U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM24195v1

Organism name:
Rahnella aquatilis CIP 78.65 = ATCC 33071 (enterobacteria)
Taxonomy check:
OK
Infraspecific name:
Culture-collection: ATCC:33071
Infraspecific name:
Strain: CIP 78.65
BioSample:
SAMN02261385
BioProject:
PRJNA60227
Submitter:
JGI
Date:
2012/01/10
Assembly type:
na
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000241955.1 (latest)
RefSeq assembly accession:
GCF_000241955.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 367638 [UID] 326598 [GenBank] 367638 [RefSeq]

See Genome Information for Rahnella aquatilis

Pathogen Detection Resources

There are 18 assemblies for this organism

See more

History (Show revision history)

Comment

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/
URL -- http://www.jgi.doe.gov
JGI Project ID: 4089211
Source DNA and organism available from Robert Martinez (rmartinez@bama.ua.edu)
Contacts: Robert Martinez (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)  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Name::GCF_000241955.1-RS_2024_03_27
Annotation Date::03/27/2024 01:38:42
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.7
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA
Genes (total)::4,997
CDSs (total)::4,889
Genes (coding)::4,821
CDSs (with protein)::4,821
Genes (RNA)::108
rRNAs::8, 7, 7 (5S, 16S, 23S)
complete rRNAs::8, 7, 7 (5S, 16S, 23S)
tRNAs::76
ncRNAs::10
Pseudo Genes (total)::68
CDSs (without protein)::68
Pseudo Genes (ambiguous residues)::0 of 68
Pseudo Genes (frameshifted)::28 of 68
Pseudo Genes (incomplete)::49 of 68
Pseudo Genes (internal stop)::6 of 68
Pseudo Genes (multiple problems)::15 of 68
CRISPR Arrays::2
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Rahnella aquatilis CIP 78.65
collection_date::Missing
lat_lon::Missing
depth::Missing
alt_elev::Missing
country::Missing
environment::Host
num_replicons::4
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::Gi06369
Type Strain::Yes
Funding Program::DOE-CSP 2010
Gene Calling Method::Prodigal 1.4, GenePRIMP
Isolation Site::drinking water
Host Name::Water, humans
Cell Shape::Rod-shaped
Temperature Range::Mesophile
Gram Staining::Gram-
##MIGS-Data-END##

Global statistics

Total sequence length5,448,900
Total ungapped length5,446,950
Gaps between scaffolds0
Number of scaffolds4
Scaffold N504,861,101
Scaffold L501
Number of contigs5
Contig N504,861,101
Contig L501
Total number of chromosomes and plasmids4
Number of component sequences (WGS or clone)4

Supplemental Content

Access the data

Assembly Information

Related Information

PubMed articles for this assembly

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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_000241965.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP003244.1=NC_016818.1
Plasmid pRahaq201CP003245.1=NC_016835.1
Plasmid pRahaq202CP003246.1=NC_016819.1
Plasmid pRahaq203CP003247.1=NC_017092.1

Assembly statistics

MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
All5,448,90045,446,9504,861,10110
Chromosome 4,861,10114,861,1014,861,10100
Plasmid pRahaq201463,9061463,906463,90600
Plasmid pRahaq202115,4871115,487115,48700
Plasmid pRahaq2038,40616,4568,40610

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Rahnella aquatilis CIP 78.65 = ATCC 33071Rahnella aquatilis

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000735505.1Rahnella aquatilis CIP 78.65 = ATCC 33071type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000735505.1Rahnella aquatilistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type99.9998.7999.93
Best-match type99.9998.7999.93

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna