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ASM16611v1

Organism name:
Desulfovibrio vulgaris RCH1 (d-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: RCH1
BioSample:
SAMN00002688
BioProject:
PRJNA32603
Submitter:
US DOE Joint Genome Institute (JGI-PGF)
Date:
2010/11/05
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_000166115.1 (latest)
RefSeq assembly accession:
GCF_000166115.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 446398 [UID] 201618 [GenBank] 446398 [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: 4085842
Source DNA and organism available from Terry C. Hazen (TCHazen@lbl.gov)
Contacts: Terry C. Hazen (TCHazen@lbl.gov)
 Tanja Woyke (microbe@cuba.jgi-psf.org)
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LANL
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 14:06:37
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)::3,280
CDSs (total)::3,190
Genes (coding)::3,171
CDSs (with protein)::3,171
Genes (RNA)::90
rRNAs::6, 5, 5 (5S, 16S, 23S)
complete rRNAs::6, 5, 5 (5S, 16S, 23S)
tRNAs::67
ncRNAs::7
Pseudo Genes (total)::19
CDSs (without protein)::19
Pseudo Genes (ambiguous residues)::0 of 19
Pseudo Genes (frameshifted)::5 of 19
Pseudo Genes (incomplete)::12 of 19
Pseudo Genes (internal stop)::5 of 19
Pseudo Genes (multiple problems)::3 of 19
CRISPR Arrays::1
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Desulfovibrio vulgaris RCH1
collection_date::Missing
lat_lon::Missing
depth::Missing
alt_elev::Missing
country::Missing
environment::Animal intestinal microflora, Fresh water, Mud, Sea water, Soil
num_replicons::1
ref_biomaterial::Missing
biotic_relationship::Free living
trophic_level::Missing
rel_to_oxygen::Obligate anaerobe
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi03939
Funding Program::DOE-GTL 2007
Gene Calling Method::Prodigal
Source of Isolate::Terry C. Hazen (TCHazen@lbl.gov)
Cell Shape::Rod-shaped
Motility::Motile
Sporulation::Sporulating
Temperature Range::Mesophile
Temperature Optimum::37C
Gram Staining::Gram-
Diseases::None
##MIGS-Data-END##

Global statistics

Total sequence length3,734,357
Total ungapped length3,734,357
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_000166125.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP002297.1=NC_017310.1
Plasmid pDEVAL01CP002298.1=NC_017311.1

Assembly statistics

MoleculeTotal
Length
All3,734,357
Chromosome 3,532,052
Plasmid pDEVAL01202,305

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Desulfovibrio vulgaris RCH1Desulfovibrio vulgaris

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000195755.1Desulfovibrio vulgaris str. Hildenboroughtype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000195755.1Desulfovibrio vulgaristype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type100.00100.0098.97
Best-match type100.00100.0098.97

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna
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