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ValleyOak3.0

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

History (Show revision history)

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 length846,070,421
Total ungapped length844,142,372
Gaps between scaffolds0
Number of scaffolds2,010
Scaffold N5066,423,012
Scaffold L505
Number of contigs3,684
Contig N50965,935
Contig L50247
Total number of chromosomes and plasmids12
Number of component sequences (WGS or clone)2,010

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_001633195.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM012293.1=NC_044904.10
Chromosome 2CM012294.1=NC_044905.11
Chromosome 3CM012295.1=NC_044906.10
Chromosome 4CM012296.1=NC_044907.10
Chromosome 5CM012297.1=NC_044908.10
Chromosome 6CM012298.1=NC_044909.10
Chromosome 7CM012299.1=NC_044910.10
Chromosome 8CM012300.1=NC_044911.10
Chromosome 9CM012301.1=NC_044912.10
Chromosome 10CM012302.1=NC_044913.10
Chromosome 11CM012303.1=NC_044914.10
Chromosome 12CM012304.1=NC_044915.10
unplacedn/an/an/a1,997

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule846,070,4212,010844,142,37266,423,0121,6740
Chromosome 1Assembled molecule55,683,757155,605,22055,683,757770
Chromosome 2AllAssembled moleculeUnlocalized scaffolds104,577,665104,436,548141,117211104,405,228104,264,111141,117104,436,548104,436,548141,1171681680000
Chromosome 3Assembled molecule74,551,540174,344,00274,551,5401700
Chromosome 4Assembled molecule97,794,414197,588,02197,794,4141910
Chromosome 5Assembled molecule89,479,036189,312,55389,479,0361670
Chromosome 6Assembled molecule54,021,141153,926,50454,021,141870
Chromosome 7Assembled molecule49,020,089148,917,14049,020,089990
Chromosome 8Assembled molecule65,456,833165,300,26165,456,8331440
Chromosome 9Assembled molecule55,012,092154,891,79755,012,0921180
Chromosome 10Assembled molecule66,423,012166,269,09466,423,0121400
Chromosome 11Assembled molecule57,729,484157,609,20157,729,4841110
Chromosome 12Assembled molecule43,132,062143,054,80543,132,062790
unplacedAssembled molecule33,189,2961,99732,918,54655,0611230
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