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Source database (GenBank or RefSeq) File type

Oner_1.0

This assembly has been replaced. See current version

Anomalous assembly.

Organism name:

Oncorhynchus nerka (sockeye salmon)

Isolate:

On170113-E2

Sex:

female

BioSample:

SAMN11519041

BioProject:

PRJNA530256

Submitter:

Fisheries and Oceans Canada

Date:

2019/06/07

Assembly level:

Chromosome

Genome representation:

full

Assembly anomaly:

contaminated

Excluded from RefSeq:

contaminated

GenBank assembly accession:

GCA_006149115.1 (replaced)

RefSeq assembly accession:

GCF_006149115.1 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

WGS Project:

SZNR01

Assembly method:

AllPaths v. 52488; Custom Gap Filling v. April-2019; ARCS/LINKS/Tigment v. April-2019

Expected final version:

yes

Genome coverage:

158.0x

Sequencing technology:

Illumina HiSeq; PacBio Sequel

IDs: 3348231 [UID] 11016728 [GenBank] 11193728 [RefSeq]

See Genome Information for Oncorhynchus nerka

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_006149115.2	≠	GCF_006149115.2	Oner_1.1	Chromosome	Latest GenBank, Latest RefSeq
GCA_006149115.1	≠	GCF_006149115.1	Oner_1.0	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

In May 2022 1367 sequences were suppressed because they were found to be contaminants.

Global statistics

Total sequence length	1,927,141,915
Total ungapped length	1,853,070,152
Gaps between scaffolds	1,903
Number of scaffolds	38,027
Scaffold N50	1,058,586
Scaffold L50	374
Number of contigs	57,813
Contig N50	329,583
Contig L50	1,232
Total number of chromosomes and plasmids	30
Number of component sequences (WGS or clone)	38,027

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Linkage Group LG1	CM016829.1	=	NC_042535.1	0
Linkage Group LG2	CM016840.1	=	NC_042536.1	0
Linkage Group LG3	CM016850.1	=	NC_042537.1	0
Linkage Group LG4	CM016851.1	=	NC_042538.1	0
Linkage Group LG5	CM016852.1	=	NC_042539.1	0
Linkage Group LG6	CM016853.1	=	NC_042540.1	0
Linkage Group LG7	CM016854.1	=	NC_042541.1	0
Linkage Group LG8	CM016855.1	=	NC_042542.1	0
Linkage Group LG9a	CM016856.1	=	NC_042543.1	0
Linkage Group LG10	CM016830.1	=	NC_042544.1	0
Linkage Group LG11	CM016831.1	=	NC_042545.1	0
Linkage Group LG12	CM016832.1	=	NC_042546.1	0
Linkage Group LG13	CM016833.1	=	NC_042547.1	0
Linkage Group LG14	CM016834.1	=	NC_042548.1	0
Linkage Group LG15	CM016835.1	=	NC_042549.1	0
Linkage Group LG16	CM016836.1	=	NC_042550.1	0
Linkage Group LG17	CM016837.1	=	NC_042551.1	0
Linkage Group LG18	CM016838.1	=	NC_042552.1	0
Linkage Group LG19	CM016839.1	=	NC_042553.1	0
Linkage Group LG20	CM016841.1	=	NC_042554.1	0
Linkage Group LG21	CM016842.1	=	NC_042555.1	0
Linkage Group LG22	CM016843.1	=	NC_042556.1	0
Linkage Group LG23	CM016844.1	=	NC_042557.1	0
Linkage Group LG24	CM016845.1	=	NC_042558.1	0
Linkage Group LG25	CM016846.1	=	NC_042559.1	0
Linkage Group LG26	CM016847.1	=	NC_042560.1	0
Linkage Group LG27	CM016848.1	=	NC_042561.1	0
Linkage Group LG28	CM016849.1	=	NC_042562.1	0
Linkage Group LG9b	CM016857.1	=	NC_042563.1	0
unplaced	n/a	n/a	n/a	36,094

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	1,927,125,257	38,026	1,853,053,494	1,058,586	19,786	1,903
Linkage Group LG1	41,065,921	52	40,663,701	1,295,189	169	51
Linkage Group LG2	61,175,412	80	60,459,197	3,461,049	242	79
Linkage Group LG3	59,001,101	86	58,142,030	1,704,976	295	85
Linkage Group LG4	63,915,030	108	62,797,344	1,065,813	346	107
Linkage Group LG5	37,979,840	84	37,378,426	759,633	185	83
Linkage Group LG6	54,634,741	78	53,774,982	2,103,397	272	77
Linkage Group LG7	58,386,872	85	57,611,525	1,679,769	239	84
Linkage Group LG8	35,046,503	58	34,315,153	1,409,600	248	57
Linkage Group LG9a	47,832,342	52	47,363,517	2,289,962	167	51
Linkage Group LG10	68,883,746	57	68,239,022	3,046,255	214	56
Linkage Group LG11	43,508,088	63	42,844,970	1,970,132	238	62
Linkage Group LG12	55,003,077	79	54,215,850	1,721,117	270	78
Linkage Group LG13	68,149,839	90	67,205,656	1,670,619	299	89
Linkage Group LG14	51,022,262	81	49,977,388	1,435,254	341	80
Linkage Group LG15	55,276,629	62	54,801,858	2,839,370	176	61
Linkage Group LG16	33,137,888	40	32,734,667	1,486,367	155	39
Linkage Group LG17	39,821,479	43	39,344,405	2,048,434	174	42
Linkage Group LG18	45,022,206	53	44,441,898	1,562,698	214	52
Linkage Group LG19	32,584,818	45	32,143,190	1,460,141	152	44
Linkage Group LG20	70,002,629	79	69,010,241	2,506,259	321	78
Linkage Group LG21	28,665,924	55	28,151,594	1,393,416	168	54
Linkage Group LG22	76,421,889	75	75,603,616	3,016,713	281	74
Linkage Group LG23	43,162,419	66	42,433,091	2,013,772	257	65
Linkage Group LG24	63,930,817	85	63,172,590	1,709,930	268	84
Linkage Group LG25	44,841,605	44	44,387,902	3,303,093	144	43
Linkage Group LG26	26,779,087	43	26,434,842	1,132,304	142	42
Linkage Group LG27	63,626,826	81	63,032,546	1,903,740	238	80
Linkage Group LG28	63,636,109	69	63,020,735	2,035,596	225	68
Linkage Group LG9b	36,765,530	39	36,266,096	2,741,404	157	38
unplaced	457,844,628	36,094	403,085,462	58,041	13,189	0

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Oner_1.0

See Genome Information for Oncorhynchus nerka

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear