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ASM22768v3

Organism name:
Thioalkalivibrio paradoxus ARh 1 (g-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: ARh 1
BioSample:
SAMN02256529
BioProject:
PRJNA52643
Submitter:
DOE Joint Genome Institute
Date:
2014/01/03
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000227685.3 (latest)
RefSeq assembly accession:
GCF_000227685.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454; Illumina

IDs: 91361 [UID] 890388 [GenBank] 1512878 [RefSeq]

See Genome Information for Thioalkalivibrio paradoxus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 401912
Source DNA and Organism available from Gerard Muyzer (g.muijzer@uva.nl)
Source DNA available from Gerard Muyzer (g.muijzer@uva.nl)
Organism available from Gerard Muyzer (g.muijzer@uva.nl)
Contacts: Gerard Muyzer (g.muijzer@uva.nl)
 Tanja Woyke (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Annotation by ... JGI-ORNL
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)
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::12/16/2020 03:31:49
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)::3,454
CDSs (total)::3,401
Genes (coding)::3,323
CDSs (with protein)::3,323
Genes (RNA)::53
rRNAs::1, 1, 1 (5S, 16S, 23S)
complete rRNAs::1, 1, 1 (5S, 16S, 23S)
tRNAs::45
ncRNAs::5
Pseudo Genes (total)::78
CDSs (without protein)::78
Pseudo Genes (ambiguous residues)::0 of 78
Pseudo Genes (frameshifted)::26 of 78
Pseudo Genes (incomplete)::52 of 78
Pseudo Genes (internal stop)::7 of 78
Pseudo Genes (multiple problems)::6 of 78
CRISPR Arrays::8
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Thioalkalivibrio paradoxus ARh 1
biotic_relationship::Free living
rel_to_oxygen::Facultative
assembly::Newbler v. 2.3
trophic_level::Chemolithoautotroph
sequencing_meth::WGS
GOLD Stamp ID::Gi07686
Current Finishing Status::Level 6: Finished
Funding Program::DOE-CSP 2010
Gene Calling Method::Prodigal 1.4, GenePRIMP
Cell Shape::Rod-shaped
Motility::Motile
Sporulation::Nonsporulating
Temperature Range::Mesophile
Salinity::Halophile
Gram Staining::Gram-
Sequencing Depth::30x
Diseases::None
Phenotypes::Alkalophile
##MIGS-Data-END##

Global statistics

Total sequence length3,756,729
Total ungapped length3,756,729
Total number of chromosomes and plasmids1

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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_000227695.2)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP007029.1=NZ_CP007029.1

Assembly statistics

MoleculeTotal
Length
Chromosome 3,756,729

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Thioalkalivibrio paradoxus ARh 1Thioalkalivibrio paradoxus

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000321415.2Thioalkalivibrio nitratireducenstype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type90.1774.5469.96

ANI result

Taxonomy check statusBest match statusComment
OKbelow-threshold-mismatchAssembly is the type-strain, mismatch is within genus and expected
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