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gadMor3.0

Organism name:
Gadus morhua (Atlantic cod)
BioSample:
SAMEA5574046
BioProject:
PRJEB33455
Submitter:
SC
Date:
2019/07/16
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_902167405.1 (latest)
RefSeq assembly accession:
GCF_902167405.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
CABHMC01
Genome coverage:
83x
Linked assembly:
GCA_902167395.1 (alternate pseudohaplotype of diploid)

IDs: 4119451 [UID] 12698358 [GenBank] 12973628 [RefSeq]

See Genome Information for Gadus morhua

There are 6 assemblies for this organism

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History (Show revision history)

Comment

The assembly gadMor3.0 of individual fGadMor1 (SAMEA5574046) is based on 83x PacBio data generated at the Wellcome Sanger Institute and the Jakobsen lab at the University of Olso in Norway, 59x 10X Genomics Chromium data and BioNano data generated ... at the Wellcome Sanger Institute, as well as 76x Arima Hi-C data generated at the Jakobsen lab. The assembly process included the following sequence of steps: initial PacBio assembly generation with Falcon-unzip, retained haplotig identification with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds were named based on a genetic map provided by the Jakobsen lab.  more

Global statistics

Total sequence length669,966,409
Total ungapped length646,392,667
Gaps between scaffolds0
Number of scaffolds227
Scaffold N5028,732,775
Scaffold L5011
Number of contigs1,442
Contig N501,015,663
Contig L50169
Total number of chromosomes and plasmids24
Number of component sequences (WGS or clone)227

Supplemental Content

PubMed articles for this assembly

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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 (GCF_902167404.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR633943.1=NC_044048.10
Chromosome 2LR633944.1=NC_044049.10
Chromosome 3LR633945.1=NC_044050.10
Chromosome 4LR633946.1=NC_044051.10
Chromosome 5LR633947.1=NC_044052.10
Chromosome 6LR633948.1=NC_044053.10
Chromosome 7LR633949.1=NC_044054.10
Chromosome 8LR633950.1=NC_044055.10
Chromosome 9LR633951.1=NC_044056.10
Chromosome 10LR633952.1=NC_044057.10
Chromosome 11LR633953.1=NC_044058.10
Chromosome 12LR633954.1=NC_044059.10
Chromosome 13LR633955.1=NC_044060.10
Chromosome 14LR633956.1=NC_044061.10
Chromosome 15LR633957.1=NC_044062.10
Chromosome 16LR633958.1=NC_044063.10
Chromosome 17LR633959.1=NC_044064.10
Chromosome 18LR633960.1=NC_044065.10
Chromosome 19LR633961.1=NC_044066.10
Chromosome 20LR633962.1=NC_044067.10
Chromosome 21LR633963.1=NC_044068.10
Chromosome 22LR633964.1=NC_044069.10
Chromosome 23LR633965.1=NC_044070.10
unplacedn/an/an/a203

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All669,949,713226646,375,97128,732,7751,2150
Chromosome 130,875,876129,725,24830,875,876580
Chromosome 228,732,775127,194,50428,732,775670
Chromosome 330,954,429130,183,98530,954,429470
Chromosome 443,798,135140,789,61443,798,135850
Chromosome 525,300,426123,976,64525,300,426530
Chromosome 627,762,770127,058,21727,762,770380
Chromosome 734,137,969133,560,24234,137,969520
Chromosome 829,710,654129,140,86129,710,654440
Chromosome 926,487,948126,104,42226,487,948350
Chromosome 1027,234,273126,131,66027,234,273560
Chromosome 1130,713,045129,369,33830,713,045560
Chromosome 1230,948,897129,335,12730,948,897580
Chromosome 1328,829,685127,874,38728,829,685520
Chromosome 1429,586,942129,100,74629,586,942420
Chromosome 1528,657,694127,124,36928,657,694390
Chromosome 1634,794,352134,174,90234,794,352560
Chromosome 1721,723,002121,039,58921,723,002400
Chromosome 1824,902,675123,814,91324,902,675490
Chromosome 1922,015,597121,142,67422,015,597420
Chromosome 2024,843,429124,275,91924,843,429390
Chromosome 2122,358,821121,983,65122,358,821560
Chromosome 2223,744,039122,932,39623,744,039620
Chromosome 2325,242,006123,824,52225,242,006560
unplaced16,594,27420316,518,040106,993330
MoleculeTotal
Length
Mitochondrion MT16,696
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