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ASM19667v2

Organism name:
Pseudonocardia dioxanivorans CB1190 (high G+C Gram-positive bacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: CB1190
BioSample:
SAMN00713596
BioProject:
PRJNA40557
Submitter:
US DOE Joint Genome Institute
Date:
2011/03/28
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_000196675.2 (latest)
RefSeq assembly accession:
GCF_000196675.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454, Illumina

IDs: 11715191 [UID] 30835788 [GenBank] 30860488 [RefSeq]

See Genome Information for Pseudonocardia dioxanivorans

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
JGI Project ID: 4083663
Source DNA and organism available from Shaily Mahendra (mahendra@seas.ucla.edu)
Contacts: Shaily Mahendra (mahendra@seas.ucla.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::01/18/2024 06:32:44
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)::7,053
CDSs (total)::6,994
Genes (coding)::6,885
CDSs (with protein)::6,885
Genes (RNA)::59
rRNAs::3, 3, 3 (5S, 16S, 23S)
complete rRNAs::3, 3, 3 (5S, 16S, 23S)
tRNAs::47
ncRNAs::3
Pseudo Genes (total)::109
CDSs (without protein)::109
Pseudo Genes (ambiguous residues)::0 of 109
Pseudo Genes (frameshifted)::33 of 109
Pseudo Genes (incomplete)::88 of 109
Pseudo Genes (internal stop)::4 of 109
Pseudo Genes (multiple problems)::15 of 109
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Pseudonocardia dioxanivorans CB1190
collection_date::Missing
lat_lon::34.299366 -79.876714
depth::Missing
alt_elev::Missing
country::USA
environment::Sludge, Fresh water
num_replicons::4
ref_biomaterial::ATCC 55486, DSM 44775
biotic_relationship::Free living
trophic_level::Missing
rel_to_oxygen::Aerobe
isol_growth_condt::Missing
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi02043
Type Strain::Yes
Greengenes ID::91804
Isolation Site::Industrial sludge contaminated with 1,4-dioxane
Isolation Comments::isolated by RE Parales, JA Romesser, for Celgene Corporation
Temperature Range::Mesophile
Temperature Optimum::30CC
Gram Staining::Gram+
Diseases::None
##MIGS-Data-END##

Global statistics

Total sequence length7,440,794
Total ungapped length7,440,794
Gaps between scaffolds0
Number of scaffolds6
Scaffold N507,096,571
Scaffold L501
Number of contigs6
Contig N507,096,571
Contig L501
Total number of chromosomes and plasmids4
Number of component sequences (WGS or clone)6

Supplemental Content

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Assembly Information

Related Information

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_000196685.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome CP002593.1=NC_015312.10
Plasmid pPSED01CP002594.1=NC_015314.10
Plasmid pPSED02n/an/an/a3
Plasmid pPSED03CP002598.1=NC_015313.10

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule7,440,79467,440,7947,096,57100
Chromosome Assembled molecule7,096,57117,096,5717,096,57100
Plasmid pPSED01Assembled molecule192,3551192,355192,35500
Plasmid pPSED02AllAssembled moleculeUnlocalized scaffolds136,8050136,805303136,8050136,80545,552045,552000000
Plasmid pPSED03Assembled molecule15,063115,06315,06300

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Pseudonocardia dioxanivorans CB1190Pseudonocardia dioxanivorans

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001313405.1Pseudonocardia tetrahydrofuranoxydanssuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type88.7512.7844.53

ANI result

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