Full Report

Send to:

Choose Destination

File
Clipboard
Collections

Download Assembly

Source database (GenBank or RefSeq) File type

Pop_tri_v3

This assembly has been replaced. See current version

Organism name:

Populus trichocarpa (black cottonwood)

Isolate:

Nisqually-1

BioSample:

SAMN02953657

BioProject:

PRJNA10772

Submitter:

US DOE Joint Genome Institute (JGI

Date:

2018/01/24

Assembly level:

Chromosome

Genome representation:

full

GenBank assembly accession:

GCA_000002775.3 (replaced)

RefSeq assembly accession:

GCF_000002775.4 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome Pltd

Data displayed for RefSeq version

WGS Project:

AARH03

Assembly method:

ARACHNE_modified v. 200721016

Genome coverage:

Sequencing technology:

Sanger; Illumina

IDs: 1532731 [UID] 5927748 [GenBank] 6309578 [RefSeq]

See Genome Information for Populus trichocarpa

Pathogen Detection Resources

There are 4 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000002775.4	≠	GCF_000002775.5	P.trichocarpa_v4.1	Chromosome	Latest GenBank, Latest RefSeq
GCA_000002775.3	≠	GCF_000002775.4	Pop_tri_v3	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000002775.2	=	GCF_000002775.3	Poptr2_0	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000002775.1	≠	GCF_000002775.2	Poptr1_1	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000002775.1	≠	GCF_000002775.1	Poptr1_1	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

Annotation was updated on the scaffolds on December 2018

Global statistics

Total sequence length	434,289,848
Total ungapped length	423,097,627
Gaps between scaffolds	247
Number of scaffolds	1,694
Scaffold N50	2,158,892
Scaffold L50	53
Number of contigs	8,318
Contig N50	552,806
Contig L50	206
Total number of chromosomes and plasmids	20
Number of component sequences (WGS or clone)	8,318

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM009290.1	=	NC_037285.1	0
Chromosome 2	CM009291.1	=	NC_037286.1	0
Chromosome 3	CM009292.1	=	NC_037287.1	0
Chromosome 4	CM009293.1	=	NC_037288.1	0
Chromosome 5	CM009294.1	=	NC_037289.1	0
Chromosome 6	CM009295.1	=	NC_037290.1	0
Chromosome 7	CM009296.1	=	NC_037291.1	0
Chromosome 8	CM009297.1	=	NC_037292.1	0
Chromosome 9	CM009298.1	=	NC_037293.1	0
Chromosome 10	CM009299.1	=	NC_037294.1	0
Chromosome 11	CM009300.1	=	NC_037295.1	0
Chromosome 12	CM009301.1	=	NC_037296.1	0
Chromosome 13	CM009302.1	=	NC_037297.1	0
Chromosome 14	CM009303.1	=	NC_037298.1	0
Chromosome 15	CM009304.1	=	NC_037299.1	0
Chromosome 16	CM009305.1	=	NC_037300.1	0
Chromosome 17	CM009306.1	=	NC_037301.1	0
Chromosome 18	CM009307.1	=	NC_037302.1	0
Chromosome 19	CM009308.1	=	NC_037303.1	0
unplaced	n/a	n/a	n/a	1,427

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	434,132,815	1,693	422,940,594	2,158,892	6,624	247
Chromosome 1	50,495,391	28	49,860,949	3,569,291	371	27
Chromosome 2	25,263,035	12	25,009,277	6,187,186	120	11
Chromosome 3	21,816,808	13	21,552,582	3,907,608	123	12
Chromosome 4	24,267,051	21	23,662,361	1,314,761	286	20
Chromosome 5	25,890,704	14	25,548,421	2,892,880	231	13
Chromosome 6	27,912,125	17	27,491,364	7,691,701	238	16
Chromosome 7	15,610,913	10	15,325,583	2,047,970	124	9
Chromosome 8	19,465,461	8	19,194,459	15,091,142	173	7
Chromosome 9	12,948,742	4	12,838,997	6,853,963	43	3
Chromosome 10	22,580,532	14	22,251,470	2,983,214	153	13
Chromosome 11	18,501,271	14	18,118,962	1,850,909	201	13
Chromosome 12	15,760,346	13	15,494,594	1,643,036	168	12
Chromosome 13	16,320,717	15	15,936,693	1,403,086	202	14
Chromosome 14	18,920,894	16	18,560,652	1,995,735	140	15
Chromosome 15	15,278,577	7	15,153,263	2,160,931	73	6
Chromosome 16	14,494,361	6	14,375,048	3,608,849	69	5
Chromosome 17	16,080,358	15	15,724,891	1,719,539	189	14
Chromosome 18	16,958,300	23	16,372,158	955,272	213	22
Chromosome 19	15,942,145	16	15,460,193	1,084,263	261	15
unplaced	39,625,084	1,427	35,008,677	129,782	3,246	0

Assembly

Genome Assembly

Result Filters

Organism group

Status

Assembly level

RefSeq category

Exclude

Annotation status

Taxonomy check status

Relation to type material

Assembly type

Sequence release date

Custom date range

Contig N50

Custom range

Scaffold N50

Custom range

Additional filters

Send to:

Download Assembly

Pop_tri_v3

See Genome Information for Populus trichocarpa

Pathogen Detection Resources

There are 4 assemblies for this organism

History (Show revision history)

Comment

Global statistics

Supplemental Content

Access the data

Assembly Information

Related Information

PubMed articles for this assembly

Recent activity

Global assembly definition

Assembly statistics

Assembly Unit Name
Primary Assembly
non-nuclear