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ASM2012v1

Organism name:
Paraburkholderia phytofirmans PsJN (b-proteobacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: PsJN
BioSample:
SAMN02598395
BioProject:
PRJNA17463
Submitter:
US DOE Joint Genome Institute
Date:
2008/05/07
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_000020125.1 (latest)
RefSeq assembly accession:
GCF_000020125.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 41168 [UID] 20928 [GenBank] 41168 [RefSeq]

See Genome Information for Paraburkholderia phytofirmans

There are 3 assemblies for this organism

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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: 4002732
Source DNA and bacteria available from James Tiedje (tiedjej@msu.edu)
Contacts: James Tiedje (tiedjej@msu.edu)
 David Bruce (microbes@cuba.jgi-psf.org)
Quality ... assurance done by JGI-Stanford
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LLNL
Finished microbial genomes have been curated to close all gaps with greater than 98% coverage of at least two independent clones. Each base pair has a minimum q (quality) value of 30 and the total error rate is less than one per 50000.
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::12/24/2023 10:17:43
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)::7,428
CDSs (total)::7,342
Genes (coding)::7,224
CDSs (with protein)::7,224
Genes (RNA)::86
rRNAs::6, 6, 6 (5S, 16S, 23S)
complete rRNAs::6, 6, 6 (5S, 16S, 23S)
tRNAs::64
ncRNAs::4
Pseudo Genes (total)::118
CDSs (without protein)::118
Pseudo Genes (ambiguous residues)::0 of 118
Pseudo Genes (frameshifted)::41 of 118
Pseudo Genes (incomplete)::97 of 118
Pseudo Genes (internal stop)::15 of 118
Pseudo Genes (multiple problems)::30 of 118
##Genome-Annotation-Data-END##

Global statistics

Total sequence length8,214,658
Total ungapped length8,214,658
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_000020135.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome 1CP001052.1=NC_010681.1
Chromosome 2CP001053.1=NC_010676.1
Plasmid pBPHYT01CP001054.1=NC_010679.1

Assembly statistics

MoleculeTotal
Length
All8,214,658
Chromosome 14,467,537
Chromosome 23,625,999
Plasmid pBPHYT01121,122

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Paraburkholderia phytofirmans PsJNParaburkholderia phytofirmans

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_004402975.1Paraburkholderia dipogonistype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type95.9981.1664.95

ANI result

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