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ASM32706v1

Organism name:
Pseudomonas stutzeri RCH2 (g-proteobacteria)
Taxonomy check:
Inconclusive
Infraspecific name:
Strain: RCH2
BioSample:
SAMN02232046
BioProject:
PRJNA60029
Submitter:
DOE Joint Genome Institute
Date:
2012/12/20
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_000327065.1 (latest)
RefSeq assembly accession:
GCF_000327065.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 515518 [UID] 515078 [GenBank] 515518 [RefSeq]

See Genome Information for Pseudomonas stutzeri

There are 319 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 4087481
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::12/18/2020 02:26:56
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::5.0
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::4,349
CDSs (total)::4,273
Genes (coding)::4,218
CDSs (with protein)::4,218
Genes (RNA)::76
rRNAs::4, 4, 4 (5S, 16S, 23S)
complete rRNAs::4, 4, 4 (5S, 16S, 23S)
tRNAs::60
ncRNAs::4
Pseudo Genes (total)::55
CDSs (without protein)::55
Pseudo Genes (ambiguous residues)::0 of 55
Pseudo Genes (frameshifted)::28 of 55
Pseudo Genes (incomplete)::29 of 55
Pseudo Genes (internal stop)::10 of 55
Pseudo Genes (multiple problems)::10 of 55
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Pseudomonas stutzeri RCH2
collection_date::Missing
lat_lon::Missing
depth::Missing
alt_elev::Missing
country::Missing
environment::Host, Rice roots, Soil
num_replicons::4
ref_biomaterial::Missing
biotic_relationship::Free living
trophic_level::Heterotroph
rel_to_oxygen::Aerobe
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi04345
Funding Program::DOE-GTL 2007
Gene Calling Method::GenePrimp, Prodigal 1.4
Cell Shape::Rod-shaped
Motility::Motile
Sporulation::Nonsporulating
Temperature Range::Mesophile
Gram Staining::Gram-
Diseases::None
Phenotypes::Non-Pathogen
##MIGS-Data-END##

Global statistics

Total sequence length4,600,489
Total ungapped length4,600,489
Total number of chromosomes and plasmids4

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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_000327075.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP003071.1=NC_019936.1
Plasmid pPSEST01CP003072.1=NC_019937.1
Plasmid pPSEST02CP003073.1=NC_019938.1
Plasmid pPSEST03CP003074.1=NC_019939.1

Assembly statistics

MoleculeTotal
Length
All4,600,489
Chromosome 4,575,057
Plasmid pPSEST0112,763
Plasmid pPSEST029,865
Plasmid pPSEST032,804

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Pseudomonas stutzeri RCH2Pseudomonas stutzeri

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000219605.1Pseudomonas stutzerisuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_003696315.1Pseudomonas songnenensistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type87.2978.7679.67
Best-match type92.8187.2292.86

ANI result

Taxonomy check statusBest match statusComment
Inconclusivebelow-threshold-mismatchna
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