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Source database (GenBank or RefSeq) File type

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

Excluded from RefSeq:

superseded by newer assembly for species

GenBank assembly accession:

GCA_000233375.4 (latest)

RefSeq assembly accession:

GCF_000233375.1 (suppressed) see latest RefSeq assembly for this species

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: 597817 unplaced scaffolds
Only in RefSeq: chromosome MT
Unplaced scaffolds shorter than 1,000 bases were omitted from the RefSeq assembly.

Data displayed for GenBank 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

Pathogen Detection Resources

There are 15 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000233375.4	≠	GCF_000233375.1	ICSASG_v2	Chromosome	Latest GenBank, RefSeq suppressed
GCA_000233375.3	n/a	n/a	ICSASG_v1	Contig	Replaced GenBank
GCA_000233375.2	n/a	n/a	ICSASG_v1	Contig	GenBank suppressed
GCA_000233375.1	n/a	n/a	ASM23337v1	Scaffold	Replaced GenBank

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 length	3,412,113,583
Total ungapped length	3,064,112,202
Gaps between scaffolds	9,418
Number of scaffolds	839,389
Scaffold N50	592,762
Scaffold L50	594
Number of contigs	965,912
Contig N50	36,085
Contig L50	14,749
Total number of chromosomes and plasmids	29
Number of component sequences (WGS or clone)	839,389

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome ssa01	CM003279.1	=	NC_027300.1	0
Chromosome ssa02	CM003280.1	=	NC_027301.1	0
Chromosome ssa03	CM003281.1	=	NC_027302.1	0
Chromosome ssa04	CM003282.1	=	NC_027303.1	0
Chromosome ssa05	CM003283.1	=	NC_027304.1	0
Chromosome ssa06	CM003284.1	=	NC_027305.1	0
Chromosome ssa07	CM003285.1	=	NC_027306.1	0
Chromosome ssa08	CM003286.1	=	NC_027307.1	0
Chromosome ssa09	CM003287.1	=	NC_027308.1	0
Chromosome ssa10	CM003288.1	=	NC_027309.1	0
Chromosome ssa11	CM003289.1	=	NC_027310.1	0
Chromosome ssa12	CM003290.1	=	NC_027311.1	0
Chromosome ssa13	CM003291.1	=	NC_027312.1	0
Chromosome ssa14	CM003292.1	=	NC_027313.1	0
Chromosome ssa15	CM003293.1	=	NC_027314.1	0
Chromosome ssa16	CM003294.1	=	NC_027315.1	0
Chromosome ssa17	CM003295.1	=	NC_027316.1	0
Chromosome ssa18	CM003296.1	=	NC_027317.1	0
Chromosome ssa19	CM003297.1	=	NC_027318.1	0
Chromosome ssa20	CM003298.1	=	NC_027319.1	0
Chromosome ssa21	CM003299.1	=	NC_027320.1	0
Chromosome ssa22	CM003300.1	=	NC_027321.1	0
Chromosome ssa23	CM003301.1	=	NC_027322.1	0
Chromosome ssa24	CM003302.1	=	NC_027323.1	0
Chromosome ssa25	CM003303.1	=	NC_027324.1	0
Chromosome ssa26	CM003304.1	=	NC_027325.1	0
Chromosome ssa27	CM003305.1	=	NC_027326.1	0
Chromosome ssa28	CM003306.1	=	NC_027327.1	0
Chromosome ssa29	CM003307.1	=	NC_027328.1	0
unplaced	n/a	n/a	n/a	829,942

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	3,412,113,583	839,389	3,064,112,202	592,762	126,523	9,418
Chromosome ssa01	159,038,749	447	151,353,067	4,117,423	5,013	446
Chromosome ssa02	72,943,711	632	64,968,669	1,373,505	3,416	631
Chromosome ssa03	92,503,428	526	84,400,352	3,422,023	3,951	525
Chromosome ssa04	82,398,023	322	77,301,500	3,482,344	2,687	321
Chromosome ssa05	80,503,876	540	72,248,006	2,317,424	3,364	539
Chromosome ssa06	87,043,187	552	77,667,875	1,158,741	3,928	551
Chromosome ssa07	58,785,265	356	54,096,097	2,292,233	2,910	355
Chromosome ssa08	26,434,011	203	23,618,527	1,574,931	1,266	202
Chromosome ssa09	141,712,163	478	130,894,457	2,848,848	5,041	477
Chromosome ssa10	116,138,521	206	111,564,273	5,172,933	3,542	205
Chromosome ssa11	93,888,508	532	85,625,781	1,740,515	3,581	531
Chromosome ssa12	91,880,962	416	84,368,765	3,586,088	3,586	415
Chromosome ssa13	107,758,822	224	103,126,604	4,981,724	3,064	223
Chromosome ssa14	93,901,823	265	87,676,932	1,982,624	3,338	264
Chromosome ssa15	103,963,436	311	96,485,278	1,981,131	3,744	310
Chromosome ssa16	87,796,322	444	81,330,560	5,182,244	3,394	443
Chromosome ssa17	57,682,537	595	50,068,798	1,266,984	2,929	594
Chromosome ssa18	70,695,409	391	66,699,202	8,432,553	2,833	390
Chromosome ssa19	82,978,132	203	78,218,687	2,198,710	2,583	202
Chromosome ssa20	86,795,997	284	81,562,207	3,961,943	2,751	283
Chromosome ssa21	58,021,487	117	55,446,222	3,474,680	1,776	116
Chromosome ssa22	63,420,196	96	61,049,830	6,107,661	1,914	95
Chromosome ssa23	49,854,004	100	47,712,391	6,695,170	1,427	99
Chromosome ssa24	48,650,976	110	46,431,631	10,225,445	1,357	109
Chromosome ssa25	51,481,326	163	48,691,058	2,447,059	1,651	162
Chromosome ssa26	47,900,953	515	42,462,615	2,444,141	2,276	514
Chromosome ssa27	43,943,985	145	41,208,119	1,639,361	1,717	144
Chromosome ssa28	39,600,944	109	37,567,275	20,002,863	1,272	108
Chromosome ssa29	42,488,238	165	38,607,991	1,354,086	1,698	164
unplaced	1,171,908,592	829,942	981,659,433	1,363	44,514	0

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ICSASG_v2

See Genome Information for Salmo salar

Pathogen Detection Resources

There are 15 assemblies for this organism

History (Show revision history)

Comment

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