071149,004,8071850
Chromosome 1223,449,2031223,444,803223,449,203100
Chromosome 2210,645,4371210,639,737210,645,437120
Chromosome 3201,318,9981201,317,498201,318,99830
Chromosome 4197,708,2861197,701,786197,708,286130
Chromosome 5165,805,7451165,794,045165,805,745240
Chromosome 6154,425,5111154,420,011154,425,511110
Chromosome 7149,004,8071148,999,567149,004,807110
Chromosome 8144,745,5941144,743,061144,745,59460
Chromosome 9144,085,4641144,080,464144,085,464100
Chromosome 10114,662,0491114,657,549114,662,04990
Chromosome 11108,787,7711108,785,771108,787,77140
Chromosome 1296,445,735196,442,23596,445,73570
Chromosome 1395,726,014195,721,51695,726,01490
Chromosome 1489,080,780189,078,28089,080,78050
Chromosome 1569,992,071169,988,57169,992,07170
Chromosome 1661,483,029161,480,52961,483,02950
Chromosome 1760,348,511160,346,51160,348,51140
Chromosome 1840,428,123140,425,92340,428,12350
Chromosome X99,689,450199,681,45099,689,450160
Chromosome Y2,249,90912,247,4092,249,90950
unplaced8,359,855238,355,355507,29190
MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Mitochondrion MT16,536116,53616,53600
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