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Source database (GenBank or RefSeq) File type

ValleyOak3.0

This assembly has been replaced. See current version

Organism name:

Quercus lobata (valley oak)

Isolate:

SW786

BioSample:

SAMN10584531

BioProject:

PRJNA308314

Submitter:

University of Maryland Center for Environmental Science

Date:

2019/01/11

Assembly level:

Chromosome

Genome representation:

full

GenBank assembly accession:

GCA_001633185.2 (replaced)

RefSeq assembly accession:

GCF_001633185.1 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: 16587 unlocalized and unplaced scaffolds; chromosome Pltd.

Data displayed for RefSeq version

WGS Project:

LRBV02

Assembly method:

MaSuRCA v. 3.2.1; Dovetail HiRise v. 1

Expected final version:

yes

Genome coverage:

280.0x

Sequencing technology:

Illumina HiSeq; PacBio; Dovetail

IDs: 2203651 [UID] 8218728 [GenBank] 14079408 [RefSeq]

See Genome Information for Quercus lobata

Pathogen Detection Resources

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_001633185.5	≠	GCF_001633185.2	ValleyOak3.2	Chromosome	Latest GenBank, Latest RefSeq
GCA_001633185.4	n/a	n/a	ValleyOak3.1	Chromosome	Replaced GenBank
GCA_001633185.3	n/a	n/a	ValleyOak3.0	Chromosome	Replaced GenBank
GCA_001633185.2	≠	GCF_001633185.1	ValleyOak3.0	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_001633185.1	n/a	n/a	ValleyOak0.5	Scaffold	Replaced GenBank

Comment

In Sept 2021 the 16,584 alternative haploid contigs (haplotigs) of assembly ValleyOak3.1 (LRBV02002015-LRBV02018598) were suppressed. Consequently, this updated assembly version (ValleyOak3.2; GCA_001633185.5) is a standard haploid assembly.

The chloroplast sequence in LRBV02000011 was updated on June 2020.

In August 2021 eight ... sequences were removed because they are contaminants, and the assembly name was updated to ValleyOak3.1. The accessions of those eight are LRBV02000234.1, LRBV02000274.1, LRBV02000464.1, LRBV02000532.1, LRBV02000701.1, LRBV02000726.1, LRBV02000790.1, LRBV02000989.1.  more

Global statistics

Total sequence length	846,070,421
Total ungapped length	844,142,372
Gaps between scaffolds	0
Number of scaffolds	2,010
Scaffold N50	66,423,012
Scaffold L50	5
Number of contigs	3,684
Contig N50	965,935
Contig L50	247
Total number of chromosomes and plasmids	12
Number of component sequences (WGS or clone)	2,010

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM012293.1	=	NC_044904.1	0
Chromosome 2	CM012294.1	=	NC_044905.1	1
Chromosome 3	CM012295.1	=	NC_044906.1	0
Chromosome 4	CM012296.1	=	NC_044907.1	0
Chromosome 5	CM012297.1	=	NC_044908.1	0
Chromosome 6	CM012298.1	=	NC_044909.1	0
Chromosome 7	CM012299.1	=	NC_044910.1	0
Chromosome 8	CM012300.1	=	NC_044911.1	0
Chromosome 9	CM012301.1	=	NC_044912.1	0
Chromosome 10	CM012302.1	=	NC_044913.1	0
Chromosome 11	CM012303.1	=	NC_044914.1	0
Chromosome 12	CM012304.1	=	NC_044915.1	0
unplaced	n/a	n/a	n/a	1,997

Molecule	Sequence Role	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	Assembled molecule	846,070,421	2,010	844,142,372	66,423,012	1,674	0
Chromosome 1	Assembled molecule	55,683,757	1	55,605,220	55,683,757	77	0
Chromosome 2	AllAssembled moleculeUnlocalized scaffolds	104,577,665104,436,548141,117	211	104,405,228104,264,111141,117	104,436,548104,436,548141,117	1681680	000
Chromosome 3	Assembled molecule	74,551,540	1	74,344,002	74,551,540	170	0
Chromosome 4	Assembled molecule	97,794,414	1	97,588,021	97,794,414	191	0
Chromosome 5	Assembled molecule	89,479,036	1	89,312,553	89,479,036	167	0
Chromosome 6	Assembled molecule	54,021,141	1	53,926,504	54,021,141	87	0
Chromosome 7	Assembled molecule	49,020,089	1	48,917,140	49,020,089	99	0
Chromosome 8	Assembled molecule	65,456,833	1	65,300,261	65,456,833	144	0
Chromosome 9	Assembled molecule	55,012,092	1	54,891,797	55,012,092	118	0
Chromosome 10	Assembled molecule	66,423,012	1	66,269,094	66,423,012	140	0
Chromosome 11	Assembled molecule	57,729,484	1	57,609,201	57,729,484	111	0
Chromosome 12	Assembled molecule	43,132,062	1	43,054,805	43,132,062	79	0
unplaced	Assembled molecule	33,189,296	1,997	32,918,546	55,061	123	0

Assembly

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ValleyOak3.0

See Genome Information for Quercus lobata

Pathogen Detection Resources

History (Show revision history)

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