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Poptr2_0

This assembly has been replaced. See current version

Organism name:: Populus trichocarpa (black cottonwood)
BioSample:: SAMN02953657
BioProject:: PRJNA10772
Submitter:: US DOE Joint Genome Institute (JGI
Date:: 2013/10/18
Assembly level:: Chromosome
Genome representation:: full
GenBank assembly accession:: GCA_000002775.2 (replaced)
RefSeq assembly accession:: GCF_000002775.3 (replaced)
RefSeq assembly and GenBank assembly identical:: yes
WGS Project:: AARH02
Assembly method:: ARACHNE v. 2007101641HA
Genome coverage:: 7.45X
Sequencing technology:: ABI 3739

IDs: 72661 [UID] 829748 [GenBank] 1008008 [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

The DNA was isolated from a single genotype, Nisqually-1, that was clonally replicated at multiple locations. The DNA itself came from leaf tissue at the University of Washington, Seattle, WA and root tissue at Oak Ridge National Laboratory, Oak ... Ridge, TN. The chloroplast genome is GenBank Accession Number EF489041.  more

Global statistics

Total sequence length	417,286,671
Total ungapped length	403,899,978
Gaps between scaffolds	0
Number of scaffolds	2,514
Scaffold N50	18,835,763
Scaffold L50	9
Number of contigs	13,561
Contig N50	242,226
Contig L50	448
Total number of chromosomes and plasmids	20
Number of component sequences (WGS or clone)	13,561

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Linkage Group LGI	CM000337.2	=	NC_008467.2	0
Linkage Group LGII	CM000338.2	=	NC_008468.2	0
Linkage Group LGIII	CM000339.2	=	NC_008469.2	0
Linkage Group LGIV	CM000340.2	=	NC_008470.2	0
Linkage Group LGV	CM000341.2	=	NC_008471.2	0
Linkage Group LGVI	CM000342.2	=	NC_008472.2	0
Linkage Group LGVII	CM000343.2	=	NC_008473.2	0
Linkage Group LGVIII	CM000344.2	=	NC_008474.2	0
Linkage Group LGIX	CM000345.2	=	NC_008475.2	0
Linkage Group LGX	CM000346.2	=	NC_008476.2	0
Linkage Group LGXI	CM000347.2	=	NC_008477.2	0
Linkage Group LGXII	CM000348.2	=	NC_008478.2	0
Linkage Group LGXIII	CM000349.2	=	NC_008479.2	0
Linkage Group LGXIV	CM000350.2	=	NC_008480.2	0
Linkage Group LGXV	CM000351.2	=	NC_008481.2	0
Linkage Group LGXVI	CM000352.2	=	NC_008482.2	0
Linkage Group LGXVII	CM000353.2	=	NC_008483.2	0
Linkage Group LGXVIII	CM000354.2	=	NC_008484.2	0
Linkage Group LGXIX	CM000355.2	=	NC_008485.2	0
unplaced	n/a	n/a	n/a	2,494

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	417,129,638	2,513	403,742,945	18,835,763	11,047
Linkage Group LGI	48,367,220	1	47,533,268	48,367,220	841
Linkage Group LGII	23,562,801	1	23,335,659	23,562,801	204
Linkage Group LGIII	20,216,275	1	19,718,531	20,216,275	315
Linkage Group LGIV	23,188,140	1	22,597,507	23,188,140	512
Linkage Group LGV	25,802,683	1	25,166,150	25,802,683	440
Linkage Group LGVI	26,894,541	1	26,410,638	26,894,541	425
Linkage Group LGVII	15,101,417	1	14,862,710	15,101,417	198
Linkage Group LGVIII	18,835,763	1	18,485,880	18,835,763	265
Linkage Group LGIX	12,942,059	1	12,763,255	12,942,059	126
Linkage Group LGX	21,538,349	1	21,282,114	21,538,349	283
Linkage Group LGXI	18,885,544	1	18,042,101	18,885,544	661
Linkage Group LGXII	14,929,429	1	14,660,141	14,929,429	256
Linkage Group LGXIII	15,658,869	1	15,285,125	15,658,869	336
Linkage Group LGXIV	17,716,633	1	17,460,192	17,716,633	201
Linkage Group LGXV	15,134,944	1	14,819,719	15,134,944	217
Linkage Group LGXVI	14,134,809	1	13,904,660	14,134,809	259
Linkage Group LGXVII	14,661,173	1	14,138,171	14,661,173	444
Linkage Group LGXVIII	14,966,190	1	14,586,788	14,966,190	272
Linkage Group LGXIX	16,008,726	1	15,368,342	16,008,726	556
unplaced	38,584,073	2,494	33,321,994	43,532	4,236

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Poptr2_0

See Genome Information for Populus trichocarpa

Pathogen Detection Resources

There are 4 assemblies for this organism

History (Show revision history)

Comment

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Assembly Unit Name
Primary Assembly
non-nuclear