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ICSASG_v2

Organism name:
Salmo salar (Atlantic salmon)
Infraspecific name:
Breed: double haploid
Isolate:
Sally
Sex:
female
BioSample:
SAMN02749551
BioProject:
PRJNA72713
Submitter:
International Cooperation to Sequence the Atlantic Salmon Genome
Date:
2015/06/10
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000233375.4 (latest)
RefSeq assembly accession:
GCF_000233375.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: 597817 unplaced scaffolds (in primary assembly-unit)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Unplaced scaffolds shorter than 1,000 bases were omitted from the RefSeq assembly.
  • Data displayed for RefSeq version
WGS Project:
AGKD04
Assembly method:
MaSuRCA v. 2.0.3
Expected final version:
yes
Genome coverage:
206.0x
Sequencing technology:
Illumina HiSeq; PacBio; Sanger; Illumina GAIIx

IDs: 487001 [UID] 1808638 [GenBank] 2308328 [RefSeq]

See Genome Information for Salmo salar

History (Show revision history)

Comment

This is a de novo whole-genome assembly of Salmo salar. The assembly was produced with the Masurca (v2.0.3) assembler and post-processed to close scaffold gaps using sequences from other assemblies. The assembler input consisted of Sanger mate pairs (insert ... sizes 3K, 35K, and 120K sequenced to 4.8X and trimmed to 3.7X read cover), Illumina PE (filtered from 113X), and Illumina MP (filtered from 89X, insert sizes 3K and larger). The source DNA was extracted from muscle tissue of a double haploid donor known as Sally.  more

Global statistics

Total sequence length2,966,890,203
Total assembly gap length347,999,900
Gaps between scaffolds9,418
Number of scaffolds241,573
Scaffold N501,366,254
Scaffold L50350
Number of contigs368,060
Contig N5057,618
Contig L509,869
Total number of chromosomes and plasmids30
Number of component sequences (WGS or clone)241,573

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_000233385.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome ssa01CM003279.1=NC_027300.10
Chromosome ssa02CM003280.1=NC_027301.10
Chromosome ssa03CM003281.1=NC_027302.10
Chromosome ssa04CM003282.1=NC_027303.10
Chromosome ssa05CM003283.1=NC_027304.10
Chromosome ssa06CM003284.1=NC_027305.10
Chromosome ssa07CM003285.1=NC_027306.10
Chromosome ssa08CM003286.1=NC_027307.10
Chromosome ssa09CM003287.1=NC_027308.10
Chromosome ssa10CM003288.1=NC_027309.10
Chromosome ssa11CM003289.1=NC_027310.10
Chromosome ssa12CM003290.1=NC_027311.10
Chromosome ssa13CM003291.1=NC_027312.10
Chromosome ssa14CM003292.1=NC_027313.10
Chromosome ssa15CM003293.1=NC_027314.10
Chromosome ssa16CM003294.1=NC_027315.10
Chromosome ssa17CM003295.1=NC_027316.10
Chromosome ssa18CM003296.1=NC_027317.10
Chromosome ssa19CM003297.1=NC_027318.10
Chromosome ssa20CM003298.1=NC_027319.10
Chromosome ssa21CM003299.1=NC_027320.10
Chromosome ssa22CM003300.1=NC_027321.10
Chromosome ssa23CM003301.1=NC_027322.10
Chromosome ssa24CM003302.1=NC_027323.10
Chromosome ssa25CM003303.1=NC_027324.10
Chromosome ssa26CM003304.1=NC_027325.10
Chromosome ssa27CM003305.1=NC_027326.10
Chromosome ssa28CM003306.1=NC_027327.10
Chromosome ssa29CM003307.1=NC_027328.10
unplacedn/an/an/a232,125

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All2,966,873,538241,5722,618,873,6381,366,254126,4879,418
Chromosome ssa01159,038,749447151,353,0674,117,4235,013446
Chromosome ssa0272,943,71163264,968,6691,373,5053,416631
Chromosome ssa0392,503,42852684,400,3523,422,0233,951525
Chromosome ssa0482,398,02332277,301,5003,482,3442,687321
Chromosome ssa0580,503,87654072,248,0062,317,4243,364539
Chromosome ssa0687,043,18755277,667,8751,158,7413,928551
Chromosome ssa0758,785,26535654,096,0972,292,2332,910355
Chromosome ssa0826,434,01120323,618,5271,574,9311,266202
Chromosome ssa09141,712,163478130,894,4572,848,8485,041477
Chromosome ssa10116,138,521206111,564,2735,172,9333,542205
Chromosome ssa1193,888,50853285,625,7811,740,5153,581531
Chromosome ssa1291,880,96241684,368,7653,586,0883,586415
Chromosome ssa13107,758,822224103,126,6044,981,7243,064223
Chromosome ssa1493,901,82326587,676,9321,982,6243,338264
Chromosome ssa15103,963,43631196,485,2781,981,1313,744310
Chromosome ssa1687,796,32244481,330,5605,182,2443,394443
Chromosome ssa1757,682,53759550,068,7981,266,9842,929594
Chromosome ssa1870,695,40939166,699,2028,432,5532,833390
Chromosome ssa1982,978,13220378,218,6872,198,7102,583202
Chromosome ssa2086,795,99728481,562,2073,961,9432,751283
Chromosome ssa2158,021,48711755,446,2223,474,6801,776116
Chromosome ssa2263,420,1969661,049,8306,107,6611,91495
Chromosome ssa2349,854,00410047,712,3916,695,1701,42799
Chromosome ssa2448,650,97611046,431,63110,225,4451,357109
Chromosome ssa2551,481,32616348,691,0582,447,0591,651162
Chromosome ssa2647,900,95351542,462,6152,444,1412,276514
Chromosome ssa2743,943,98514541,208,1191,639,3611,717144
Chromosome ssa2839,600,94410937,567,27520,002,8631,272108
Chromosome ssa2942,488,23816538,607,9911,354,0861,698164
unplaced726,668,547232,125536,420,8695,92344,4780
MoleculeTotal
Length
Mitochondrion MT16,665
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