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Source database (GenBank or RefSeq) File type

fSalTru1.1

This assembly has been replaced. See current version

Organism name:

Salmo trutta (river trout)

BioSample:

SAMEA994732

BioProject:

PRJEB32115

Submitter:

Date:

2019/06/02

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_901001165.1 (replaced)

RefSeq assembly accession:

GCF_901001165.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

WGS Project:

CAAJIE01

Genome coverage:

68x

IDs: 3286621 [UID] 10890548 [GenBank] 11512478 [RefSeq]

See Genome Information for Salmo trutta

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_901001165.2	n/a	n/a	fSalTru1.2	Chromosome	Latest GenBank
GCA_901001165.1	≠	GCF_901001165.1	fSalTru1.1	Chromosome	Latest RefSeq, Replaced GenBank

Comment

The assembly fSalTru1.1 is based on 
68x PacBio data and 
70x coverage 10X Genomics Chromium data generated at the Wellcome Sanger Institute, as well as BioNano data generated at the Rockefeller University Vertebrate Genome Laboratory and 
28x coverage Hi-C ... data generated by Arima Genomics. 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, 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 confirmed by the Hi-C data have been named on the following basis: first they were assigned as metacentric versus acrocentric based on a Salmo trutta linkage map and synteny with the Salmo salar assembly GCA_000233375.4; numbers 1 to 11 are metacentric, numbers 12 to 40 are acrocentric, and within each of those two categories they are named in order of size.  more

Global statistics

Total sequence length	2,371,880,186
Total ungapped length	2,298,279,497
Gaps between scaffolds	0
Number of scaffolds	1,441
Scaffold N50	52,209,666
Scaffold L50	18
Number of contigs	5,378
Contig N50	1,703,178
Contig L50	294
Total number of chromosomes and plasmids	41
Number of component sequences (WGS or clone)	1,441

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	LR584410.1	=	NC_042957.1	0
Chromosome 2	LR584445.1	=	NC_042958.1	0
Chromosome 3	LR584416.1	=	NC_042959.1	0
Chromosome 4	LR584420.1	=	NC_042960.1	0
Chromosome 5	LR584433.1	=	NC_042961.1	0
Chromosome 6	LR584406.1	=	NC_042962.1	0
Chromosome 7	LR584430.1	=	NC_042963.1	0
Chromosome 8	LR584407.1	=	NC_042964.1	0
Chromosome 9	LR584409.1	=	NC_042965.1	0
Chromosome 10	LR584419.1	=	NC_042966.1	0
Chromosome 11	LR584438.1	=	NC_042967.1	0
Chromosome 12	LR584441.1	=	NC_042968.1	0
Chromosome 13	LR584428.1	=	NC_042969.1	0
Chromosome 14	LR584411.1	=	NC_042970.1	0
Chromosome 15	LR584415.1	=	NC_042971.1	0
Chromosome 16	LR584431.1	=	NC_042972.1	0
Chromosome 17	LR584426.1	=	NC_042973.1	0
Chromosome 18	LR584435.1	=	NC_042974.1	0
Chromosome 19	LR584427.1	=	NC_042975.1	0
Chromosome 20	LR584429.1	=	NC_042976.1	0
Chromosome 21	LR584437.1	=	NC_042977.1	0
Chromosome 22	LR584440.1	=	NC_042978.1	0
Chromosome 23	LR584421.1	=	NC_042979.1	0
Chromosome 24	LR584412.1	=	NC_042980.1	0
Chromosome 25	LR584436.1	=	NC_042981.1	0
Chromosome 26	LR584439.1	=	NC_042982.1	0
Chromosome 27	LR584424.1	=	NC_042983.1	0
Chromosome 28	LR584422.1	=	NC_042984.1	0
Chromosome 29	LR584418.1	=	NC_042985.1	0
Chromosome 30	LR584432.1	=	NC_042986.1	0
Chromosome 31	LR584423.1	=	NC_042987.1	0
Chromosome 32	LR584408.1	=	NC_042988.1	0
Chromosome 33	LR584414.1	=	NC_042989.1	0
Chromosome 34	LR584434.1	=	NC_042990.1	0
Chromosome 35	LR584444.1	=	NC_042991.1	0
Chromosome 36	LR584442.1	=	NC_042992.1	0
Chromosome 37	LR584417.1	=	NC_042993.1	0
Chromosome 38	LR584425.1	=	NC_042994.1	0
Chromosome 39	LR584413.1	=	NC_042995.1	0
Chromosome 40	LR584443.1	=	NC_042996.1	0
unplaced	n/a	n/a	n/a	1,400

