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ASM18770v1

Organism name:
Rahnella aceris (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: Y9602
BioSample:
SAMN00713582
BioProject:
PRJNA50601
Submitter:
US DOE Joint Genome Institute
Date:
2011/02/02
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
GenBank assembly accession:
GCA_000187705.1 (latest)
RefSeq assembly accession:
GCF_000187705.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454-Titanium, Illumina GAii

IDs: 276048 [UID] 242848 [GenBank] 276048 [RefSeq]

See Genome Information for Rahnella aceris

There are 8 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 4089210
Source DNA and organism available from Robert J. Marinez (rmartinez@bama.ua.edu)
Contacts: Robert J. Marinez (rmartinez@bama.ua.edu)
 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)
The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::02/07/2024 01:47:30
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.6
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::5,233
CDSs (total)::5,127
Genes (coding)::5,058
CDSs (with protein)::5,058
Genes (RNA)::106
rRNAs::8, 7, 7 (5S, 16S, 23S)
complete rRNAs::8, 7, 7 (5S, 16S, 23S)
tRNAs::76
ncRNAs::8
Pseudo Genes (total)::69
CDSs (without protein)::69
Pseudo Genes (ambiguous residues)::0 of 69
Pseudo Genes (frameshifted)::22 of 69
Pseudo Genes (incomplete)::60 of 69
Pseudo Genes (internal stop)::7 of 69
Pseudo Genes (multiple problems)::17 of 69
Pseudo Genes (short protein)::1 of 69
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Rahnella sp. Y9602
collection_date::Missing
lat_lon::36.010 -84.263
depth::Missing
alt_elev::Missing
country::USA
environment::Fresh water, Human intestinal microflora
num_replicons::3
ref_biomaterial::Missing
biotic_relationship::Missing
trophic_level::Missing
rel_to_oxygen::Facultative
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi05347
Funding Program::DOE-CSP 2010
Isolation Site::DOE Field Research Center (FRC), Oak Ridge, TN (Area 3)
Host Name::Homo sapiens, freshwater
Cell Shape::Rod-shaped
Motility::Motile
Temperature Range::Mesophile
Gram Staining::Gram-
##MIGS-Data-END##

Global statistics

Total sequence length5,614,252
Total ungapped length5,614,252
Total number of chromosomes and plasmids3

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_000187715.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP002505.1=NC_015061.1
Plasmid pRAHAQ01CP002506.1=NC_015062.1
Plasmid pRAHAQ02CP002507.1=NC_015063.1

Assembly statistics

MoleculeTotal
Length
All5,614,252
Chromosome 4,864,217
Plasmid pRAHAQ01616,549
Plasmid pRAHAQ02133,486

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Rahnella acerisRahnella aceris

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_011684115.1Rahnella aceristype

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_011684115.1Rahnella aceristype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.3989.5096.02
Best-match type99.3989.5096.02

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna