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ASM1548v1

Organism name:
Desulfovibrio vulgaris DP4 (d-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: DP4
BioSample:
SAMN02598381
BioProject:
PRJNA17227
Submitter:
DOE Joint Genome Institute
Date:
2007/01/03
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000015485.1 (latest)
RefSeq assembly accession:
GCF_000015485.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 36588 [UID] 16288 [GenBank] 36588 [RefSeq]

See Genome Information for Desulfovibrio vulgaris

There are 5 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 4001787
Source DNA and bacteria available from Christopher Walker (cbwalkdr@u.washington.edu)
Contacts: Christopher Walker (cbwalkdr@u.washington.edu)
 Paul Richardson (microbes@cuba.jgi-psf.org)
Quality assurance done by JGI-Stanford
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LLNL
Finished microbial genomes have been curated to close ... all gaps with greater than 98% coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000.
The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis.
(http://www.genome.gov/page.cfm?pageID=10506376)  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::09/23/2020 14:05:10
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::4.13
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::3,168
CDSs (total)::3,079
Genes (coding)::3,059
CDSs (with protein)::3,059
Genes (RNA)::89
rRNAs::6, 5, 5 (5S, 16S, 23S)
complete rRNAs::6, 5, 5 (5S, 16S, 23S)
tRNAs::69
ncRNAs::4
Pseudo Genes (total)::20
CDSs (without protein)::20
Pseudo Genes (ambiguous residues)::0 of 20
Pseudo Genes (frameshifted)::7 of 20
Pseudo Genes (incomplete)::16 of 20
Pseudo Genes (internal stop)::3 of 20
Pseudo Genes (multiple problems)::4 of 20
CRISPR Arrays::1
##Genome-Annotation-Data-END##

Global statistics

Total sequence length3,661,391
Total ungapped length3,661,391
Total number of chromosomes and plasmids2

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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_000015495.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP000527.1=NC_008751.1
Plasmid pDVUL01CP000528.1=NC_008741.1

Assembly statistics

MoleculeTotal
Length
All3,661,391
Chromosome 3,462,887
Plasmid pDVUL01198,504

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Desulfovibrio vulgaris DP4Desulfovibrio vulgaris

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_902167245.1Desulfovibrio vulgaris str. Hildenboroughtype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_902167245.1Desulfovibrio vulgaristype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.8393.6892.00
Best-match type98.8393.6892.00

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna
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