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	2,371,863,509	1,440	2,298,262,820	52,209,666	3,937
Chromosome 1	81,542,925	1	78,193,696	81,542,925	133
Chromosome 2	75,345,318	1	70,965,486	75,345,318	106
Chromosome 3	74,753,489	1	72,656,599	74,753,489	108
Chromosome 4	73,168,960	1	72,012,674	73,168,960	83
Chromosome 5	67,763,595	1	65,535,357	67,763,595	94
Chromosome 6	60,103,141	1	58,142,327	60,103,141	91
Chromosome 7	59,837,330	1	59,341,591	59,837,330	54
Chromosome 8	51,188,276	1	49,564,258	51,188,276	104
Chromosome 9	49,359,203	1	48,289,359	49,359,203	53
Chromosome 10	46,595,448	1	45,691,478	46,595,448	56
Chromosome 11	22,956,941	1	21,546,378	22,956,941	25
Chromosome 12	97,529,106	1	93,696,289	97,529,106	170
Chromosome 13	91,488,822	1	87,690,935	91,488,822	202
Chromosome 14	86,253,525	1	83,335,986	86,253,525	133
Chromosome 15	66,900,148	1	65,544,810	66,900,148	63
Chromosome 16	61,349,433	1	60,561,849	61,349,433	57
Chromosome 17	59,764,774	1	59,149,526	59,764,774	44
Chromosome 18	59,142,494	1	58,153,648	59,142,494	52
Chromosome 19	56,583,805	1	55,568,374	56,583,805	58
Chromosome 20	55,161,844	1	54,347,064	55,161,844	52
Chromosome 21	52,728,040	1	50,407,115	52,728,040	56
Chromosome 22	52,209,666	1	50,573,017	52,209,666	69
Chromosome 23	51,488,243	1	49,569,978	51,488,243	58
Chromosome 24	50,333,583	1	49,556,830	50,333,583	60
Chromosome 25	48,970,219	1	47,803,914	48,970,219	66
Chromosome 26	48,699,937	1	47,561,180	48,699,937	105
Chromosome 27	46,405,705	1	45,749,440	46,405,705	45
Chromosome 28	46,383,311	1	45,200,545	46,383,311	62
Chromosome 29	46,063,367	1	44,184,629	46,063,367	71
Chromosome 30	45,787,633	1	44,346,287	45,787,633	65
Chromosome 31	45,589,842	1	44,844,874	45,589,842	41
Chromosome 32	44,953,446	1	42,941,730	44,953,446	86
Chromosome 33	44,893,998	1	43,896,032	44,893,998	44
Chromosome 34	42,900,288	1	39,738,901	42,900,288	72
Chromosome 35	41,918,599	1	40,157,007	41,918,599	49
Chromosome 36	41,684,595	1	39,116,956	41,684,595	79
Chromosome 37	35,205,783	1	34,227,675	35,205,783	46
Chromosome 38	34,894,132	1	33,841,191	34,894,132	54
Chromosome 39	25,826,328	1	25,148,998	25,826,328	44
Chromosome 40	25,483,426	1	24,394,909	25,483,426	40
unplaced	202,654,791	1,400	195,013,928	694,601	987

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fSalTru1.1

See Genome Information for Salmo trutta

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear